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Hyperthermia Treatment Planning with HyperPlan

1. poop Konrad Zuse Zentrum D 14195 Berlin Dahlem fur Informationstechnik Berlin Germany DETLEV STALLING MARTIN SEEBASS MALTE ZOCKLER HANS CHRISTIAN HEGE Hyperthermia Treatment Planning with HyperPlan User s Manual Z1B Report 00 27 October 2000 Hyperthermia Treatment Planning with HyperPlan User s Manual Detlev Stalling Martin Seebass Malte Z ckler Hans Christian Hege Abstract HyperPlan is a software system for performing 3D simulations and treatment plan ning in regional hyperthermia It allows the user to understand the complex effects of electromagnetic wave propagation and heat transport inside a patient s body Opti mized power amplitudes and phase settings can be calculated for the BSD radiowave applicators Sigma 60 and Sigma 2000 eye applicator HyperPlan is built on top of the modular object oriented visualization system Amira This system already con tains powerful algorithms for image processing geometric modelling and 3D graph ics display HyperPlan provides a number of hyperthermia specific modules allowing the user to create 3D tetrahedral patient models suitable for treatment planning In addition all numerical simulation modules required for hyperthermia simulation are part of HyperPlan This guide provides a step by step introduction to hyperthermia planning using HyperPlan It also describes the usage of the underly
2. Size of points for draw style Points Only visible in Points mode Complexity 3 Complexity 4 02 Set complexity of displayed spheres Reducing the complexity leads to coarser spheres and improved rendering performance If draw style 1s set to plates the complexity controls the size of the texture maps containing the sphere s images The smallest texture size is 32x32 the biggest is 512x512 The port is not visible for draw style points Options a Options show test I transparency Po buffer only A toggle list of options e Show text If selected vertex numbers are drawn This might be quite slow especially for large vertex sets Alternatively you may select a vertex by clicking on it Then its number is printed in the console window e Transparency Optionally the spheres and plates may be drawn transparent Note that the vertices are not sorted along the z axis Thus the appearance of the vertex set may look flawed e Buffer only The default is to display all spheres of the vertex set By clicking this toggle you can display only those vertices that were previously added to the buffer o gt e YN pi N O 3 Text Size A 7 0 00023931 Specify textsize 1f show text is active Transparency a Transparency AA 0 5 Allows you to specify the degree of transparency of the spheres 6 86 VERTEX VIEW 177 Buffer a Buffer Add Remove Clear Show Hide Box Invert A list of buttons that all
3. This slider lets you select the number of samples for the histogram Normally the default values should be adequate Histogram If you select this toggle a plot window appears showing the histogram of qualities for all tetrahedra selected by the Grid Volume module If no tetrahedra have been selected the plot window will not be shown 6 82 TissueStatistics This module takes a uniform label field as well as an optional scalar field as input and computes some statistical quantities for the regions defined in the label field The results are stored in a spreadsheet object The different columns of the spreadsheet have the following meaning e Number Enumerates all materials of the label field e Material Denotes which material is stored in a row 172 CHAPTER 6 ALPHABETIC INDEX OF MODULES e Count Number of voxels contained in a region e Volume Number of voxels times size of a single voxel e CenterX X coordinate of the region s center e CenterY Y coordinate of the region s center e CenterZ Z coordinate of the region s center If an additional scalar field is connected to the module then four more columnns will be generated e Mean Mean value of the field in a particular region e Deviation Standard deviation of the field in a region e Min Min value of the field in a particular region e Max Max value of the field in a particular region The scalar field will be evaluated at the center of each voxel
4. Colormap 3 Cooma B Ap This port becomes visible only if a scalar field has been connected to the ColorField port For further details see section Colormap 128 CHAPTER 6 ALPHABETIC INDEX OF MODULES Buffer E Buffer Add Remove Clear Show Hide Draw This port lets you add and remove highlighted triangles being displayed in red wireframe to an internal buffer For a further description and for the functionality of each of the port buttons see ViewBase Materials Materials E This port provides a menu where all materials of the input grid are listed If you choose a material all tetrahedra of that material are selected and displayed using a red wireframe model You may crop the selection domain by turning the viewer into interactive mode and moving the green handles of the bounding box to a position of your choice Only the tetrahedra inside the bounding box can be added to the buffer Color mode a Color mode nomal mixed twisted Here you may choose among several color modes For details see the module Surface View Commands getSelectedTetra Displays a run length encoded list of all currently selected tetrahedra The list consists of pairs of integer numbers The first number is the index of a selected tetrahedron The second value denotes the number of subsequent selected tetrahedra setSelectedTetra lt list gt Adds some tetrahedra to the internal buffer so that they become visible The a
5. Refinement Steps Here you can set the number of adaptive grid refinements It is recommended to perform at most 2 refinement steps Action Button El Properties invokes an editor window which allows you to specify the electric material properties Same functionality as button Materials in module E Field Simulation Note the electric parameters stored in HyperPlan s material database refer to a frequency of 90 MHz Buttons Parameters and Therm Properties invoke editor windows which allow you to specify the thermal material properties Same functionality as buttons Parameters and Materials in module Static Heat After you have setup the simulation you can commit it by pressing the Submit button If one of the specified output files did already exist a warning message is issued If you don t want to overwrite the file press Cancel and change the filename When the job has been submitted the job dialog window appears showing the status of the job queue If you press the Start button the first pending job of the queue starts running 154 CHAPTER 6 ALPHABETIC INDEX OF MODULES 6 63 Resample This module works on any 3 dimensional field with regular coordinates e g complex and non complex scalar or vector fields or RGBA color fields It lets you resample the data 1 e enlarge or shrink the dimensions of the regular grid while recalculating the data according to it The first port displayed is Input Resolution which indicates th
6. unary negation unary minus The modulo operator gt lt lt gt The basic comparison operators stand for greater less less equal greater equal not equal equal If the comparison is true the result of these operators is 1 otherwise 0 amp amp The logical operators and or xor the result is either 1 or 0 There are also some builtin functions pow Power function with two arguments note that there is no power operator sin cos tan Trigonometric functions asin acos atan Inverse trigonometric functions sqrt Square root Inf exp Logarithm and exponent For better understanding some examples on the usage of the Arithmetic module follow A B The result is the difference between input objects A and B 255 A gt 127 Simple thresholding For every value of A the result is set to 255 if the value is greater than 127 otherwise the result is 0 A The result is a copy of input object A If A is based on a tetrahedral grid and the result type is set to regular together with an appropriate resolution this expression leads to a conversion from an unstructured tetrahedral grid to a structured regular grid 6 5 AXIS 99 Connections Data required Input data object of type Scalar Field InputA is the master input object i e the type of the resulting object is determined by the type of the object connected to port InputA InputB optional Input data object of type Scalar Fiel
7. z Edit mode Query z Marker type Point z Marker position 149 696 131 554 68 4998 Figure 9 5 User interface of landmark editor Changing the size of the bounding box You change the size of the bounding box by setting new values explicitly in the bounding box fields This does not affect the stored data but its representation as displayed by a viewing module e g OrthoSlice by way of a different scaling for the specified dimensions The boundig box of a data set with uniform coordinates specifies the world coordinates of the center of the lower left front voxel min values and the center of the upper right back voxel max values For example if your input is 256 pixels wide and the size of each voxel is Imm then you may set xMin to 0 and xMax to 255 Flipping slices in one dimension Invoke one of the three flip buttons to revert the order of slices in the corresponding dimension e g click on FlipX to flip the slices in the x dimension Exchanging two dimensions Invoke one of the three exchange buttons to interchange the corresponding dimensions e g click on X Y to interchange the x and y dimension CAUTION The exchange operations are not rotations they change the spatial orientation of the dataset 9 7 Landmark Editor This component allows you to edit landmark sets It operates by directly interacting with the 3D geometry in the viewer window cf Section 4 1 6 In order to do so the viewer has to be switch
8. Commands setResolution lt res gt Allows you to adjust the resolution of the line segments The higher the value the smaller the point spacing The default value is 256 resulting in a point distance of 1 256 of the length of the surface s bounding box 6 53 MAGANDPHASE 141 6 53 MagAndPhase The MagAndPhase module connects to a UniformComplexScalarField For each point in space it computes the phase and the squared magnitude and creates a UniformColorField from this information The squared magnitude is used to determine the alpha value 1 e the opacity of a voxel The phase determines the color using an arbitrary colormap This module can be used to visualize quantum mechanical wave functions Connections Data required Complex scalar field defined on a regular grid Colormap optional A colormap that is used to visualize the phase In order to avoid that phase values are being clipped the range of the colormap should extend from 7z to 7 Ports Colormap 3 Colomap 0 TT af Phase colormap input port Action Action I Dolt Pushing this button triggers the computation 6 54 Magnitude The Magnitude module computes the magnitude of the vectors of a vector field 1 e Vl V2 V2 V2 These vectors might be located on regular or on irregular grids Regular or complex vector fields are typically defined by uniform stacked rectilinear or curvilinear coordinates Vectors located on vertices of tri
9. The Snakes filter automatically adjusts the contour of a selected region to edges in the image Edges are regions with a sharp contrast Key Bindings If the mouse cursor is placed somewhere in theGI window some panel commands are available by keys the key bindings are the following e Changing the slice number By holding Shift while you press one of these keys the current markings are copied to the target slice Space CursorDown CursorRight Go to next slice Backspace CursorUp CursorLeft Go to previous slice PgDn Go forth over the next five slices PgUp Go back over the previous five slices Home Go to the first slice End Go to the last slice e Selection c Clear all markings 230 CHAPTER 9 ALPHABETIC INDEX OF EDITORS i Invert all markings a Add current marking to active region s Subtract current marking from active region e Tools 1 Lasso 2 Brush 3 Magic Wand 4 Pick Tool e Zoom Z Decrease zoom Z Increase zoom e Display style d Change display style of the regions i e change the appearance of every region to one of the above described with every new key press cycling through the possible appearances 9 6 ImageCrop Editor This editor works on a scalar data field defined on a uniform cartesian grid It lets you crop such a field 1 e discard all voxels lying outside of a specified subvolume Alternatively you may rescale the field by changing the values of the bounding box Note tha
10. 5 7 Acknowledgements and Copyrights We thank the Department of Genetics at the University of W rzburg the Hermann Fottinger Institut of the Technical University of Berlin and the Rudolf Virchow Klinikum Berlin for providing demo data sets The Amira software project was started at the scientific visualization group at Konrad Zuse Zentrum Berlin ZIB Since 1999 Amira is being jointly developed further by ZIB and by Indeed Visual Concepts GmbH a spin off company from ZIB Amira is based on the latest release of the Open Inventor toolkit from TGS Template Graphics Software Inc Indeed Visual Concepts GmbH has selected TGS Template Graphics Software Inc as the worldwide distributor for Amira Copyright C 1995 2000 Konrad Zuse Zentrum Berlin ZIB Copyright C 1999 2000 Indeed Visual Concepts GmbH Berlin Copyright C 1999 2000 Template Graphics Software Inc USA Amira uses the following non commercial libraries e The Tcl library developed by John Ousterhout subject to following license terms This software is copyrighted by the Regents of the University of California Sun Mi crosystems Inc and other parties The following terms apply to all files associ ated with the software unless explicitly disclaimed in individual files The authors hereby grant permission to use copy modify distribute and license this software and its documentation for any purpose provided that existing copyright notices are retained in a
11. Commands setLineColor lt color gt Lets you adjust the default line color which is used if color mode is set to No Color The color may be specified as an RGB color triple or as a X11 color name setSphereColor lt color gt Lets you adjust the default sphere color which is used if sphere color mode is set to No Color The color may be specified as an RGB color triple or as a X11 color name 6 52 LineStreaks This module takes a surface and randomly distributes a number of short line segments on it The line segments are computed as field lines of a 3D vector field projected onto the surface or as field lines of a vector field directly defined on that surface The latter can for example be produced by the GetCurvature module in Max Direction mode Instead of being visualized directly the resulting line streaks will be stored in a LineSet data object Connections Data required The surface where the streaks will be put on VectorField required The vector field from which the streaks will be computed May be either a surface vector field or a 3D vector field Ports StreakLength a 5 treakLength 10 Relative length of the field line segments The length is scaled by the length of the diagonal of the surface s bounding box NumStreaks amp NumStreaks 100 Number of line streaks to be computed The number of streaks per surface area will be approximately constant Action E Action I Dolt Starts computation
12. Ports Histograms amp Histograms absolute relative differential If you select one of these toggles a plot window appears showing the corresponding histogram for all tetrahedra selected by the Grid Volume module If no tetrahedra have been selected the plot window will not be shown For the three different modes of representation see above Samples This slider lets you select the number of samples for the histogram 6 40 IlluminatedLines This module displays line segments of a line set object taking into account ambient diffuse and specular illumination The illumination effect is implemented internally using the same texture mapping technique which is also applied in module DisplayISL Connections Data required The line set to be visualized 6 41 INTERSECTION 131 Ports Fade Factor Fade Factor I Al fi Values smaller than 1 have the effect that line segments become more and more transparent in back ward direction Transparency Transparency R 0 Base transparency of the line segments 6 41 Intersection The Intersection module shows the intersection of a tetrahedral grid and a cutting plane Depending of the setting of the All toggle only material boundaries are shown or the boundaries of all cut tetrahedra Whenever this module is invoked from a popup menu of a data object it comes together with a module EmptyPlane that constructs a cutting plane Connections Data require
13. To read in raw data use the Load Load Data menu select the file in the file browser and click OK Since Amiracan not recognize the file format automatically a dialog will popup Within this dialog choose Raw Data as file format and click OK Since the raw data file does not contain any information on how to format the data some user specifications are required Amira will bring up a dialog Now adjust the parameters e Data Types Primitive type of data byte for 8 bit data short for 16 bit data int32 for 32 bit integer data float for 32 bit float data double for 64 bit floating point data In addition the number of data values per data point has to specified 1 for scalar data 3 for vector data 6 for complex vector fields e Dimensions Size of the three dimensional array If wrong dimensions are specified the data will be scrambled e Min Max Coords The bounding box of the data These parameters are not as critical as the other ones In particular the bounding box can be adjusted afterwards using the crop editor e Header Many file formats consist of a raw data block with a prepended header If such files are read with this method the size of the header can be specified here The header will then simply be skipped when reading the file e Endianess The byte order of data types other than byte is system dependend If you read your files on the same type of processor as on which they have been produced the default setting will
14. viewer lt number gt saveScene lt filename gt Saves all of the geometry displayed in a viewer in Open Inventor 3D graphics format Warning Since many Amira modules use custom Inventor nodes the scene usually can not be displayed correctly in external programs like ivview viewer lt number gt viewAll Resets the camera so that the whole scene becomes visible This method is called automatically for the first object being displayed in a viewer viewer lt number gt show This command opens the specified viewer and ensures that the viewer window is displayed on top of all other windows on the screen viewer lt number gt hide This command closes the specified viewer viewer lt number gt setTransparencyType lt type gt This command defines the strategy used for rendering transparent objects The argument type may be a number between 0 and 6 corresponding to the entries Screen Door Add Add Delay Add Sorted Blend Blend Delay and Blend Sorted as described for the View menu Most accurate results are obtained using mode 6 which is the default However some objects may not be recognized correctly as being transparent In this case you may switch them off and on again in order to force them to be rendered last Also if lines are to be rendered on a transparent background problems may occur In this case you may use transparency mode 4 and ensure the correct rendering order manually viewer lt number gt getTranspar
15. Commands applyTransform This command changes the coordinates of the vertices of the data object according to the object s current transformation matrix This matrix can been defined using the Transform Editor After the vertices have been transformed the transformation matrix is reset to the identity This command is useful in order to make transformations permanent In particular it should be issued before a transformed data object is written to a file Otherwise the transformation will be ignored by most file formats 194 CHAPTER 7 ALPHABETIC INDEX OF DATA TYPES translate Sax gt lt dy gt Q2 gt Translates all vertices by a constant amount Scale lt i gt XEx gt lt Ey gt lt EzZ gt Scales all vertices by a common factor If three arguments are specified the x y and z coordinates are scaled by different factors jitter lt d gt lt dx gt lt dy gt lt dz gt The coordinates of the vertices are jittered randomly The arguments indicate the maximal amount of jitter Each coordinate of a vertex will be changed change by at most d 2 The method is useful in order to resolve problems due to degenerate configurations in certain geometric algorithms getNumPoints Returns the number of vertices of the data object getPoint lt n gt Returns the coordinates of the specified vertex setPoint lt n gt lt x gt lt y gt lt z gt Sets the coordinates of the specified vertex Chapter 8 Alphabetic Inde
16. The Remove button removes highlighted faces from the buffer The Clear button removes all faces from the buffer The Hide button deselects all faces but does not change the buffer Draw Style Draw Style Outined This option menu lets you select between different drawing styles e Outlined The faces are shown together with their edges Shaded The faces are shown Lines The edges of the faces are rendered as a wireframe Flat The edges of the faces are rendered as a wireframe without lighting Points Only the vertices of the faces are rendered as points 6 8 Bounding Box The Bounding Box module can be connected to any spatial data object in order to visualize its bounding box The bounding box of a data object encloses its geometrical domain More precisely it is obtained by determining the minimum and maximum coordinates in x y and z direction Connections Data required Any spatial data object 6 9 CALCAREAVOLUME 103 Ports Text Text show Shows or hides the coordinates of the lower left front and upper right back corner of the box 6 9 CalcAreaVolume Calculates the area and volume of materials or patches Connections Data required description Ports Mode Mode material patches Allows the choice between a spreadsheet representing the materials or the patches a surface type object consits of The choice of the material port results in a spreadsheet exhibiting th
17. To compute temperature increase the transport of heat inside the body has to be simulated as well Unfor tunately there is no equivalent to Maxwell s equations which describes the phenomenon exactly Instead in HyperPlan a simplified model is used the bio heat transfer equation This equation does not take into account individual blood vessels Instead it assumes that heat exchange between tissue and blood occurs only in the capillaries Thus the thermal effect of blood flow is described by an isotropic term Relevant parameters are the blood perfusion as well as the thermal conductivity 13 14 CHAPTER 1 HYPERTHERMIA PLANNING Tomographic HYPERPLAN image data N Threshold An E Field Simulation segmentation FDTD method Interactive Generation E Field Simulation Simulation of Temperature segmentation of patient grid modified FDTD heat transport optimization Bolus Grid E Field Simulation Processing Finite Elements All in gt one Finite Element Simulation Device with adaptive grid refinement parameters Figure 1 1 Work flow in hyperthermia simulation The system reads tomographic image data of a patient and outputs optimized amplitudes and phase settings for the hyperthermia applicator Several different simulation methods are provided All data can be analysed using powerful visualization methods Figure 1 1 illustrates the different algorithmic steps of hyperthermia simulation as implemen
18. We recommend using Windows 98 or Windows 2000 instead of Windows 95 Graphics Hardware You should use a graphics board with OpenGL support which is the case for almost all newer boards and texture mapping capabilities 5 6 3 Silicon Graphics Graphics Hardware To get optimal graphics performance the machine should support texture mapping in hardware Currently this is the case for all O2 systems and for Octane systems with High Impact and Maximum Impact graphics not Solid Impact Amira provides a number of modules which make use of texture mapping e g slicing pseudo coloring or volume rendering On machines without hardware texture mapping these modules either run much slower or may not work at all The advantage of the Octane is a higher speed in polygon rendering For a complex model with an isosurface of 100 000 triangles the frame rate is 10 per second for an Octane compared to 3 per second for an O2 The MXE and MXI Octanes have larger texture memory than the SSE and SSI Thus the MXE and MXI enable a direct volume rendering using 3D textures which is not possible on an SE SI or O2 Software The current version of Amira requires IRIX 6 5 x or higher We recommend you install the newest version of the operating system see http www sgi com support 5 6 4 HP UX Amira performs pretty well on HP workstations equipped with Visualize fx 4 fx 6 and fx 10 graphics cards under HP UX 10 20 Probably 1t will run on other machi
19. between all pairs of successive knots for each color channel This function manipulates all color channels simultaneously Snap This operation behaves much like a local Snap All i e snapping occurs only between the left and the right neighboring knots of the focus by tightening all color channels as if they were ropes between the knots Snap Red Snap Hue Depending on the chosen color model see Mode the first color channel Red or Hue is snapped between the left and right neighboring knots of the focus leaving the other color channels untouched See Snap for an explanation of snapping Snap Green Snap Saturation Like in Snap Red this entry manipulates the second color channel between the left and the right knot leaving the other color channels untouched Snap Blue Snap Value Like in Snap Red this entry manipulates the third color channel between the left and the right knot leaving the other color channels untouched Snap Alpha This entry is only shown if Show Alpha see Mode has been activated By selecting it the alpha channel will be locally snapped as described in Snap between the left and the right neighbouring knots of the focus leaving the other color channels untouched b Mode Menu Here you control the appearance of the colormap in a certain color model or whether the alpha value transparency is shown or not L Red Green Blue By
20. including image segmentation extraction of boundary faces surface simplification and finally grid gener ation The tutorial in Section 3 4 of the user s guide illustrated this process in more detail The actual grid generation step is performed by the computational module TetraGen The quality of a tetrahedral grid may be improved by applying certain operations provided by the Grid Editor Commands hasMaterial lt name gt Returns true if the specified material is defined in the material section of the TetraGrid hasDuplicatedNodes Returns the number of duplicated nodes 1 e nodes with exact identical coordinates Such nodes may be used in order to represent discontinous piecewise linear fields removeDuplicatedPoints Removes all duplicated points from the grid No field object must be connected to the grid add lt othergrid gt Copies all vertices and tetrahedra from an other tetrahedral grid into this one removeTetra lt n gt Marks the tetrahedral cell specified by lt n gt as obsolete cleanUp Removes all obsolete tetrahedra from the grid fixOrientation Fixes the orientation of all tetrahedra so that the enclosed volume is positive 7 14 TETRAHEDRAL PATIENT MODELS 193 7 14 Tetrahedral Patient Models Tetrahedral patient models are represented as objects of type HxTetraGrid This class stores geometric information in terms of vertices edges faces and tetrahedra Although the generation of patient specific tetra
21. it is useful to pin the three ports on the landmark editor In order to do so select the grey pin toggles left from the port s labels e Connect a second LandmarkView module to the Landmarks object e Select the first LandmarkView module and choose Point Set Point Set 1 e Shift select the second LandmarkView module and choose Point Set Point Set 2 e Adjust the viewer toggles of the two display modules such that the first is visible in the first viewer and the second in the second viewer Before starting to set landmarks it is helpful to rotate the two lobes in their viewers such that they are approximately aligned This will make it easier to locate corresponding features in the two objects and to select reasonable positions for landmarks e Rotate the two lobes to align them roughly Now we are ready to define and set corresponding landmarks Select the LandmarkSet object if necessary and choose the option Edit mode Add To set corresponding landmarks simply click with the left mouse button anywhere on the surface in the first viewer first and click on the surface in the second viewer subsequently The landmarks are visualized as small spheres the first landmark in yellow and the corresponding landmark in blue Make sure to always set the first landmark on the first yellow surface and the second landmark on the second blue surface 52 CHAPTER 3 FIRST STEPS IN AMIRA SHEH Lamdmak Se 0 markers 2 sets no lppes no o e
22. resample Two toggle buttons are provided If update min max is set then the isoline thresholds are automati cally reset to some default values whenever the data range of the incoming scalar field changes The toggle called resample allows you to compute isolines using the resampling approach even if the incoming scalar field is defined on a tetrahedral grid Colormap 8 Colormap 0 EE 7 of Port to select a colormap 6 43 ISOLINES SURFACE 133 6 43 Isolines Surface This solines module computes isolines for a scalar field defined on a surface made of triangles Inside the triangles the scalar field is linearly interpolated if the scalar field contains values for every node If the field contains values for every surface triangle only the isolines will follow the triangle edges if the values of the neighboring triangles are appropriate Connections Data required A scalar field defined on a Surface can be connected to this port Colormap optional A colormap is used to map the values represented by the isolines to a corresponding color If no colormap is connected a constant color is used See also Colormap Ports Spacing amp Spacing uniform explicit Controls how isoline thresholds are being defined In uniform mode a certain number of isovalues are distributed equidistantly within a user defined interval In explicit mode the threshold for each isoline can be set manually Values a Values ol 100 n
23. s guide This guide as well as additional information is provided on the Amira web site www amiravis comand also onwww tgs com If you have specific questions you will find contact information on these web sites How do I see what command line options Amira accepts Command line option are documented in the user s guide in Section 5 2 In addition starting Amira with help gives you a short summary of options How can I check the version of my Amira package To get the version of Amira type app version in Amira s console window In order to see when Amira was compiled use app built Please indicate the version string or compilation date 84 CHAPTER 5 TECHNICAL INFORMATION whenever your report bugs or problems 22 Are there any examples or demos Yes The Amira 2 2 distribution contains tutorials and example with demo data The tutorials are contained in Chapter 3 of the user s guide Demos are listed in the reference section of the user s guide 23 Is there a specific newsgroups There is no Amira specific newsgroup yet 24 Is there a mailing list Not yet 25 Is there a web site For technical information refer to www amiravis com For sales and marketing contact www tgs com 26 Where can I find free modules for Amira Is there a public repository for 3rd party contributions With the availabilty of the developer version a public repository for 3rd party contributions will be set up at www amiravis com 2
24. the grey values in the OrthoSlice are completely replaced by the colors it is sometimes useful to switch fore and back between these two modes 6 14 CombineLandmarks This module merges an arbitrary number of HxVertexSet objects into one HxLandmarkSet Connections Data required Accepts a VertexSet object As soon as this port gets connected to a data object an additional source port will appear This allows the merging of a practically unlimited number of data objects Source2 optional See above Ports Unify Sets amp Unify Sets If this option is chosen the resulting landmark set will only contain one set of landmarks Otherwise the input vertices of the individual input data sets will be mapped to different sets Action Action I Dolt Triggers the computation 6 15 ComponentField This class 1s a special data object which helps you to analyze uniform complex scalar fields The class itself is a uniform real scalar field However it can be attached to a complex scalar field like an ordinary display module The component field provides an option menu allowing you to select which real quantity should be computed from the complex input values These real quantities may be visualized using standard modules like OrthoSlice Isosurface or Voltex Connections ComplexField optional Complex scalar field for which a real quantity should be computed Ports Component Field Component Field Imagina
25. viewer lt number gt setSize lt width gt lt height gt Sets the size of the viewer window The visible part of the 3D window exactly matches the given size if decorations are switched off see below 4 1 INTERFACE COMPONENTS 65 viewer lt number gt setVideoFormat pal ntsc Sets the size of the viewer window according to PAL 601 or NTSC 601 resolution 1 e 720x576 pixels or 720x486 pixels The current setting of the decoration is taken into account viewer lt number gt setVideoFrame lt state gt If state is 1 a frame is displayed in the overlay plane of the viewer This frame depicts the area where images recorded to video are safely shown on video players Setting state to O switches the frame off Note Objects displayed in the overlay planes are not saved to file with the snapshot command see above viewer lt number gt getSize Returns the size of the viewer window viewer lt number gt getCamera This command returns the current camera settings 1 e camera position camera orientation and camera focal distance The values are returned as Amira commands which can be executed in order to restore the camera settings viewer lt number gt setCameraPosition lt x gt lt y gt lt z gt Defines the position of the camera in world coordinates viewer lt number gt setCameraOrientation lt x gt lt y gt lt z gt lt a gt Defines the orientation of the camera By default the camera looks in negative z
26. with the name defined at port Grid already exists a warning occurs If you don t want to overwrite the file press Cancel and change the filename Then press button Run again The job dialog window appears that shows you the status of the job queue If you press the Start button the first pending job of the queue starts running When tetrahedron generation is finished and HyperPlan is still running the tetrahedral grid is automati cally loaded 6 The tetrahedral grid generated in the previous step only covers the water bolus and the surrounding medium air You must combine this grid with the tetrahedral patient model from which you started Select the icon representing the patient model Then point to the icon of the bolus grid and press the right mouse button Select module Combine from the popup menu Make sure that Combine is connected to both tetrahedral grids If not you can point to the small rectangle at the left hand side of the Combine 1 6 TEMPERATURE SIMULATION 25 icon and press the right mouse button Now you can create connect the inputs of the Combine module to both grids manually We recommend that you use the default settings all toggles are set Just press button Dolt After a few seconds a new green icon will appear which represents the combined tetrahedral grid Save the combined grid into a file We recommend to use the filetype ExtendedGrid Applying the FE Method Now you are ready to start the E field calcula
27. 112 data import 77 DataProbe 113 default directories 79 Delaunay2D 115 Digital Image Filters 220 DisplayColormap 115 DisplayISL 116 Divergence 118 Duplicate Nodes 119 E Field Sets 188 E Field Simulation 119 editors 29 Encapsulated Postscript 203 environment variables 78 FDTD 120 Field Cut 121 File dialog changing directories 71 filename filter 71 popup menu 71 selecting files 71 File dialog box 70 File menu Jobs 56 Load 55 Quit 56 Save Data 56 Save Data As 56 Save Network 56 font size 79 function key 80 GetCurvature 123 GMC 122 Gradient 124 Grid Boundary 125 Grid Cut 126 Grid Editor 222 Grid Volume 127 GridView 128 HeightField 129 INDEX Histogram 129 hot key procedure 80 HxSurface 204 Icol 207 IlluminatedLines 130 Image Segmentation Editor 224 ImageCrop Editor 230 Intersection 131 Inventor 207 Isolines 131 Isolines Surface 133 Isosurface Regular 133 Isosurface Tetrahedra 135 IvDisplay 135 IvToSurface 136 Job dialog box 69 JPEG Image Format 208 Label Field 188 Label Voxel 136 Landmark Editor 232 Landmark Set 189 Landmark View 138 Leica Microscope 3D TIFF 208 Leica Microscope Slice Series 208 Line Probe 138 Line Set 190 LineSet Editor 233 LineSetView 138 LineStreaks 140 MagAndPhase 141 Magnitude 141 Object Pool 61 ObliqueSlice 142 OpenGL driver 88 OptTemp 143 OrthoSlice 144 Para
28. 124 GrdBoOundal f7 7 a dedos de a ym ls E ee RO a ee es See Ee ee 125 GIG CUl ss Aa bn Ea e OE Oe RS BS S a 126 Cda VOM te arp at oe AA eo a as AA ER ee 127 CHOVE au a Bn hae ae AA Oh eee ees SE a 128 HOM IG Gy 5 8 fs Aa eee at ae Sete ee wats te Dena ee ee age Ge ees Ee oe 129 PASO OTA amp Soe at iss id ee tae Sle A ee a ee Be ee amp ee 129 Miinainatedlages a 2 6 t te Be Dee Sok oe at Bee OS BOSS OAS SG oS 130 MCT SCCW ON ea Be Been Sak Bese A a SA ee 131 DOUNE Dad a Oe ee Bice ieee de A ee O ee E eis 131 TSO MES SUTTACE Nu ui das E ee we ee ee ea a los lens 133 Sosuttace Resular sac id e a De ada E Bee oS 8 ee 133 Sosurtace Tetrabiedrd s 0 2 4 ee a oo SO AA SS 135 INDISPIAVE arca a ere AE a jo A ee me de a a ee nas 135 CONTENTS 7 6 47 6 48 6 49 6 50 6 51 6 52 6 53 6 54 6 55 6 56 6 57 6 58 6 59 6 60 6 61 6 62 6 63 6 64 6 65 6 66 6 67 6 68 6 69 6 70 6 71 6 72 6 73 6 74 6 75 6 76 6 77 6 78 6 79 6 80 6 81 6 82 6 83 6 84 6 85 DV TOS URAC Ct ue AA ARA ra 136 EaD INOR T ue Sy ca do eh a oh US Seva Oo Gt oe a Bae A E er 136 Landmark VOW haa bl amp Oe OES AAA A ok eS 138 Re PEO ic aoe Gaye oes Oe ae ee camera Dae hes a E ee G 138 Ici SCUVICW 4 4 2h oes oe oe Boe eee DA O ee eee G amp G 138 PMC SEPCAKS 2 Dt AAA ES ee ae E Bes 140 Masnatura pd Saute a o ad ee Ber ae ee OO 141 NS mitudes e sb e Bek eS Ra A EE BE EA AE Oe 141 OBIqueSlce oi as Bee is de A in AA A A oe 142 Opt as d
29. 7 ALPHABETIC INDEX OF DATA TYPES setPosition lt set gt lt index gt gt lt y gt lt 25 Sets the coordinate values of the specified marker lt index gt in a particular set 7 7 Line Set A LineSet data object is able to store independent line segments of variable length Optionally for each vertex one or more scalar data items can be stored LineSet objects inherit the vertex set interface cf Section 4 2 5 In order to visualize the line segements of a LineSet object the module LineSetView can be used Finally line sets can be stored using the AmiraMesh file format Commands adadPoint lt x y z gt Adds a new point to the line set s vertex array The new point will not yet be referenced by any line segment adatain pk pz os 2 Adds a new line segment to the line set The line segment is defined by indices referencing elements of the vertex array removeAllLines Removes all lines but leaves the vertex array unchanged 7 8 Plan Data Power amplitudes and phase shifts for the hyperthermia applicator may be stored as separate data objects of type HxPlanData The plan data also contain a scaling factor which determines the total absorbed power inside the patient A general problem is that the control units of the BSD Sigma applicators use a simplified steering which allows the user to specify a subset of all possible amplitude and phase settings only An appropriate conversion of the input parameters will be provided in fu
30. Amira up with NO display in order to do batch processing of data or to generate pictures and plots without displaying anything on the console You can start Amira with the no_gui command line option in order to execute scripts in batch mode How does Amira behave with large data sets Amira is an interactive visualization system Therefore data sets must be loaded into main memory in order to be processed In some projects very large dynamic data sets up to several 100 GB have been visualized with Amira In this case special reader modules have been used which only read subsets of the data at once How can I change the background color of the viewer There are three different background modes namely uniform gradient and checkerboard These modes can be set for all viewers via the View Background menu of the main window or via the command viewer lt n gt setBackgroundMode lt mode gt fora particular viewer The primary background color can be adjusted via the camera icon in the upper left corner of the viewer window or via the command viewer lt n gt setBackgroundColor lt color gt The secondary color used in gradient and checkerboard mode can be adjusted via the command viewer lt n gt setBack GrouncdColorz lt color gt You can also place an arbitrary raster image in the background using the command viewer lt n gt setBackgroundImage lt filename gt Any image file in TIFF SGI RGB JPEG PNM BMP or PNG format can be read H
31. Description of every item Let us first take a course in what the items of this colormap editor are and what they do A Menu Bar The menu bar consists of the three sub menus Edit Mode and Brush a Edit Menu This sub menu offers two opportunities for editing the colormap The first group deals with the undoing and the opposite redoing changes you made in the colormap The second group snaps one or more channels like tightening a rope between the left and right neighboring knots of the focus 1 Undo If you think that your last changes to the colormap have been a mistake this entry lets you take back your last changes You can easily go back to a point of editing when you were content with the colormap and 9 2 COLORMAP EDITOR 217 start editing again The colormap editor memorizes up to 50 of your last changes Redo If you took back too much this entry undoes the last undo i e redoes the undone changes This is the reverse function of Undo You may undo redo your changes as often you wish but if you modify the colormap by another function not Undo Redo you lose the opportunity to redo the last undos Redo is only activated if your last action was invoking Undo Snap All By selecting this entry all colormap entries will be tightened like a rope snapped between their left and right neighboring knots leaving the knots itself untouched This means that lines are drawn
32. FR rR FP OO OC O Use float 3 in order to encode a vector field instead of a scalar field Likewise you may modify the field s primitive data type Instead of ScalarField you may use any other name in the data definition statement Label fields for segmentation Label fields are closely related to ordinary scalar fields with uniform coordinates However the data values at each voxel are interpreted as labels denoting the different materials or regions the voxels have been as signed to during a segmentation process Therefore the most important difference of label fields compared to uniform scalar fields is the occurence of a Materials section in the AmiraMesh file Whenever such a section occurs and elements of type byte denoted Labels are found the AmiraMesh file is interpreted as a label field Here is a simple example of a label field containing two different materials AmiraMesh ASCII 1 0 define Lattice 2 2 2 Parameters CoordIype uAito m BoundingBox is xmin xmax ymin ymax zmin zmax BoundingBox 01 30 QI 8 2 AMIRA MESH FORMAT Materials Id 0 Name Exterior Id 4 Name Something Lattice byte Labels Q1 Lattice byte Probability 2 Q1 Oe 0074 O 0 4 4 2 255 2oo LSO ds 0 200 ZOO LIO 230 201 Each material is supposed to have a parameter Id specifying the correspondence between labels and mate rials In the example above all voxels labeled with O belong to material Exterior whil
33. Home 64 interaction mode 62 Perspective Ortho toggle 64 Pick 63 rotate button 64 Seek 63 Set Home 64 Snapshot 63 View 63 View All 64 viewing directions YZ XZ XY 64 viewing mode 62 zoom 62 virtual memory 88 Voltex 180 voxel size 212 232 Voxel View 182 Working Area 62 INDEX
34. HxAnnaScalarField3 data object and entering the point s cordinates by the Coord port of that module An expression consists of variables and mathematical and logical operators the syntax is basically the same as for C expressions The following variables are always defined e x the x coordinate of the current point e y the y coordinate of the current point e Z the z coordinate of the current point If data objects ScalarField A or ScalarField B are connected to port InputA resp InputB the following variables are also defined e a the values of input object A e b the values of input object B The same C style mathematical and logical operators as well as built in functions that are availabe for arithmetic expressions can be used here see HxArithmetic module description Connections InputA optional Optional scalar field InputB optional Optional second scalar field 185 186 CHAPTER 7 ALPHABETIC INDEX OF DATA TYPES Ports Expr a Expr E Input field for arithmetic expression defining the scalar field values 7 2 Analytical Vector Field This data class represents a user defined 3D vector field based on a regular grid It provides ports X Y Z by which arithmetic expressions can be entered that define the component mappings with respect to uniform Cartesian coordinates x y and z The default domain is the unit cube thus for each point x y z in it the associated vector X Y Z is given by scalar
35. If you want to look for multiple words you must prepend them with a plus sign e g surface editor Running demo scripts In the demo section of the on line manual you can easily start any demonstration just by clicking on the marked text The script will be loaded and executed immediately You may interrupt running demo scripts by using the stop button in the lower right of the Amira main window 60 CHAPTER 4 PROGRAM DESCRIPTION Online Help Piel ES amira Visualization and 30 Reconstruction Werslon 2 1 Users Guide 1 Introduction including a list of features 2 First steps in Amira including a geting stared tutorial 3 Program description covering gui components and dala classes 4 Technical information including a section on data import User s Reference Rantial Modules Dala Tenes Edi File Formats Other Components Demos Fulltable of content Figure 4 1 Amira s help window Commands help Makes the help dialog appear and loads the home page of the online help help getFontName Returns the name of the font of the browser help setFontName Sets the font of browser help getFontSize Returns the size of the font of the browser help setFontSize Sets the size of the font of the browser In order to permanently change the font size put this com mand in the Amira file in your home directory or in an Amira init file in the current working directory For details see Section
36. Save Network You may save the complete network of icons and connections shown in the object pool using the Save Network button The file dialog will appear and you will carry out the same steps as for single data files This feature is useful for resuming work at a point where it was left in a previous Amira run When loading the network script all data objects and modules will be restored automatically Note that usually all data objects must have been stored in a file in order to be able to save the network If this is not the case a dialog is popped up listing all the data objects that still need to be saved In the dialog you can also specify that all required data objects should be saved automatically in the same directory where the network script will be written auto save feature Jobs This button brings up Amira s job dialog which is used to control the execution of batch jobs running in the background For example tetrahedral grids can be generated in a batch job see module TetraGen However for most users the batch queue will be of minor interest Quit This button terminates Amira The current network configuration will be lost unless you explicitly save it using Save Network 4 1 2 Edit Menu The Edit menu provides control on the visibility of object icons and lets you delete and create objects Depending on how many icons are selected in the Object Pool some menu options might be disabled Hide The Hide button hide
37. The antenna parameters are used as default values for superposition For more information see the Plan Data description Ports Action If you press the button Save the actual antenna parameters power amplitudes and phase delays are stored into a file If the button Reset is pressed the last interactive changes of the antenna parame ters are removed and the actual default values synchronous mode or antenna parameters read from a file are restored The option menu on the right allows to select between different antenna steerings Default means a synchronous steering of all antennas If files containing antenna parameters suffix Plan have been loaded their file names occur in the menu In this way the E field or SAR distribu tion corresponding to an optimized temperature distribution see module Opt Temp can be shown by loading the file containing the optimal antenna parameters and selecting its filename from the option menu 6 76 SUPERPOSE TEMPERATURE DISTRIBUTIONS 165 Power and Scale Factor The power amplitudes for the single channels see below should only be used to do a relative weight ing between the channels Using port Factor you can define an additional over all scaling factor for all channels Using port Power the scale factor can be defined indirectly by prescribing the total power absorbed in the patient Note The value displayed at port Power means the total power absorbed in the patient model not the total power
38. a set of inde pendent temperature fields is computed This makes it possible to change amplitudes and phases without rerunning the whole simulation Finally an optimization module is provided which computes individually optimized device parameters The optimization procedure tries to maximize the heating of the tumor while not exceeding user defined maximal temperatures in the other tissue compartments HyperPlan also provides an all in one simulation module which performs E field simulation temperature simulation and optimization at once This has the advantage that adaptive grid refinement takes place at locations required by the optimized temperature distribution Using this approach is the recommended way of performing hyperthermia simulations because it is the most accurate one In Figure 1 1 the corrsponding work flow is marked by solid black lines while alternative paths are shown in light gray 1 2 Filename Conventions Some of the planning steps described in the following require a number of sub steps We recommend to group all planning data for a single patient into a separate directory Furthermore we recommend to compose filenames used to store intermediate planning results as follows 1 3 SEGMENTATION 15 name filetype version number The meaning of the different parts of the name is described below e name might be the patient s name or a short form of it Make the name part of the filename a unique identification of the pa
39. a unique way so that we can define an inner region and an outer region The triangle normals point into the outer region For each patch an InnerRegion and an Outer Region may be specified in the file format If one of these specifiers is missing it is assumed that the patch delimits the exterior space Otherwise the exterior region should be called OUTSIDE Patches may be closed or may be delimited by so called boundary curves Boundary curves are specified by a list of signed integers The sign denotes the orientation of the curve segment for a particular patch In addition for each patch inner branching points may be specified if necessary e BoundaryCurve At a boundary curve multiple patches join The curves are defined by a set of vertex indices For closed curves the first and the last index must be equal e BranchingPoint A point where multiple regions join The start and end points of a boundary curve are branching points In addition there may be also branching points inside a patch which are not part of a boundary curve e Vertices These are the points from which the surface triangles are built In the file format the vertex co ordinates are specified after the indentifier Vert ices followed by the number of vertices First branch 206 CHAPTER 8 ALPHABETIC INDEX OF FILE FORMATS ing points should be specified then points on boundary curves and then inner points of the patches In the definition of boundary curves and patches the verti
40. additional vertex data values can be defined Multiple values should be distinguished by denoting them Data2 Data3 and so on Colormaps An Amira colormap consists of a one dimensional array of RGBA components accompanied by two num bers min max specifying which data window should be linearly mapped to the RGBA values The RGBA array should have 256 elements in order to be able to edit the colormap using the colormap editor Colormaps are encoded in an AmiraMesh file as follows AmiraMesh ASCII 1 0 define Lattice 256 Parameters ContentType Colormap MinMax 10 180 Lattice lost 14 Date el O 0 BOOS IZLI 10 O OOS IZ SL OO sOU SIZ Ley OTIS EE OW OOS 2215 7 OLIGO O WOLLIGE UL PASE Us QOS IZ EFT 00196075 hehe OS DO G The RGBA values are stored in floating point format A component value of 0 means no intensity black while a component value of 1 means maximum intensity white The fourth component denotes opacity alpha Here a value of 0 indicates that the color is completely transparent while a value of 1 indicates that the color is completely opaque 8 3 BMP Image Format BMP is a standard image format mainly used on the Microsoft Windows platform Image data is stored with 8 or 24 bits per pixel without applying any compression When writing RGBA color fields the alpha channel will be discarded When reading BMP images an alpha value of 255 full opacity will be assumed BMP files are automatical
41. an axis just click on the appropriate tab If you want to change the range you have to set off the Auto toggle Now the range fields are sensitive The Nice Num toggle sets the range to the next good looking boundaries A tick delta can be typed in after the number of ticks are set to 1 It is possible to zoom interactively into your data using the mouse For this purpose drag a rectangle within the plot area by pressing the shift key and the left mouse button while moving the mouse To go back to the automatic ranges click into the plot area with the left mouse button while the alt key 1s pressed at the same time Every axis object has a hidden grid child object which is not active by default To show the grid just open the grid child and select it Then set the is active toggle to on Editing annotation parameters To position an annotion on your plot you can switch between world coordinates or normalized coordinates The usage of world coordinates is useful if you like to annotate a certain feature e g an extrema of a curve In this case you have to insert the annotion after that curve object You can also position an annotation in the plot window interactivly by pressing the left mouse button on the annotation move the mouse and release 150 CHAPTER 6 ALPHABETIC INDEX OF MODULES Annotation Text sin x 3 14 cos y s 14 sin f2 3 14 Position oS loa ve World Normal Font helvetica 26 4 Color Figure 6 4 Editable a
42. an ellipse that fits it The filter operates in the current slice in the active viewer Fill This selects all unselected pixels which are comletely sourrounded by selected pixels in the current slice in the active viewer Interpol Pressing this button interpolates selections between all slices where areas have been selected Pressing this button again after corrections in certain slices will interpolate the selections between all 9 5 IMAGE SEGMENTATION EDITOR 229 slices where changes have been made Label Filters e Fill holes This filter removes islands of arbitrary size in the current material i e an island is assigned to the active region if it is totally surrounded by a segment that belongs to the active material The filter can be applied to the current slice in the active viewer or to all slices e Remove Islands This filter removes islands in or between the regions depending on the size and percent values that are set in the filters dialog An island is a connected area of voxels in which the number of voxels is less than or equal to the size specified in the dialog If such an island is encountered the percentages of the surrounding regions with respect to the total number of voxels adjacent to the island are calculated and compared with the percent threshold The island is added to the region with the highest percentage value greater than or equal to percent If no region exceeds the percent threshol
43. and the focus are represented by white and black vertical lines respectively The left edge of the color chart shows the values of the leftmost index of the colormap and the right edge those of the rightmost index C Color Bar Like in the colormap port this color bar displays a continuous form of the chosen colormap by linearly interpolating the colors between the colormap entries If Show Alpha is enabled alpha values are represented by a certain amount of transparency in the colors 1 e you see the colors translucent over a white and black chequer For an alpha value of 0 0 you see no color information but only the white and black chequer for a value of 1 0 you do not see a chequer because the colormap entry is not translucent D Color Buttons An entry of the color button panel is also called a color cell Each color cell shows the color associated to a color index without the alpha value the indices are counted from left to right and from top to botom Thus the color cell in the upper left corner shows the color of the leftmost colormap entry and the color cell in the lower right corner shows the color of the rightmost colormap entry The index of the focus cell is displayed below the color button panel A knot is represented by a small black box in the middle of the color cell with white outlines and the focus has additional black and white surroundings E Color Sliders In the lower area of the Colormap Editor window there are thre
44. ara a da e eR SS Ba A235 Coordinate San NES e A E E O ls AD Suae Data rra ara a A dl A a EB A ee E 4207 EranstormalOldS e 5 ie AAA A a A Batamelers a os ase as AER A A a he As 5 Technical Information 5 1 32 5 3 5 4 5 5 5 6 Data IMPOR e ee ar fen E ee a a AA E Bees Command Ling Opuons s arsa A be ep BS A eee hw ee eh ee oe EE eS Environment Variables 2 ieem aen 6825 06 be 84 44 BSEREHSE CEES User deiined Start upscnp lt 4 bed 2 2 54d eA DOS DERE SESS Frequently Asked Questions a SYSE REGUITCINEMIS ete a a da te de a AAA ee Be eS SOLT On Systemr Stability ds A A A Se a 5 0 2 Microsoft WiNdOWS e si E AAA CA we AAA DUG MMC APIS ads e Ate ade ome neve E a eee es MOR HPUX 0000 e Reece a e Boe ad a e a A A O ARA 6 0 AUX ear ad SES SS a a III Amira Reference Manual 6 Alphabetic Index of Modules 6 1 6 2 6 3 6 4 6 5 6 6 6 7 AMOO lt A A Ge re a e ROS a Oe Ee a da a S AMEMA a a NA ADTA COU hes da ee OVE amp Re Sey Bk eM A es Oe ee aA e a oe ot T a ACOE a hs Yh cok ee A ee a N 62 66 69 70 71 72 12 73 74 74 75 75 75 77 T1 78 78 79 80 88 88 89 89 89 89 90 90 93 6 8 6 9 6 10 6 11 6 12 6 13 6 14 6 15 6 16 6 17 6 18 6 19 6 20 6 21 6 22 6 23 6 24 6 25 6 26 6 27 6 28 6 29 6 30 6 31 6 32 6 33 6 34 6 35 6 36 6 37 6 38 6 39 6 40 6 41 6 42 6 43 6 44 6 45 6 46 CONTENTS BOUNCING BOX 4 ere gst aoe Bee hod he A
45. are axis aligned and have equal spacings The coordinates of such a uniform grid can be obtained from a simple bounding box containing the origin vector and increments for all directions Stacked coordinates are another example Here the spacing in z direction between subsequent slices may be different In any case scalar values inside a hexahedral grid cell are obtained from the eight vertex values using trilinear interpolation While the OrthoSlice module can only be used to visualize scalar fields with uniform or stacked coordinates other modules like ObliqueSlice or Isosurface work for all scalar fields with regular coordinates Yet another example of a scalar field is the class HxAnnaScalarField3 It represents an analytically defined scalar field To create such a field select ScalarField from the Edit Create menu of Amira s main window You have to specify a mathematical expression which is used to evaluate the field at each requested position 74 CHAPTER 4 PROGRAM DESCRIPTION Up to three other fields can be connected to the object These can be combined to a new scalar field even if they are defined on different grids Vector Fields As for scalar fields Amira provides a number of vector field classes these are derived from the base classes HxVectorField3 and HxComplexVectorField3 While ordinary vector fields return a three component vector at each position complex vector fields return a six component vector Complex vector fields ar
46. are manipulated by dragging the small triangles alternatively values in fix point format may be entered directly into the text fields to the right of the sliders The last three buttons named OK Apply and Cancel are for quitting the editor applying your changes to the underlying Colormap data object and quitting the editor without applying your changes The important elements for manipulation 1 Focus The focus marks the color cell for which you can change the value by the sliders Its representation is a surrounding black and white box of a color cell and a black vertical line in the color chart You set the focus by clicking with the left mouse button on a colormap entry in the color button panel A focus cell also gets a knot marker see below clicking again on a focus cell removes the knot and places the focus on to the leftmost color cell just setting the focus to a different cell does not remove a knot 2 Knot Knots are fixed points in the colormap 1 e they retain their values while the colormap is being manip ulated by snapping see Menu bar Edit Snap or by dragging the focus Knots are represented by a small black box with a white surrounding in a color cell and a white vertical line in the color chart You set a knot by setting the focus and remove a knot with the focus by clicking another time on a color cell with the focus The knots on the first and last cells of the colormap cannot be removed
47. be snapped i e the color channels will be tightened like a rope between the focus and the left or right knot When you move in a new region between two knots the old region will be restored and the new region will be affected by snapping When you release the button the focus cell s color values the one which you dragged will be copied to its last position and the colormap remains in this state 1 e with the copied color values in the focus cell and the snapped color values between the focus and the left or right knot While moving the color chart is refreshed with the new color course The color sliders stay the same because the focus cell s values remain the same remember you drag the focus and copy its cell s values C Using the color sliders The color sliders offer you three ways to modify the values associated to the focus cell Either by setting the value explicitly in the text field by dragging the small triangle or by clicking into the true slider s area All modifications have effect on the surrounding colormap entries between the next knots to the left and to the right of the focus cell A modification of a value changes the surrounding colormap entries relative to their distances to the focus This is similar to raising lowering a rubber band between the left and right knot in the focus position This could be best explained graphically in the color chart l Setting a value explicitly in the text field Simply do th
48. case namely scalar fields with regular structure Each step builds on the step before In particular the following topics will be discussed orthogonal slices simple threshold segmentation resampling the data displaying an isosurface cropping the data DD uu BW NY na volume rendering We start by loading the data you already know from Section 3 1 Getting Started a 3D image data set of a part of a fruit fly s brain The data set has been recorded with a confocal laser scanning microscope at the 3 2 VISUALIZATION OF SCALAR FIELDS 39 rl it F i Fi i y Ea Pi i y do j al ma a Figure 3 7 Lobus data set visualized using three orthogonal slices University of Wuerzburg e Load the file Lobus am located in subdirectory data tutorials 3 2 1 Orthogonal Slices The fastest and in many cases most standard way of visualizing 3D image data is by extracting orthog onal slices from the 3D data set Amira allows you to display multiple slices with different orientations simultaneously within a single viewer e Connect a BoundingBox module to the data use right mouse on lobus am e Connect an OrthoSlice module to the data e Connect a second and third OrthoSlice module to the data e Select OrthoSlice2 and press coronal in the orientation port e Similarly for OrthoSlice3 choose sagittal orientation e Rotate the object in the viewer to a more general position e Change the slice n
49. connected to the module This field determines how the isosurface is colored If no color field is connected to the module the isosurface has constant color Connections Data required The scalar field defined on a regular 3 dimensional grid ColorField optional Arbitrary scalar field which is mapped onto the isosurface using pseudo coloring Colormap optional The colormap is used for pseudo coloring the isosurface PointProbe optional If this port is connected to a PointProbe module as isovalue the value at a certain point within the scalar field will be chosen For details see PointProbe Ports Draw Style amp Draw Style shaded more options The draw style port 1s inherited from class ViewBase For a description of this port see there Colormap 3 Colomap 2 B Ap In case a colormap is connected to the isosurface module this colormap will be shown here If no colormap is connected to the module the port s default color is used To change this color click into the color bar with the left mouse button This will bring up the color selection dialog To connect the port to a colormap use the popup menu under the right mouse button See also Colormap Buffer Buffer Add Remove Clear Show Hide Draw This port must be enabled explicitly with the command Isosurface showBuffer For a de tailed description see the Viewbase documentation Threshold Threshold 4 2 Determines the value use
50. controls of an object or a module are organized in Ports Each port has a pin button on its left If a port is pinned it will still be visible even when the object is deselected The ports are composed of various widgets that reflect an operational meaning e g a value is entered by a slider a state is set by radio buttons a binary choice is presented as a toggle button The control elements have a uniform layout and are divided into several basic types A description of the basic port types is contained in the component index section of the User s Reference Manual 4 1 6 Viewer Window The 3D viewer plays a central role in Amira Here all geometric objects are shown in 3D space The 3D viewer offers powerful and fast interaction techniques It can be regarded as a virtual camera which can be moved to an arbitrary position within the 3D scene The left mouse button is used to change the view direction by means of a virtual trackball The middle mouse button is used for panning while the left and the middle mouse button pressed together allow you to zoom objects Sometimes you need to manipulate objects directly in the 3D viewer For example this technique called 3D interaction is used by the transform editor The editor provides special draggers that can be picked and translated or rotated in order to specify the transformation of a data object Before you can interact with these draggers you must switch the viewer into interaction mode This is
51. corners or edges of the TabBox and drag them around e To move the whole TabBox click with the right mouse button in the box and move it Try to get the TabBox into a shape and position as shown in the image Press Dolt button again in order to recalculate the stream lines Now some information about Console Window commands Most Amira modules provide more control features than those that are available by the ports displayed in the Working Area All of them are available by commands that you type in the console window You can get a list of commands associated with a particular module currently in use just by entering its name Now we will use such commands to form and position the TabBox exactly as in the image above 46 CHAPTER 3 FIRST STEPS IN AMIRA pF Le a Pia i s y os gt yl rF a aj inh Figure 3 14 Illuminated streamlines around a wing e Type DisplayIST into the Console Window e Type DisplayISL getBox into the Console Window The first command lists all commands of the DisplayISL module and the second shows the scale and trans lation of the current TabBox The first word of a command always has to be the name of a module as shown on its icon Note that module commands are not recognized unless corresponding modules have been loaded into the object pool However you do not need to select a module for typing in its commands e Type DisplayISL setBoxTranslation 0 31 0 00 0
52. data objects and modules can be modified in Amira s interaction area For some data objects such as surfaces or colormaps there exist special purpose interactive editors that allow the user to modify the objects All Amira components can be controlled via a Tcl command interface Commands can be read from a script file or issued manually in a separate console window The biggest part of the screen is occupied by a 3D graphics window Additional 3D views can be created if necessary Amira is based on the latest release of the TGS Open Inventor graphics toolkit In addition several modules apply direct OpenGL rendering to achieve special rendering effects or to maximize perfor mance In total there are more than 120 data object and module types They allow the system to be used for a broad range of applications User defined extensions are facilitated by the Amira developer version 2 2 Features Amira provides a large number of module types allowing you to visualize various kinds of scientific data as well as to create polygonal models from 3D images All visualization techniques can be arbitrarily combined to produce a single scene Moreover multiple data sets can be visualized simultaneously either 29 30 CHAPTER 2 INTRODUCTION E Gun E nasteriata j an Figure 2 1 Data objects and modules are represented as little icons in the object pool top right In the 3D graphic window a surface colored according to its curvature
53. de reporting on this error If possible determine the Cmd Directory of the batch job it is shown in the job dialog window when you select the job and attach all files existing in that directory to the e mail 1 5 E Field Simulations For E Field simulation HyperPlan offers three alternative approaches They differ with respect to the un derlying geometric model regular cubic grid or tetrahedral grid and the numerical method used FE or FDTD Each of HyperPlan s E field calculation modules computes a separate field for each channel of the hyper thermia applicator In particular 4 channels are computed for the Sigma 40 and Sigma 60 applicators and 12 channels are computed for the Sigma 2000 eye applicator 1 5 1 General Remarks About the FDTD Method The current release of HyperPlan contains two different FDTD modules which use different geometry models as input The first method directly works on a LabelField while the second one requires a tetrahedral patient grid Internally both methods operate on a cartesian grid consisting of cubic cells so called Yee cells Both methods currently only support the Sigma 60 applicator 22 CHAPTER 1 HYPERTHERMIA PLANNING e FDTD on label fields This algorithm merely requires roughly segmented CT data as input After importing the CT data and resampling it to 256 x 256 pixel resolution the LabelVoxel module should be activated This module transforms the Hounsfield values of the CT images pi
54. demo script illustrating the isoline module click here Connections Data required Scalar field for which isolines are to be computed Module optional Module defining cutting plane used for isoline computation Colormap optional Colormap used for pseudo coloring If no colormap is connected all isolines have equal color Ports Spacing a Spacing uniform explicit Control how isoline thresholds are being defined In uniform a certain number of isovalues are dis tributed equidistantly within a user defined interval In explicit mode the threshold for each isoline has to be set manually Values a Values 0 3 Furr 5 In uniform mode this port contains three text fields allowing the user to define the lower and upper bound of the isoline interval as well as the number of isolines being computed in this interval Values Values 0 75 2 25 In explicit mode an arbitrary number of blank separated threshold values can be defined in this text field For each threshold a corresponding isoline is displayed a o my O O e D amp Parameters resolution 128 line width 2 The resolution value determines the resolution of the sampling raster used for computing isolines This parameter is ignored if the incoming scalar field is defined on a tetrahedral grid and the resample option is off The second input of this port determines the width of the isolines in pixels Options a Options update min max
55. determine which color channel you want to edit This is controlled by your mouse buttons When you push the first mouse button you edit the first color channel with the second the second and by pushing the third button you modify the third channel If you want to manipulate the alpha channel provided that Show Alpha is set you have to hold the Control key while pushing the first mouse button This is summarized by the following table Color channel Mouse button Control key iret RA First No second G S second No third B V Enira No alpha ELCs Yes Editing the channel This is simply done by clicking with the desired channel s mouse button including pressing the Control key if you want to edit the alpha channel on the color chart The brush appears and you can move it all around the color chart The brush vanishes if you release the button Depending on whether you start above or below the channel the brush is fixed to lower or raise the channel When the brush touches the corresponding color channel the others will not be affected 1t moves the color channel up down depending on from which side it comes to the first pixel outside the brush s area No color channel can be moved below its minimum or beyond its maximum When you move the color channel to its minimum maximum it simply stops there and is not affected by further movements When you want to raise lower a channel already in its minimum maximum you have to m
56. done by clicking on the arrow button in the upper right corner If the viewer is in interaction mode the mouse cursor will be an arrow instead of a hand symbol You can use the ESC key in order to quickly switch between interaction mode and viewing mode If the viewer is in interaction mode use the Alt key to temporarily switch to viewing mode More than one viewer can be active at a time Standard screen layouts with one two or four viewers can be selected via the view menu Additional viewers can be created using the Tcl command viewer lt n gt show where lt n gt is an integer number between 0 and 15 While viewers 0 to 3 will be placed in a common 4 1 INTERFACE COMPONENTS 63 Amira View Rob Roty EIS Za El Dll 45 0 Doty Figure 4 3 Amira s viewer window provides a virtual trackball for easy navigation The decoration frame contains several controls allowing you for example to switch between viewing mode and interaction mode to choose certain orienations or to take snapshots panel window viewers 4 to 15 will create their own top level window For more specific control the viewer provides an extensive command set which is documented below The decoration of the viewer window provides several buttons and controls see Figure 4 3 The precise meaning of these controls is described below e Edit Background Color Pops up a color editor which
57. few options for his work with the color dialog The sliders and the corresponding text fields and arrow buttons let the user choose a color by hue saturation and value HSV or by the levels of red green and blue RGB The color picker allows the user to pick a color by sight Moreover the user can choose a predefined color from a palette of custom colors displayed by some of the color cells The buttons are used to apply or reset changes and to quit the dialog Here is a detailed description of the interface components Menu Bar The menu bar holds two pop up menus the Edit and the Options menu There are two items in the Edit menu allowing the user to toggle between different editing modes the Immediate Mode and WYSIWYG Mode EdH r Immediate Mode Ctr r WYSIWYG Mode Cirih W If Immediate Mode is selected each modification of the color to be changed is effective immediately e g if you are changing the background color of the 3D viewer and Immediate Mode is active the effect of every slider or picker operation can be observed directly in the viewer The WYSIWYG What You See Js What You Get Mode determines the background of the color sliders If WYSIWYG Mode is active the background of a slider shows a color range representing how the current color would change by moving this slider The user has the option of displaying and manipulating two different combinations of sliders RGB and HSV The Options menu holds two items repr
58. for finite element calculation If you want to visualize the surfaces select module Surface View from the surfaces popup menu 4 Before starting tetrahedron generation it is a good idea to check if the surfaces contain intersecting triangles Click on the green icon representing the surfaces Then invoke the Surface Editor by clicking on the button with the pencil icon Press Compute in order to perform the intersection test The number of intersections is shown in HyperPlan s Console window Click again on the pencil icon to leave the editor If there are intersections you can try to remove them by going back to the Antenna module and slightly changing the applicator position You can also change the Offset in module BolusGrid Normally a smaller offset value reduces the probability of intersections Caution If you want to use surface editing operations to remove the intersections as described in Section 1 4 2 you have to be very careful You must not change any triangles belonging to the patient s surface at this time because they are prescribed by the patient model If such triangles are changed the bolus grid and the patient model will not fit together later on 5 If there are no intersections select the TetraGen module from the surface s popup menu This module will generate a volumetric tetrahedral grid from the surfaces Tetrahedron generation is performed as a batch job Press button Run to submit the batch job If a file
59. graphics board A typical limit will be 2048x2048 pixels per tex ture On some architectures there is also a limit to the total amount of texture memory available This is of special importance for texture based volume rendering Details are given in the documentation for the Voltex module Does Amira support the VolumePro volume rendering hardware Yes Amira supports the VolumePro board on the Windows NT and Windows 2000 platforms If you need VolumePro support for other platforms please contact us Resources examples documentation 16 17 18 19 20 21 Where should I start to learn how to use Amira Probably the best starting point are the tutorials in the user s guide They provide a step by step learning by doing introduction How long does it take to learn how to use Amira Amira is easy to use After going through one of the tutorials for 15 minutes you will have an idea of the basic functionality Usually this is sufficient in order to be able to do first visualizations of your own data Of course becoming an Amira wizard and becoming familiar with all the features available in the system will take substantially more time Can I get training courses Yes training courses and consulting services are available For more information refer to the web sites www amiravis comorwww tgs com What is the relevant documentation Where can I find help The primary source for documentation is the Amira user
60. graphics cards support 2D texture mapping Older SGI systems like Indigo2 Extreme and the Linux platform currently do not offer hardware acceleration Using this module on the latter platforms can be extremely slow Note that on some systems a significant slow down can occur if the data set is larger than the available texture memory which typically is 4 16 MB 6 88 VOLTEX 181 Connections Data required The 3D scalarfield to visualized Colormap optional Colormap used to vizualize the data Ports Mode a Mode mip em ab max intensity shows the brightest data value along each ray of sight No absorption is used This mode is especially useful for very sparse data sets like e g angiographic data or images of neurons em ab Uses emission and absorption as described above Range a Range min 200 mas 200 If no colormap is connected data values are mapped according to this range Values smaller than the minimum are mapped to completely transparent no absorption and no emission Values larger than the maximum appear completely opaque and emit the maximum amount of light Values in between are mapped proportionally amp Lookup alpha luminance alpha rgba a Only available if a colormap is connected In Alpha mode the colormaps alpha value is used for both absorption and emission In LumAlpha mode the colormaps alpha value is used for absorption while the luminance o
61. green title bar in the Working Area that shows a pencil In response the image segmentation editor is popped up e Change the slice slider in the upper part of the editor s window to slice 39 e Choose a magnifiaction ratio of 4 1 by pushing the zoom up button in the left part of editor s window The image segmentation editor shows the image data to be segmented lobus am as well as green contours representing the borders between interior and exterior regions as contained in the lobus Labels data object As you can see the borders are not so smooth and there are many little islands bordered by green contours This is what we want to improve now 48 CHAPTER 3 FIRST STEPS IN AMIRA Figure 3 16 Surface representation of optical lobus as triangular grid e Choose Remove Islands from the editor s Label Filter menu In response a little dialog window appears e In the dialog window select the all slices mode Then press Apply in order to apply the filter in all slices Note how the segmentation results become less noisy e To further clean up the image choose Smooth Labels from the editor s Label Filter menu Another dialog box appears e Select the 3D volume mode and push the Apply button in order to execute the smoothing operation e To examine the results of the filter operations browse through the label field slice by slice In addition to the slice slider you may also use the cursor up and cursor down keys for this e
62. icol is connected to Colorwash automatically but the connection is not shown in the Object Pool display area This happens whenever one of the predefined colormaps is used otherwise you have to load your own colormap and connect it to Colorwash If you want to make changes in the input colormap invoke the Colormap Editor on the Colormap data object the Colormap port of Colorwash lets you set or replace the current input Colormap data object only it also provides two sliders for setting Min and Max values that define the subrange of the scalar data as required in the first mapping step Connections Data required The second scalar field to be visualized via a colormap Module required Connection to the OrthoSlice or ObliqueSlice module Colormap optional Connection to a Colormap Ports Colormap 3 Colomap 2 ET a The input Colormap If no Colormap is connected to the module the port s default color is used 1 e a Colormap with constant value To change this color click into the color bar with the left mouse button this brings up a color selection dialog To connect the port to a Colormap use the popup menu under the right mouse button See also PortColormap Mode Mode multiply replace 6 14 COMBINELANDMARKS 107 The Colorwash module offers two modes In the default multiply mode the RGB values from the colormap are multiplied with the grey values in the OrthoSlice as described above In the replace mode
63. is defined for the function key F2 You can define such a procedure for any other function key as well In addition procedures like onKeyShiftF2 or onKeyCtr1F2 can be defined These procedures are executed when a function key is pressed with the Shift or the Ctrl modifier key being pressed down 5 5 Frequently Asked Questions Questions General 1 What is Amira 2 What is the latest version of Amira 3 How can I try Amira Are there demo or evaluation keys 4 Is Amira Y2K compliant Installation hardware and platform related questions 5 What are the supported platforms for Amira Is Amira available on Windows 98 NT Compatibility between Windows and Unix version Can I display Amira on a remote screen Oo 0 2 D Do I need to have root or administrator privileges in order to install the product 10 What are the software and hardware requirements 11 What is the minimum configuration required for my platform 12 What is the recommended hardware for my purpose 13 What is the resource consumption of Amira for memory disk cpu graphics 14 Are there any limits to the size of textures that graphics boards can use 15 Does Amira support the VolumePro volume rendering hardware Resources examples documentation 16 Where should I start to learn how to use Amira 17 How long do I need to learn how to use Amira 18 Can I get training courses 19 What is the relevant documentation available 20 How do I see wha
64. lines setOutlineColor color Sets color of lines in outlined mode seCHIGOLIGNCCOLOr color Sets wireframe color of selected triangles setEmissiveColor color Sets the emissive color of the surface setSpecularColor color Sets the specular color of the surface This will only take effect if specular lighting has been enabled in port Draw Style setShininess shininess Sets the shininess of the surface showBox Shows box that is used for selecting triangles hideBox Hides box that is used for selecting triangles 6 88 Voltex Direct Volume Rendering is a very intuitive method to visualize 3D scalar fields Each point in a data volume is imagined to emit and absorb light The amount and color of emitted light and the amount of absorption is determined from the scalar data by using a color map which includes alpha values Default colormaps for volume rendering are provided with the distribution and can be edited using the colormap editor Then the resulting projection from the shining data volume is computed This module provides you with a hardware accelerated implementation which uses 2D and 3D texture hardware to allow for real time rendering Note that this currently is not supported by all grahics hardware Currently hardware acceleration for 2D and 3D textures is available on e g SGI Octane SSI MXI MXE SGI Reality and InfiniteReality SGI High Max Impact HP fx 4 and fx 6 The SGI O2 supports 2D textur ing Most PC
65. of the data probing modules determine the locations where the samples are to be taken PointProbe has one controlpoint which is the samplepoint LineProbe has two controlpoints which are the endpoints of a line which is subdivided into a number of segments given by the Samples port or by the Distance port and SplineProbe has at least three controlpoints that define a spline that goes through the endpoints and approximates the points in between The spline curve is subdivided into a number of segments given by the Samples port or by the Distance port by which the sample points are obtained To place the controlpoints within the bounding box of the given geometry you can either type in the coordi nates in the port Points see below or you can shift the points interactively with the mouse The latter can be done by turning the 3D viewer into interactive mode and picking and moving the crosshair dragger of the current point The plot immediately changes if the immediate mode toggle is set Usually the sampled values are plotted against the length of the probe line or as a bar in case of PointProbe in an extra plot window If you use more than one data probing module of the same type all plotted curves will be shown in one plot window PointProbe displays the value at the sample point and the material if material values are set LineProbe and SplineProbe display the length of the line resp spline Connections Data required Can be connected to arbit
66. part of HyperPlan The first part of this guide provides a step by step introduction to hyperthermia planning using HyperPlan The underlying software system Amira is described in the second part Before reading the following sec tions it is a good idea to become more familiar with Amira At least one of the introductory Amira tutorials should have been worked through An overview of the planning process is given in section Overview Technical prerequistes like file name con ventions used throughout the guide are described in section Filename Conventions The following sections are devoted to segmentation grid generation E field simulation temperature simulation and optimization issues 1 1 Overview Before discussing the technical aspects of HyperPlan let us first discuss some basic principles of hyperther mia simulation In regional hyperthermia two different physical processes have to be considered The first one is electromagnetic wave propagation inside the patient s body Simulating this process means to solve Maxwell s equations numerically For every point inside the patient we need to know the dielectric constant and the electric conductivity Given these parameters it is possible to obtain an approximate E field pattern as well as a corresponding power absorption also called SAR Specific Absorption Rate However from the therapeutic point of view the power deposition is less important than the resulting temperature increase
67. store colormaps The Icol file format and the col Colormap Editor originate from the Graphics and Visualization Lab GVL of the Army High Performance Computing Research Center AHPCRC Minnesota The Colormap Editor in Amira shares many ideas with the original AHPCRC tool The structure of an col format can be immediatly understood by looking at the examples in Amira s demo data directory 8 7 Inventor The Inventor file format is used for storing 3D geometries The format is very powerful The VRML format 208 CHAPTER 8 ALPHABETIC INDEX OF FILE FORMATS known from the World Wide Web is very similar to Inventor Since Amira is built on top of Inventor it naturally supports this format However Amira has added a lot of special purpose components to Inventor Therefore currently some geometries which can be displayed in Amira s 3D viewer cannot be saved in Inventor file format 8 8 JPEG Image Format JPEG is a standard format which can be used to store RGB and greyscale images in a highly compressed form However note that the compression algorithm is lossy When writing RGBA color fields the alpha channel will be discarded When reading RGB images an alpha value of 255 full opacity will be assumed JPEG files are automatically identified by the file name extensions jpg or jpeg Regarding the import and export of multiple slices the same remarks apply as for the TIFF image format When reading JPEG images the channel conversion
68. stored automatically e Push the Run now button in port Action A pop up dialog appears asking you whether you really want to start the grid generation Click Continue in order to proceed Once grid generation is running the progress bar informs you about the number of triangles which already have been created In some situations grid generation may fail for example if the input surface intersects itself In this case try to create a simplified surface with the fast toggle of the Surface Simplification Editor disabled You can also invoke the Surface Editor to interactively fix any intersections After the tetrahedral grid has been successfully created a new icon called lobus grid will be put in the Object Pool You can select this icon in order to see how many tetrahedra the created grid contains If grid generation takes too long on your computer you may also load the pre computed grid lobus grid from the data tutorials directory As the very last step you may want to have a look at the fruits of your work e Attach a Grid Volume module to the lobus grid e Select the Grid Volume icon and push the Add to button of port Buffer The Grid Volume module maintains an internal buffer and displays all tetrahedra stored in this buffer By default the buffer is empty but all tetrahedra are highlighted 1 e they are displayed using a red wireframe representation The Add to button causes the highlighted tetrahedra to be added to the buffer You ma
69. the filetypes ThermGridFD and ThermValsFD or ThermGridFE and ThermValsFE If you press the Parameters button a dialog window is popped up allowing you to change some global parameters for temperature simulation You can also change the thermal properties of the different tissue types For certain tissue types default values are taken from the HyperPlan material database 3 Temperature calculation will take ca 10 minutes CPU time It is performed as a batch job Press the Submit button to submit the job If one of the output files did already exist a warning message is issued If you don t want to overwrite the file press Cancel and change the filename When the job has been 26 CHAPTER 1 HYPERTHERMIA PLANNING submitted the job dialog window appears showing you the status of the job queue If you press the Start button the first pending job of the queue starts running When temperature calulation is finished and HyperPlan is still running the ThermGrid and Therm Vals files are automatically loaded 1 7 Temperature Optimization This section describes how to perform a temperature optimization The result of temperature optimization 1s a so called plan file containing the power amplitudes and phase settings of the individual channels of the applicator Before optimization can be started a temperature simulation on a tetrahedral patient grid has to performed as described in the previous section 1 From temperature simulation you will
70. the wrong triangles are removed auto matically The number of inconsistently oriented triangles and the number of removed triangles are printed in Amira s console window If triangles have been removed automatically you must subse quently select Fix Coplanars from the Surface Simplication Editor to remove them permanently If the automatic method could not remove all incorrect orientations you can proceed as in the case of intersections and try to repair them manually Important A prerequisite for the orientation test is that the outer triangles of the surface are assigned to material Exterior If the surface does not con tain such a material or if the assignment to Exterior is not correct the test will report falsely oriented triangles Buttons Aspect Ratio Dihed Angle and Tetra Quality sort all surface triangles according to different quality measures The aspect ratio is the ratio of the radii of the circumscribed and the inscribed circle of a triangle The largest aspect ratio should be below 20 better 10 The dihedral angle is the angle between two adjacent triangles at their common edge The smallest dihedral angle should be above 5 degree better 10 Button Tetra Quality may be useful if you want to create a tetrahedral volume mesh from the surface For each surface triangle the aspect ratios of the tetrahedra which will probably be created for that triangle are calculated The largest tetrahedral aspect ratio should be below 50 better
71. to crop a data set to enlarge it by replicating boundary voxels or to modify its coordinates i e to scale or shift its bounding box sources It determines how much light reaches each voxel on the ray and is emitted or absorbed by the voxel Then it computes what can be seen from the current viewing point as implied by the current placement of the volume relative to the viewing plane simulating the casting of sight rays through the volume from the viewing point You can choose between two different methods for these computations maximum intensity projections or an ordinary emission absorption model Remove all objects in the Object Pool other than the lobus am data record Connect a Voltex module to the data Select the data icon and read off the range of data values printed on the first info line 22 254 Select the Voltex module and enter the range in the Colormap port Click the Do t button in order to perform some texture preprocessing which is necessary for visualizing the data By default emission absorption volume rendering is shown The amount of light being emitted and absorbed by a voxel is taken from the color and alpha values of the colormap connected to the Voltex module In our example the colormap is less opaque for smaller values You may try to set the lower bound of the colormap to 40 or 60 in order to get a better feeling for the influence of the transfer function In order to compute maximum intensity projections
72. tour become a triangle in the resulting surface The result is almost guaranteed to be an oriented manifold Connections Data required The input point set Ports Probe Radius a ProbeRadius A 0 0177834 This slider specifies the radius of the probe sphere It is only relevant if the module is run in the fixed radius mode and when looking for an initial triangle If the algorithm is unable to find an initial triangle try increasing this value amp Search xis xO pO z YN O pao oe O z gt gt ji o UN The direction the probe is initially dropped from to find a starting triangle If no such triangle can be found try a different axis a ProbeMode fixed adaptive a a a Here you can choose the probe radius to be fixed throughout the whole computation or to adapt it to local feature size Adaptive probe size is faster than fixed probe size and gives better details on point sets that are relatively well behaved However it is less robust Enlargement amp Enlargement EA 1 15 6 62 REFINED E FIELD SIMULATION 153 If the algorithm is run in adaptive probe size mode the local probe size might be too small to find any more triangles If that happens the size is enlarged by this factor and the local search is restarted MaxlIterations amp Maxlterations AR As The iterative process described under Enlargement is repeated no more times than the nu
73. used by the script Ports File a File test hx File name of the TCL script Action a Acton Restart Call Call simply executes the script as a change of any other dynamically created port would do Restart deletes all dynamically created ports sets the isFirstCall flag to 1 and calls the script 6 65 SeedSurface This module extends the vector field visualization module DisplayISL It allows you to compute illuminated field lines of a vector field with seed points distributed across an arbitrary surface 6 66 SHEAR 157 First load both the vector field and the surface into Amira Then attach DisplayISL to the vector field From the popup menu of DisplayISL choose SeedSurface The SeedSurface module automatically connects itself to the first surface found in the object pool Of course you may change the surface connection at any time later on Properties of the illuminated field lines such as base opacity fade factor or color will be determined by DisplayISL Connections Data required Module of type DisplayISL which is used to display the illuminated field lines DisplayISL required The surface on which the field lines will be distributed Ports Z a j a NumLines za 100 Number of field lines to be displayed This port will only be visible if distribution mode on surface has been selected The distribution algorithm tries to achieve a constant seed density per surface area Length 3 Le
74. used to show or hide the decoration area Hiding the decoration is useful when multiple viewers are open and the size of a single viewing window is rather small viewer lt number gt setBackgroundColor lt r gt lt g gt lt b gt This command sets the color of the background to a specific value The color may be specified either as a triple of integer RGB values in the range 0 255 as a triple of rational RGB values in the range 0 0 1 0 or simply as plain text e g white where the list of allowed color names is defined in POST VANS yee x 66 CHAPTER 4 PROGRAM DESCRIPTION viewer lt number gt setBackgroundColor2 lt r gt lt g gt lt b gt Sets the secondary background color which is used by non uniform background modes viewer setBackgroundMode lt mode gt Allows you to specify different background patterns If mode is set to O a uniform background will be displayed Mode 1 denotes a gradient background while mode 2 causes a checkerboard pattern to be displayed This might help to understand the shape of transparent objects viewer setBackgroundImage lt imagefile gt This command allows you to place an arbitrary raster image into the center of the viewer s back ground The image must not be larger than the viewer window itself The format of the image file will be detected automatically by looking at the file name extension All formats mention for the snapshot command are supported except of Encapsulated Postscript
75. value will be mapped to white e Change the minimum and maximum values of the data window port until these values are the same and a suitable segmentation result is obtained For this data set 85 should be a good threshold value A more powerful way of quantitatively examining intensity values of a data set is to use a data probing module PointProbe or LineProbe However we will not discuss these modules in this introductory tutorial 3 2 3 Resampling the Data Now we are going to compute and display an iso surface Before doing so we will resample the data The resampling process will produce a data set with a coarser resolution Although this is not necessary for the iso surface tool to work it decreases computation time and improves rendering performance In addition you will get acquainted with another type of module The Resample module is a computational module Computational modules are represented by red icons and typically have a Dolt button to start the computation After you press this button they produce a new data object containing the result e Connect a Resample module to the data and select it e Enter values for a coarser resolution e g x 64 y 64 z 43 e Press the Dolt button A new green data icon representing the output of the resample computation named lobus Resampled is created You can treat this new data set like the original lobus data In the popup menu of the resampled lobus you will find exactly the same attachab
76. vector field wing am and select it Choose the slice number 22 in the Translate port Set filter length to 40 and resolution to 200 Press the Do It button of the Action port Whenever the projection plane of the PlanarLIC module is changed or other values for filter length or resolution are taken the LIC texture must be recalculated i e the Do It button must be pressed again Otherwise a checkerboard pattern will be displayed Experiment with different filter lengths and resolution values to see what kinds of textures can be produced To get an impression of the magnitude of the vectors you can apply a colormap to the image Some default colormaps are already loaded when Amira starts up The corresponding icons usually will be hidden In order to use one of the colormaps you have to select 1t explicitly e From the main window s Edit Show menu select temperature icol or any other colormap the correspond ing icon becomes visible e Select Magnitude from port Colorize of the PlanarLIC module A new port labeled Colormap appears in the working area e Connect the colormap port to temperature icol by clicking with the right mouse button in the red rectangle and choosing temperature icol from the appearing popup menu The two integer values of the colormap port specify the range of values to which the colormap is applied Vector magnitudes within this range are depicted symbolically by coloring streamline pixels such that each 3 3 VIS
77. 00000 00300000 Oe 500000 Lo OB 000 0 000000 0 000000 0 000000 1 000000 1000000 1 000000 0 900000 0000000 1 000000 0000000000 0 500000 1 000000 Oraa LO 10 5253 09 Patches 3 InnerRegion Green OuterRegion Yellow Triangles 7 le N E 11 le Le 11 I deal e N CO ODD amp N CO O1 Ma W Magenta OrRrRrR OOD ODO OF SIVIH 000000 000000 000000 00000 500000 9 00000 000000 OOO OOO 000000 200004 8 5 HXSURFACE 205 InnerRegion Magenta OuterRegion Yellow Triangles 1 Dize a InnerRegion Magenta OuterRegion Green Triangles 2 A KO oF TZ The first line is required and identifes the surface format Additional comments starting with a hashmark may appear at any point in the file Next an optional parameter section and a material section follow These sections have the same format as in an AmiraMesh file The parameter section may contain an arbitrary number of name value items The material section contains additional information about imaginary regions the surface patches are supposed to separate In contrast to an AmiraMesh file individual materials need not to have an d since they are referenced via their names The statement Vertices 11 indicates that the x y and z coordinates of 11 vertices follow Likewise the statement Patches 3 indicates that 3 patches follow The definition of each patch is enclosed by a pair of brackets and Inside these brackets InnerRegion and OuterRegio
78. 17 e Type DisplayISL setBoxScale 0 11 0 04 0 14 Now the sub field that corresponds to the clipping of the vector field as implied by the settings of the TabBox should look like the one shown in the image above 3 4 Grid Generation from 3D Image Data By following this step by step tutorial you will learn how to generate a surface grid and a volumetric tetrahedral grid for an object embedded in a voxel data set A surface grid 1s suitable for producing a 3D view of the object s surface a volumetric tetrahedral grid is the basis for producing various views of inner parts of the object e g cuts through it and both kinds of grids are frequently used for numerical simulations The generation process consists of these steps Threshold Segmentation Refining Segmentation Results Extracting Surfaces from Segmentation Results Simplifying the Surface Mm BB WO N e Generation of a Tetrahedral Grid 3 4 1 Threshold Segmentation The first step is to separate the object from the background This is done by segmenting the volume into exterior and interior regions on the basis of the voxel values 3 4 GRID GENERATION FROM 3D IMAGE DATA 47 Figure 3 15 Data from confocal microscopy is segmented using Amira s image segmentation editor Load the lobus am data record from the directory data tutorials Attach a Label Voxel module to the data icon and select it Type 85 into the text field of port Exterior Inside You m
79. 17 TIFF Image Format This is the 2D TIFF file format It can be used to read and write one or more 2D images If multiple images of equal size have been selected in the file dialog they will be combined into a single 3D image volume 8 17 TIFF IMAGE FORMAT 211 ee Image Read Parameters Files 1 Image Size 1 slices 6454453 1 channel Channel Conversion Channel 1 Bounding Box xMin o xMax 644 yHin o yHMax 452 zMin o Max 10 Object label 005 jpg Cancel Figure 8 2 Amira s channel conversion dialog 1 e a uniform scalar field of bytes or an RGBA color field TIFF files will be automatically identified by looking at the file header irrespectively by the actual file name extension Likewise if a 3D image data set is to be saved in TIFF format in fact for each slice a separate file will be created If you choose the 2D TIFF format in the file dialog s format menu a sequence of hashmark characters will be automatically inserted into the filename When saving the images the hashmark sequence will be replaced by the current slice number formatted with leading zeros For example if the base filename if image tif the files actually being written will be named image 0000 tif image 0001 tif and so on Note that not all variants of the TIFF format are supported In particular the following limitations apply e The number of channels must be 1 3 or 4 e The number of bits per pixel
80. 2 254 uniform coords Voxel Size 1 56963 x 1 56863 x 1 58386 3 Filter Median 20 y 8 Orientation lt planes y E Kemel Size 3 3 Action Apply Undo Figure 9 1 Digital image filters in two dimensional slices only In the latter case the orientation of the 2D slices can be selected via an option menu Currently the following filters are supported e 2D Median Filter e 2D Minimum Filter e 2D Maximum Filter e Unsharp Masking e 2D Histogram Filter e 3D Gauss Filter e 3D Lanczos Filter Ports Filter Specifies which filter is to be applied to the image Orientation This port will only be visible if a 2D filter has been selected It allows you select whether the filter should be applied in the XY XZ or YZ slices of the 3D image Action Starts computation 2D Median Filter The median filter is a simple edge preserving smoothing filter It may be applied prior to segmentation in order to reduce the amount of noise in a stack of 2D images The filter works by sorting pixels covered by a NxN mask according to their grey value The center pixel is then replaced by the median of these pixels 1 e the middle entry of the sorted list The size of the pixel mask may be adjusted via the text field labeled kernel size A value of 3 denotes a 3x3 mask An odd value is required 2D Minimum Filter The minimum filter replaces the value of a pixel by the smallest value of neighboring pixels covered by a NxN mask Th
81. 25 The worst triangle according to the selected quality measure is displayed and the worst quality is printed in the console window Using the buttons of port Display you can cycle through all other triangles and edit the surface if necessary Display This port provides three buttons First Next and Previous Depending on the last operation these buttons allow you to cycle through the list of all triangles sorted by quality or through the list of intersecting triangles These lists are not updated if you perform manual surface editing Instead you have to press one of the buttons of port Check again Undo Using this port you can undo the last editing operations edge flip edge collapse and ver tex movement in reversed order Currently the undo buffer is constrained to a maximum of 100 operations 9 12 TRANSFORM EDITOR 257 Info 224 4 161 59 labels 0 12 uniform coords Voxel Size 00187733 0 187734 1 a Manipulator Trackball a Reset All Translation Rotation Scale a Action undo eaa Figure 9 9 User interface of transform editor 9 12 Transform Editor This editor allows you to add a transformation to a data set or modify an existing one A transformation may be a translation rotation and scaling or a combination thereof The transformation can be edited interactively in the 3D viewer using standard Inventor draggers Make sure to switch the viewer to the interaction mode Details can be found i
82. 5 4 help load file html Load the specified hypertext document in the file browser Note that only a subset of HTML is supported help reload Reload the current document 4 1 INTERFACE COMPONENTS 61 Figure 4 2 The object pool contains data objects and module icons 4 1 5 Main Window Amira s main window consists of two components the Object Pool in the upper part of the window and the Working Area in the lower part The Object Pool contains icons representing data objects and modules currently in use as well as lines connecting icons indicating dependencies between objects and modules The Working Area is the place where the user interface of selected objects is displayed Typically the interface consists of buttons and sliders arranged in Ports They can be thought of as ports because the user can pass information to a module solely through them Object Pool Once a data object has been loaded or a module has been created it will be represented by an icon in the Object Pool Some objects especially colormaps may not be visible here Such hidden objects are listed in the Edit Show menu of the main window Selecting an object from this menu causes the corresponding icon to be made visible in the Object Pool Icon colors indicate different object types Data objects are shown in green computational modules in red and visualization modules in yellow Orange icons represent visualization modules of slicing type Such modules may
83. 55 56 57 58 59 Can I display axes Can I do image processing with Amira Does the surface reconstruction support non manifold topologies Is it possible to start Amira up with NO display in order to do batch processing of data or to generate pictures and plots without displaying anything on the console How does Amira behave with large data sets How can I change the background color of the viewer Can I display a colormap in the viewer window as legend How can I adjust color and transparency of individual parts of a surface How can I create an iso surface with fewer polygons than the iso surface module extracts How do I visualize data with holes in it How can I read a series of single image files such that I get a 3D stack How can I quickly switch between two different data sets How can I compare two data sets Specific features 60 61 62 Does Amira support Stereo viewing Does Amira support VR devices such as 3D mouse head mounted displays or CAVE systems Can I use antialiasing 82 CHAPTER 5 TECHNICAL INFORMATION Answers General l Ze 4 What is Amira Amira is a professional general purpose visualization and 3D reconstruction software Visualization means that you can display various data sets notably 3D image data vector fields and finite element data 3D reconstruction means that you can create polygonal surface models as well as tetrahedral grids from 3D image data What i
84. 7 How can I learn Tcl There are many good Tcl books For example you can try Tcl and the Tk Toolkit by John K Ouster hout the creator of Tcl Like many others this book also covers the Tk GUI toolkit Note that Tk is not used in Amira Technology 28 What graphics libraries are used by Amira Amira is based on the Open Inventor graphics toolkit Furthermore Amira contains a number of custom Inventor nodes which implement special visualization techniques These nodes apply direct OpenGL rendering 29 What is Open Inventor Open Inventor is a C library allowing you to describe and render 3D scenes Open Inventor is built on top of OpenGL This guarantees portability and hardware accelerated performance across a wide range of platforms 30 What is OpenGL OpenGL is a library for rendering 3D graphics OpenGL is the industry standard for professional 3D graphics It is supported by all professional graphics hardware and by an increasing number of consumer graphics cards 31 What is Tcl Tcl is a popular scripting language Tcl has a simple syntax so you can learn Tcl in one afternoon Amira has a built in Tcl interpreter This way Amira is scriptable 32 What is Qt Qt is a multi platform GUI software toolkit developed by Troll Tech www troll no An appli cation written with Qt can be compiled on Unix X11 as well as on Windows While the user interface of Amira 2 0 was based on Motif all releases of Amira 2 1 and later includ
85. 7 12 Temperature Sets Temperature simulations can only be performed for tetrahedral patient models Similar to the E field sim ulation linear independent temperature fields are computed The set of independent temperature fields 1s stored as an object of type HxTetraTemperatureSet From these fields the temperature distribution for any setting of the applicator parameters can be computed by simple superposition Again this is done by a Superpose module Like the SAR pattern the final temperature distribution is represented as an object of type HxTetraScalarField3 However notice that temperature distributions are defined on ThermGrid models while E fields and SAR distributions are defined on EF ie1dGrid models The latter may contain duplicated vertices at the tissue boundaries to represent field discontinuities 7 13 Tetrahedral Grid A data object of type TetraGrid represents an unstructured finite element grid composed of tetrahedra The geometric information is stored in terms of vertices edges faces and tetrahedra For instance such data objects are useful as patient models Like a LabelField with its uniform hexahedral grid structure a tetrahedral grid also contains a dictionary of different material types or regions In addition to the material names the dictionary may contain colors and other parameters related to material properties Amira is able to reconstruct tetrahedral grids from 3D image data This procedure involves several steps
86. A histogram is constructed for the selected tetrahedra only This is done in the following way The range of scalar values is divided into subranges given by the number of sample points With respect to each subrange one or more sub volumes of the tetrahedral grid are determined where the scalar field values fall into that range Then the volumetric sizes of the sub volumes are computed and these are depicted as differential histogram function values over the total range of scalar field values or used to calculate cumulative histogram values If the selected tetrahedra are members of different regions histograms are calculated separately for each region as well as for all selected tetrahedra called total Volume The histograms can be shown in several ways e differential shows a differential form of the histogram e absolute and relative show an integral form of the histogram 1 e for each value the partial volume is shown where at least that value is assumed For the integral form either the absolute volume ccm or the relative volume i e the percentage of the total volume of the corresponding region can be shown With the latter type of representation you can easily find out which value is at least assumed in 90 percent of a selected region Connections Data required A scalar field defined on a tetrahedral grid PortGridVol required A Grid Volume module that selects the tetrahedra for which the histogram is calculated
87. CHAPTER 6 ALPHABETIC INDEX OF MODULES ColorMode amp ColorMode Colormaps RGB Planes This port is only visible if all source fields are of equal dimensions and if they are all byte fields It means that faster algorithms are now in use and offers the special choice RGB planes which makes sourcel source2 and source3 the R G B compoment of the result respectively Action Action I Dolt Pushing this button triggers the field computation 6 13 Colorwash The Colorwash module helps you to visualize two scalar fields in combination e g medical images like CT data and a temperature distribution It can also be used for fusion of medical images from different modalities The first scalar field is mapped to a greyscale the second is mapped to colors Apply an OrthoSlice or an ObliqueSlice module to the first scalar field which must be a uniform or stacked field Select the green icon of the second scalar field and invoke Colorwash from the popup menu of the OrthoSlice or ObliqueSlice module The map used to determine the colors is a succession of three maps namely a linear ramp map of the scalar value range or a subrange thereof to an index set e g 0 255 a map of the index set to RGB values by a Colormap connected to the Colorwash module by an input port and a multiplication of an RGB value with a grey value from the underlying OrthoSlice module In the example above the predefinied colormap temperature
88. Click onto the pencil icon in the Working Area to close the image segmentation editor 3 4 3 Extracting Surfaces from Segmentation Results Now we let Amira construct a triangular surface of the segmented object A method called generalized marching cubes GMC is used for this purpose This method can handle probabilities associated to the voxels They were calculated when you applied the smoothing filter of the image editor and can also be computed by the Label Voxel module If the sub voxel accuracy option is set the GMC algorithm takes the probabilities into account to compute a smoother surface e Connect a GMC module to the lobus Labels data e Make sure that the toggles sub voxel accuracy and add border are set e Push Triangulate in the Action port The option add border ensures that the created surface is closed A new data object lobus gmc surf is generated Again it is represented by a green icon in the Object Pool 3 4 4 Simplifying the Surface Usually the number of triangles created by the GMC module is far to high for subsequent operations Thus the number of triangles has to be reduced in a surface simplification step In Amira a Surface Simplification Editoris provided for this purpose e Select the surface lobus gmc surf e Click on the triangle mesh icon second from the right in the title bar in the Working Area e Set the desired number of faces to 3500 in port Simplify 3 5 REGISTRATION AND WARPING TWO 3D OBJECTS U
89. Commands viewer lt number gt snapshot offscreen lt width gt lt height gt lt filename gt This command takes a snapshot of the current scene and saves it under the specific filename The image format will be automatically determined by the extension of the file name The list of available formats includes TIFF tiff tiff SGI RGB rgb sgi bw JPEG jpg jpeg PNM pgm ppm BMP bmp PNG png and Encapsulated PostScript eps If the viewer number is not given the snapshot is taken from all viewers if you have selected the 2 or 4 viewer layout from the View menu If the offscreen option is specified offscreen rendering with a maximum size of 2048x2048 is used In this case the viewer number is required even if viewer 0 is addressed If the width and height is not specified explicitly the size of the image is the current size of the viewer Caution If you have more than one transparent object visible in the viewer and you want to use offscreen rendering set the transparency mode to Blend Delayed and check to see if all objects are rendered properly prior to taking a snapshot viewer lt number gt setPosition lt x gt lt y gt Sets the position of the viewer window relative to the upper left corner of the screen The allowed range of x and y values is defined by the resolution of the screen Typically this will be 1280 x 1024 viewer lt number gt getPosition Returns the position of the viewer
90. Connections Data required Label field defining the regions Field optional Optional scalar field Ports Action E Action Dolt Triggers the computation 6 83 TriangleQuality The TriangleQuality module computes the triangle qualities for a triangular surface You can attach to the result a Surface View module to visualize the triangle qualities or a Histogram module to plot a histogram of triangle qualities You can also use the TriangleQuality module in conjunction with the Surface Editor to detect the worst triangles and manually repair them Connections Data required A triangular surface Ports Average edge length E Average edge length 0 0126384 Displays the average length of triangle edges in the input Output amp Output m This option menu lets you select between different quality measures 6 84 VECTORPROBE 173 Velocity shear Convergence 4 Divereence Acceleration Figure 6 7 Components of the vector field probe e R r Ratio of diameters of circumscribed and inscribed circle The optimal minimal value is 2 e Largest Angle Computes the largest angle degree of each triangle For numerical applications obtuse angles above 90 degree should be avoided e Dihed Angle Computes the dihedral angle degree for each pair of adjacent triangles Small dihedral angles below 5 10 degree should be avoided e Triangle Number For testing purposes only assigns the
91. D viewer Select the Antenna icon You may change parameters like position and inclination angle of the applicator The relative position of the applicator is specified in centimeters Caution The Sigma Eye button merely changes the geometric representation of the applicator Currently the FDTD solver only works for the Sigma 60 applicator 4 Attach the FDTD solver to the applicator by selecting FDTD from the popup menu of the Antenna icon A red icon appears representing a computational module Select the icon to bring up the user interface of the FDTD solver If you want to change dielectric constants or electric conductivities for some tissue types click on button Materials and enter the new values in the editor window Note The electrical parameters stored in HyperPlan s material database refer to a frequency of 90 MHz 5 In the field labeled EFieldVals you can specify the name of the file containing the simulation results We recommend to include the filetype EFieldValsFD into the filename 6 An E field simulation is expected to run several hours on a workstation Therefore it is performed as a batch job Press the Submit button to submit the job If the output file did already exist a warning message is issued If you don t want to overwrite the file press Cancel and change the filename When the job has been submitted the job dialog window appears showing you the status of the job queue If you press the Start button the first pendin
92. DITORS Ctrl Buttonl The picked triangle as well as all its neighbors are deselected and disappear Shift Ctrl Buttonl The picked triangle and all its neighbors become visible All other triangles are deselected Button2 If a vertex is picked a dragger is attached to that vertex The dragger allows you to change the position of the vertex If an edge is picked the start and end points of the edge are displayed Shift Button2 This operation flips an edge of the surface i e a common edge of a pair of triangles is removed and the alternative triangle defining edge with respect to the corresponding quadrupel of surface vertices is introduced as a surface edge thus the triangular layout is changed locally Flipping the edge a second time restores the original state Ctrl Button2 Collapses an edge of the surface Warning There is no undo for this operation Ports Check This port allows you to control the part of the surface being displayed Button Intersections checks the surface for intersecting triangles The number of intersections is printed in Amira s console window If intersections have been found they can be subsequently viewed using port Display Notice that a single intersection often will be reported multiple times because multiple triangles are involved Button Orientation checks the surface for correct orientation You should have removed all intersec tions before applying this check For simple configurations
93. IPTION The format option lets you select the file format EPS or Raster Image to be produced for file output If raster image has been selected the file format will be determined from the file name suffix The following formats are supported TIFF tif tiff SGI RGB rgb sgi bw JPEG jpg jpeg PNM pgm ppm BMP bmp PNG png and Encapsulated Postscript eps Note On many computers you may get better quality snapshots if you first switch the viewer into single buffer mode You can do this using the right mouse button popup menu in the viewer window By default the viewer uses double buffer mode This mode avoids flicker effects by rendering new images in the back buffer before copying the final image into the front buffer for visibility However since two buffers are used on some platforms the color depth is reduced and dithering is applied This may deteriorate image quality In single buffer mode you can observe some flickering resulting from images being rendered in the front buffer whose content becomes visible immediately On the other hand on some platforms the color depth in single buffer mode is higher than in double buffer mode Therefore when taking snapshots choose single buffer mode to obtain best quality 4 2 General Concepts This section contains some general comments on how data objects are organized and classified in Amira In particular the following topics are discussed e Amira Class Str
94. ITOR 215 al Colormap Editor Edit Mode Brush _ F Color cell O 0 o oC ay ol oo cof Blue 0 467 ME ars o i A Apply Cancel Help the color can be set with the picker One component corresponds with the vertical extent of the color picker and the other with the horizontal The selected component can not be changed with the picker To select a color using the color picker 1 move your mouse cursor on top of the color picker 2 press down on the left mouse button and move your mouse As you move your mouse around the picker the current color is set to the color beneath the intersection of the vertical and horizontal grey line 3 release the mouse button when the grey cross is on top of the color you like 9 2 Colormap Editor To change existing colormaps push the edit button pencil icon which is visible when the colormap is selected The colormap editor pops up As you can see there is a menu bar near the top border of the window with the sub menus Edit Mode and Brush which help you to control the behavior of the colormap editor and to change components of the chosen colormap 216 CHAPTER 9 ALPHABETIC INDEX OF EDITORS Below the menu bar a so called color chart is displayed The red green and blue lines are the graphs of the color channel components of the colormap the underlying color model is RGB at startup The axes are not shown directly the x axis ranges from the l
95. Immediate mode however the previous state of the colormap cannot be restored by Cancel If you think that your manipulations have gone totally wrong you can always decide to keep the old col ormap and throw away your changes This is done by pressing the Cancel button which also closes the editor window Cancel restores the colormap to the last state when the Apply button was pressed or to the initial if Apply was left untouched How to modify a colormap This section describes how to modify a colormap in various ways For the effects of invoking the various menu items see Menu bar A Using the color chart The only but possibly most comfortable manipulation you can do is to move a brush over a color channel and therefore raising lowering it in the brush s region 1 Choosing the right brush 9 2 COLORMAP EDITOR 219 You choose the brush in the menu bar s sub menu Brush where you see a choice of three brushes a square a circle and a diamond By its form you determine how much a colormap entry will be raised lowered e g when you select the diamond brush all channels you touch will be raised lowered by a small amount on the brush s edges corresponding to the sharp form of the diamond on the outer sides But with a square brush all color channels will be raised lowered by the same big amount in response to the square s form 1 e all positions have the same height Choosing the color channel Now it s up to you to
96. MODULES 6 73 Static Heat Nonlinear The Static Heat Nonlinear module performs a temperature simulation on a tetrahedral patient model The underlying heat transfer model is a nonlinear version of the Bio Heat Transfer Equation taking into account that blood perfusion depends on temperature The superposition principle see module Static Heat is no longer valid for the nonlinear case Therefore module Static Heat Nonlinear calculates only one temperature distribution corresponding to a specific optimal set of antenna parameters which are also determined by this module Note Nonlinear temperature simulation can only be done if the preceding E field calculation was per formed using the FE method module E Field Simulation On default a nonlinear behaviour is assumed for the following tissue types Fat Muscle and Target For the temperature dependence of blood perfusion a sigmoidal curve is assumed which is characterized by 4 parameters TLowForPerfusion lower bound for temperature THighForPerfusion upper bound for temperature PerfusionAtLow perfusion at lower bound and below PerfusionAtHigh perfusion at upper bound and above First you have to load a tetrahedral patient model as well as a set of E field channels into HyperPlan The patient models normally are called EFie1dGridFE while the files containing the E field channels have a suffix EFieldValsFE Connections Data A set of E field distributions as created by module E F
97. Material These properties can be changed as described above The Viewer Window In the center of the Image Segmentation Editor window you see the presently chosen slice with colored contours for the segments at startup Near the top border you find a slider to control which slice of the 3D volume is currently displayed The orientation e g XY XZ or YZ of the slice can be changed with the menu entry View Orientation in the menu bar As from version 2 1 of Amira there are two different viewer arrangements Single viewer and 4 viewer display You can choose between those with the View Layout menu In the 4 viewer mode three 2D viewers with the major orientations and an additional 3D viewer are displayed The orientation menu is disabled in this mode You can arbitrarily switch between the viewers during work One of the viewers is the active viewer It is depicted with a red frame A viewer can be made the active viewer by clicking on its title bar or into the viewer itself be careful when clicking into the image in 3D mode if the Pick tool or the Magic Wand tool is active All 2D operations like the or are allways performed in the active viewer i e in the slice and orientation currently shown in the active viewer See also the description of the Edit Options menu and the Zoom buttons in the toolbox Using the Zoom buttons These buttons control the size of the image An info line on the right hand side of th
98. Ok button all images will be combined in a single 3D data stack Note that the images should be of the same size How can I quickly switch between two different data sets Click with the left mouse on the blue line connecting one of the data icons and the visualization module icon in the Working Area and holding the left mouse button down move the line to the icon of the other data object How can I compare two data sets One solution is to display each data set in a different viewer You can activate up to four viewers via the View Layout menu If two viewers are visible attach a display module to each data set You can control in which of the viewers the output of a module is displayed by selecting the module and setting or unsetting the orange viewer toggles If you are using two OrthoSlice modules make sure that the same slice is displayed in both viewers In order to get the same camera settings in both viewers use the Tcl command viewer 0 set SlaveViewer 1 Whenever you navigate in viewer 0 the camera of viewer will be adjusted as well An alternative method to compare two different data sets is to compute and visualize the difference of both To subtract two fields from each other use the Arithmetic module Connect the module to both data sets by activating the popup menu over the small rectangle of the module s icon Then enter an expression like A B in order to compute the difference You can visualize the result of the Arithme
99. Rec eed swe A A Ree wh Ea eh Ee 102 CalcArca volume 2474s ido e td Y ee hs Bed te ole kta amp Sew af 2G ee 103 Casthicld e unes sa SSeS SS ee SBE ORES SSA ORS 103 Chippire Plane a road a SCR ee eB eR BE ve eR ee 104 COLOR OMDING 4 02 4 ie dd be SO Ad eee a a a 105 COLONS o Ps te es ge Brae Pet e A Ee eee Re Sek 106 Combine Land marks cs ido ah Spee ds te ed ed ee we ee See of oy 107 Componenthicld sarge 4 34 68 Se eek ee eB ESSER ACRE GSS 107 Compute SAR amp 4 518 bad lee Wa ee A hte bed ine a Se aoe 108 Compute ContoUes e isa Be he Ee ee oe Oe ee hee eee So eS 108 Connected Component Analysis rae 4 a ak od ew A ek Be BR a Ee 109 COMODI W e oasis So ce oe Soa a ll ee te ee eee oe Sew af ot 110 Contras COMIOL amp oa 2 6 A OS oA AA eS AAA OR a 110 Sl AA E AS 112 Daa OG es nino o lc ds GL os de See gh a ee a 113 Delay 21 she Se ger fate Ree ep sth od GE chee eed hve cae ce eet ch Re Th lla de AR 115 Displaveolonnap 2 ta hd de ee a See clas a le Se 115 Display IS gee oe rd BE OR ee Hav A ar BS SES OR OS 116 DIVE GENCE al 6 132 rena eet A o eo a td Be ea 118 Iu plcateiNOGes ws he Bi ee o oe ee oie fates a SE oe He 119 ES Pield S1milavl Ons gate 9h Gets Ba ee ee ee oe RA a Ee tee 119 FIO tse ay Ste alee y a re De A he Ee ee a AAN ee es 120 Pedut sanar BE Bre OE OD GEO EEE ORD Bae BAS RS 121 CI hara oh Wray De ae econ So a eo Rs o a eve a E es 122 A E a ia EA 123 aadi Ngee on o loas a r e e oe Soe ne aie do yee E
100. Resolution r_a Controls the resolution of the discretized stream surface or more precisely the preferred edge length of the triangulation Smaller values results in more details Length amp Length n 20 mp with 5 Value n determines how far the surface should be traced in backward direction Value m determines how far the surface should be traced in forward direction Value width determines the extent of the seed line The actual lengths in physical space depend on the value of port resolution All values may be changed using the right mouse buttons by means of a virtual slider Action Action Add ta Fesul Clear Result z axis This port provides push buttons allowing you to store the current stream surface in a surface object add to result respectively to remove all triangles from this surface again clear result More over the port provides an option menu allowing you to select the mode used for automatic seed line definition The following modes are supported Binormal The seed line will be traced in a direction perpendicular to both the stream line s tangent and normal curvature direction Often this gives quite meaningful results However note that in 164 CHAPTER 6 ALPHABETIC INDEX OF MODULES general the stream surface s normal vectors do not conicide with the stream line s curvature vectors except at the seed line Normal The seed line will be traced along the field line s normal cu
101. SING LANDMARKS 49 e Turn on the fast toggle in port Options This option disables some time consuming intersection tests e Push the Simplify button in port Action The number of triangles is reduced to about 3500 now The progess bar tells you how much of the simplifi cation task has already been done To examine the simplified surface attach a Surface View module to the lobus gmc surf data object e Attach a Surface View module to the lobus gmc surf surface More closely investigate the simplified geometry in the 3D Viewer e Before making the next step deactivate the display of the Surface View module by hitting the Viewer Toggle located in the module s yellow title bar For an explanation of the buffer concept employed in the Surface View module see the short description of the Grid Volume module below 3 4 5 Generation of a Tetrahedral Grid The last step 1s the generation of a volumetric tetrahedral grid from the surface This means that the volume enclosed by the surface 1s filled with tetrahedra Because the computation of the tetrahedral grid is time consuming it may be performed as a batch job You can then continue working with Amira while the job is running However in this case we want to compute the grid right inside Amira e Connect a TetraGen module to the lobus gmc surf surface e Clear the text field called Grid If the text field is not empty it specifies a filename under which the resulting tetrahedral grid is
102. SSIBILITY OF DAMAGE AND ON ANY THEORY OF LIABILITY ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE e The zlib library developed by Jean Loup Gailly and Mark Adler e The JPEG input and output routines are based in part on the work of the Independent JPEG Group e On Linux the Mesa OpenGL library developed by Brian Paul is used The library is subject to the GNU Library General Public License http www gnu org copyleft lesser html Itis linked as a Shared object so you may replace or upgrade it without recompiling Amira Amira is a registered trademark of ZIB Berlin OpenGL Open Inventor Silicon Graphics and IRIX are registered trademarks of Silicon Graphics Inc Sun and Solaris are registered trademarks of Sun Microsystems Inc 92 CHAPTER 5 TECHNICAL INFORMATION Part III Amira Reference Manual 93 Chapter 6 Alphabetic Index of Modules 6 1 Annotation This module displays a 2D text in the 3D viewer Position and color of the text can be specified by the user The module is useful to annotate snapshots For color legends refer to module DisplayColormap Ports Color a Color mu Choose text color with the ColorDialog Position E Position 40 y 40 Position of the text measured in pixels from the lower left corner If negative values are specified position is measured from the top or right border respectively Text a Text Some annotation best The te
103. Start button the first pending job of the queue starts running Connections Data A set of temperature distributions as created by module Static Heat The data files usually have a suffix ThermVals 6 57 OrthoSlice The OrthoSlice module is an important tool for visualizing scalar data fields defined on uniform cartesian grids For instance stacks of tomographic images are commonly displayed using OrthoSlice Such data are visualized by extracting an arbitrary axial frontal or sagittal slice out of the volume Within the slice the data are mapped to colors or grey levels by one of three mapping methods The most simple mapping technique uses a linear grey ramp In addition a data range can be specified This range determines which data values are mapped to black and which are mapped to white Alternatively a contrast limited histogram equalization technique may be applied With this method there is no unique correspondence between grey levels and data values any more The method tries to visualize all features of an image As a third mapping method an external colormap can be used in OrthoSlice Connections Data required The scalar or color field to be visualized Currently uniform cartesian grids of type HxUniform ScalarField3 HxUniformStackedScalarField3 and HxUniformColorField3 are supported Colormap optional The colormap used to map data values to colors This port is ignored when linear or histogram equalized mapping i
104. TER 6 ALPHABETIC INDEX OF MODULES Connections Data optional Data object the axes should be adapted to Ports Axis This port lets you select for which direction axes should be drawn Options E Options W arrows text Po grid This port provides three toggles If arrows is set arrows are drawn at the top of each axis If text is set labeled ticks are drawn indicating the coordinate values If grid is set a coordinate raster is drawn between every pair of visible axes Thickness a Thickness A Lets you adjust the thickness of the axes Colors a Colors mi anis Ej anis L z anis Of tent o ticks Provides buttons for changing the colors of different parts of the geometry On default the x y and z axes are drawn in red green and blue respectively Commands getFontName Returns the name of the text font Default is Helvetica setFontName lt name gt Lets you change the text font getFontsize Returns the size of the text font Default is 10 points setFontSize lt size gt Lets you change the size of the text font getBoundingBox Returns the bounding box of the volume enclosed by the axes setBoundingBox lt xmin gt lt xmax gt lt ymin gt lt ymax gt lt zmin gt lt zmax gt Lets you change the bounding box of the axis module Once the bounding box has been set automat ically the box will not be updated automatically anymore unless the set BoundingBox command is issued again with
105. TION interaction mode and viewing mode e Home Resets camera to the home position e Set Home Sets the current position as the new home position e View All Repositions the camera so that all objects become visible The orientation of the camera will not be changed e Perspective Ortho Toggles between a perspective and an orthographic camera By default a perspective camera is used You may want to use an orthographic camera in order to measure distances or to exactly align objects in 3D space e YZ XZ and XY Views Adjusts the camera according to the specified viewing direction The viewing direction is parallel to the coordinate axis perpendicular to the specified coordinate plane Medical doc tors are used to viewing series of tomographic images parallel to the X Y plane with the y axis pointing downwards This convention is followed by the XY button The opposite view direction is used if the Shift key is pressed e Rotate Rotates the camera around the current view direction By default a clockwise rotation of one degree is performed If the Shift key is pressed while clicking a 90 degree rotation is done If the Ctrl key is pressed the rotation will be counterclockwise Viewer Commands Commands to a viewer can be entered in the console window The syntax is viewer lt number gt command where lt number gt specifies the viewer being addressed The value 0 refers to the main viewer and may be omitted for convenience
106. The fields for all channels are written into a single file In HyperPlan the simulation results are represented as objects of type HxTetraEFieldSet or Hx VoxelEFieldSet depending on whether the simulation has been performed using a tetrahedral patient model or using the raw tissue labels In both cases the SAR distribution for a given set of power amplitudes and phases can be obtained using the Superpose module In the tetrahedral case the Superpose module can also be used to compute the resulting electromagnetic field The field will be stored as an object of type HxTetraComplexVectorField3 In case of a voxel based simulation this 1s not possible because the E field components have already been pre multiplied by sqrt o 2 where o denotes the electric conductivity of the tissue This makes it possible to compute SAR patterns without referencing the labeled volume which has been used for the simulation again The amount of data to be stored is smaller and data management becomes easier 7 5 Label Field Data objects of type LabelField are used to represent the result of a segmentation applied to a 3D image volume A LabelField is a regular cubic grid with the same dimensions as the underlying image volume For each voxel it contains a label indicating the region that the voxel belongs to Use module Label Voxel to create a LabelField from an image data stack You can manually modify a LabelField using Amira s image editor GI In addition to t
107. UALIZATION OF VECTOR FIELDS 45 3 a E B Ei ta pl Figure 3 13 Air flow around the wing visualized using Line Integral Convolution pixel gets the unique color associated with the magnitude value by the temperature icol colormap e Select the wing am icon and read off the magnitude range e Shift select the PlanarLIC icon and enter the magnitude range into the Colormap port 3 3 3 Illuminated Stream Lines Illuminated Stream Lines is a technique for interactive 3D vector field visualization which makes use of large numbers of properly illuminated stream lines A realistic shading model is employed which signifi cantly increases realism of the resulting images and enhances spatial perception Now you will learn which tools are used for illuminated stream line visualization and how to use them to get a 3D impression of our airflow vector field Remove the PlanarLIC module or disable its display Connect a DisplayISL module to the vector field wing am e Set Num Lines to 300 Press the Dolt button of the Distribute port Click on the TabBox button of port Box and zoom out the viewer if you cannot see a box A TabBox appears in the viewer Only stream lines flowing through this box are visible The green ticks at the corners and edges of the box allow you to change the dimensions of the box Switch the viewer into interaction mode Try out what happens if you click with the right mouse button on one of the green ticks on the
108. abelled tetrahedral volume grids e g tetrahedral patient models Views on various sub grids can be specified e g a view on a sub grid corresponding to one of the tissue compartments of a patient model The module maintains an internal buffer which contains all currently visible tetrahedra Tetrahedra belonging to a particular compartment can be selected and added to the buffer Selected tetrahedra are displayed using a red wireframe Having been added to the buffer they are displayed in their associated colors The selection can be restricted by means of an adjustable selection box In addition individual tetrahedra can be removed from the buffer by Ctrl clicking on one of their faces but notice that the viewer has to be turned into interactive mode for this Similarly a simple click on a face adds the tetrahedra in front of it to the buffer Connections Data required The labelled tetrahedral grid to be visualized ColorField optional Arbitrary scalar field which is mapped onto the grid volume using pseudo coloring Colormap optional The colormap is used for pseudo coloring the grid volume Ports Draw Style a Draw Style outined more options This port is inherited from the ViewBase class and therefore the description will be found there In contrast to other modules derived from the ViewBase class this module does not provide the possibility to consider vertex and direct normals The triangles will always be drawn flat
109. aces are most commonly used for analyzing arbitrary scalar fields sampled on a discrete grid Ap plied to 3D images the method provides a very quick yet sometimes sufficient method for reconstructing polygonal surface models Beside standard algorithms Amira provides an improved method which gener ates significantly fewer triangles with very little computational overhead In this way large 3D data sets can be displayed interactively even on smaller desktop graphics computers Like other polygonal models iso surfaces can be colored in order to visualize a second independent data set Another highlight comprises the realistic view dependent way of rendering semi transparent surfaces By correlating transparency with lo cal orientation of the surface relative to the viewing direction complex spatial structures can be understood much more easily 2 2 FEATURES 31 2 2 3 Segmentation Amira also provides a component for 3D image segmentation with several special purpose features This component is called image segmentation editor It offers a large set of segmentation tools ranging from purely manual to fully automatic Among others the following tools are provided brush painting lasso contouring magic wand region growing thresholding intelligent scissors contour fitting snakes con tour interpolation and extrapolation various filters including smoothing cleaning and connected compo nent analysis Although the display is slice orie
110. ach step builds on the steps described before We recommend that you read the text online and to carry out the instructions directly on the com puter Instructions are indicated by a dot so you can execute them quickly without reading the explanations between the instructions 33 34 CHAPTER 3 FIRST STEPS IN AMIRA hj i e m Ot at fat Figure 3 1 The Amira user interface consists of four major parts the 3D viewer 1 the object pool 2 the working area 3 and the console window 4 e On a Windows system select the Amira icon from the start menu On a Unix system start Amira by entering ami ra in a shell window If there is no such command the software has not been properly installed In this case try to execute the script bin start located in the Amira root directory When Amira is running windows like those shown in Figure 3 1 appear on the screen The user interface is divided into four major parts The 3D viewer window displays visualization results e g slices or iso surfaces The object pool will contain small icons representing data objects and modules The working area displays interface elements ports associated with Amira objects Finally the console window prints system messages and lets you enter Amira commands Amira provides an integrated hypertext browser You may use this browser to read the user s guide online In order to activate the browser type help in the console window or select User s G
111. ach vertex is shifted according to its neighbors coordinates Special care is taken in the case of boundary vertices for which not all the neighbors are considered but only those that are also on the boundary In this way the boundaries are preserved The smooth operation is controlled by two tunable parameters the number of iterations to be performed and a lambda coefficient which should be in the range 0 1 and describes the step for each iteration 6 69 SPLATS 159 Connections Data required The surface to be smoothed Ports Parameters a Parameters iterations 2 lambda 0 6 Contains two parameters Iterations specifies the number of steps for the smoothing lambda is a shifting coefficient which should be in the range 0 1 Action Action T Dalt Reset The Dolt button starts the smoothing pressing the Reset button the original surface will be restored 6 69 Splats This module visualizes scalar fields defined on tetrahedral grids using a direct volume rendering technique called cell projection splatting The principle of this method is to display a kind of semi transparent clouds The higher the data values the brighter and more opaque these clouds are Often meaningful results are obtained if this technique is used in conjunction with a standard isosurface module In order to get correct results for linearly varying functions a special texture mapping technique is applied On machines where texture m
112. ain the resulting tetrahedral grid is automatically loaded 1 5 E FIELD SIMULATIONS 21 If tetrahedron generation failed the job is also marked as being completed but some kind of error message is displayed If you want to determine the reason for a failure select the job and press the button View Output Look at the last lines of output created by the tetrahedron generation program e If you find the following message ERROR surface of current region is not closed surface can t be filled with tetrahedra an open surface occured for some tissue type The most probable reason for this failure is that toggle add empty slices was not set in the GMC module e If the message is ERROR surface of current region contains intersecting triangles surface can t be filled with tetrahedra some intersecting triangles have been generated during surface simplification If the surface intersection test has been passed successfully see Section 1 4 2 this error should not occur e If the message is ERROR surface triangles of current region don t have a uniform orientation surface can t be filled with tetrahedra some triangles with wrong orientation have been generated during surface simplification If the surface orientation test has been passed successfully see Section 1 4 2 this error should not occur e If none of the above three error messages occurs we would ask you to send an e mail to amira zib
113. alized ColorField optional Scalar field used for pseudo coloring the selected triangles Pseudo coloring also requires that a colormap has been connected to the module Colormap optional A colormap is used to map the data values of the optional scalar field Ports Draw Style a Draw Style outined more options This port is inherited from the ViewBase class and therefore the description will be found there In contrast to other modules derived from the ViewBase class this module does not provide the possibility to consider vertex and direct normals The triangles will always be drawn flat Colormap 3 Colomap 0 MU a This port becomes visible only if a scalar field has been connected to the ColorField port For further details see section Colormap 126 CHAPTER 6 ALPHABETIC INDEX OF MODULES Buffer a Buffer Add Remove Clear Show Hide Draw The Buffer buttons give you some control of the internal face buffer of the GridBoundary module Only the faces present in the buffer are displayed according to the current drawing style The Add button adds the highlighted faces to the buffer The Remove button removes highlighted faces from the buffer The Clear button removes all faces from the buffer The Hide button deselects all faces but does not change the buffer See also PortButtonList Materials Materials Exterior y E This port provides two menus where all different materials of the input grid are li
114. aller than the crease angle The default value is 60 degrees This command lets you overwrite this value Note that discontinuities will appear if the triangles of the input surface are not oriented in the same way In order to fix this use the command fixOrientation of the surface 6 78 SurfaceView This module allows you to visualize triangular surfaces 1 e data objects of type Surface Derived from the generic ViewBase class the module provides an internal buffer of visible triangles You can add triangles to this buffer by means of two special option menus For example if your surface contains regions FAT and MUSCLE you may first highlight all triangles separating these two regions by choosing FAT and MUSCLE in port Materials Highlighted triangles are displayed in red wireframe By pressing button Add to of port Buffer highlighted triangles can be added to the internal buffer which causes them to be displayed in their own colors You may restrict highlighting by means of an adjustable box In order to resize the box pick one of the green handles at the corners of the box Highlighted triangles may also be removed from the buffer by pressing button Remove In addition individual triangles may be removed from the buffer by shift clicking them Connections Data required The surface to be visualized ColorField optional In conjunction with a colormap an optional field can be visualized on top of the surface in pseudo color mode The
115. allows you to change the main background color of the viewer In order to change the secondary background color which is used if a non uniform back ground pattern has been selected use the Swap colors option of the main winodw s View Background menu see Section 4 1 3 Alternatively you may use the viewer command setBackgroundColor2 e Snapshot Takes a snapshot of the current rendering area and saves it in a file The filename as well as the desired output format have to be entered through the snapshot dialog Snapshots may also be taken using the viewer command snapshot e Seek Pressing the seek button and then clicking on an arbitrary object in the scene causes the object to be moved into the center of the viewer window Moreover the camera will be oriented parallel to the normal direction at the selected point Seeking mode may also be activated by pressing the S key in the viewer window e Animate Camera If this button is pressed the first camera path object found in the Object Pool will be used for animation No action is performed if no camera path is found In order to create a camera path select KeyframeCamPath from the Edit Create menu and invoke the camera path editor e Pick Switches the viewer into interaction mode You can also use the ESC key to toggle between viewing mode and interaction mode e View Switches the viewer into viewing mode You can also use the ESC key to toggle between 64 CHAPTER 4 PROGRAM DESCRIP
116. alue The Ok button of the editor window saves your changes After you have setup the simulation you can commit it by pressing the Submit button The Job Dialog window should appear showing you the status of the job queue If you press the Start button the first pending job of the queue starts running Display A bounding box of the calculation domain with size given by NumCubes times Cube Size is shown in the 3D viewer by pressing the box toggle 6 30 Field Cut The Field Cut module is a tool for visualizing cross sections of a 3 dimensional scalar field defined on a tetrahedral grid In general such grid volumes are made up of several materials A 2 dimensional cutting plane has to be defined for this purpose and may be shifted through the 3 dimensional tetrahedral grid in orthogonal direction an Orientation port is provided for setting the orientation of the cutting plane perpendicular to one of the main axes and a Translate port for specifying an orthogonal translation FieldCut renders a slice with the values of the scalar field mapped to colors of a connected colormap This is called pseudo coloring The cutting plane is usually clipped to a rectangle With the 3D viewer turned into interactive mode you can pick one of its edges and shift it through the grid volume To define arbitrary cutting planes you have to set the rotate toggle which makes a rotation handle appear in the center of the cutting plane Having turned the viewer into i
117. an includes an interactive editor for 3D image data called the image segmentation editor This editor lets you display and browse through the 2D slices of the data set You can activate it by first selecting the green icon representing a LabelField object and then pressing the pencil shaped edit button For a detailed description of the image segmentation editor please refer to the Amira reference manual When the editor is activated HyperPlan checks whether a CT data set with the same dimensions as the LabelField has been loaded If such a CT data set exists it is displayed as a background in the 2D viewing window of the segmentation editor Without a background image segmentation doesn t make much sense The background image may also be set manually by connecting the image port of the LabelField to the corresponding CT data set click with the right mouse button into the small rectangle left of the LabelField icon and choose ImageData Before starting the manual segmentation at least the following two filters should be applied e Remove Islands This filter removes small segments by assigning them to their surrounding segments In order to activate it choose Remove Islands from the Label Filter menu This causes a small dialog window to appear which allows you to adjust the maximal size in pixels of segments to be deleted as well as some percentage value Islands will be assigned to the tissue type that most of its neighbouring pixels belo
118. ancel and change the filename When the job has been submitted the job dialog window appears showing you the status of the job queue If you press the Start button the first pending job of the queue starts running More information is given in the reference documentation of the FDTD module 1 5 3 FDTD On Tetrahedral Grids This section describes how to start HyperPlan s FDTD solver for tetrahedral grids 1 Load one of the tetrahedral patient models filetype grid into HyperPlan Select module DuplicateN odes from the popup menu of the green data icon representing the patient model The popup menu is activated using the right mouse button Press the button Do it After a few seconds a new green icon appears It represents essentially the same tetrahedral grid as the original one but now containing dupli cated nodes at the boundaries between tissue compartments These duplicated nodes are necessary for representing the discontinuities of the electromagnetic field Save the new grid to a file We recommend to use the filetype EFieldGridFD 2 Load one of the tetrahedral patient models named EFieldGridFD into HyperPlan To visualize the patient model in the 3D viewer select a GridVolume module from the popup menu of the green data icon representing the patient model The popup menu is activated using the right mouse button 3 Select the Antenna module from the grid s popup menu A geometric representation of the applicator appears in the 3
119. and choose volrenRed icol e Set Lookup to RGBA and change the min and max values of the colormap to 40 and 150 e Finally press Do It in order to initialize the Voltex textures Whenever you choose a different colormap or change the min and max values of the colormap you must press the Do It button again This causes the internal texture maps to be recomputed An exception are SGI systems with Infinite Reality graphics On these platforms a hardware specific OpenGL extension is exploited causing colormap changes to take effect immediately 3 3 Visualization of Vector Fields This step by step tutorial briefly explains some Amira modules for vector field visualization The use of these modules is explained by way of data representing the flow around an airfoil The two methods referred to in steps 2 and 3 are independent of each other These topics will be covered 1 Loading the Wing and the Flow Field 2 Line Integral Convolution 3 Illuminated Stream Lines 3 3 1 Loading the Wing and the Flow Field As in the previous tutorials we use the file dialog to import data e Import the geometry of the wing by loading the file wing iv from the directory data tutorials e Attach an vDisplay module to this data object e Load the vector field data set called wing am from the directory data tutorials The extension iv indicates that the wing geometry is defined in the Open Inventor file format The vDisplay module can be used for displaying
120. angular surface meshes or tetrahedral grids are defined by irregular coordinates The result of Magnitude is a field of scalars located at positions according to the underlying grid of the input data Connections Data required Vector field or complex vector field defined on a regular grid Reg VectorField3 RegComplexVector Field3 Vector field on an irregular grid either specified by nodes of a surface or a tetrahedral grid TetraVec torField3 Surface VectorField 142 CHAPTER 6 ALPHABETIC INDEX OF MODULES Ports Number of Vectors amp Vectors 110592 Shows number of input vectors for computing the magnitude field Compute E Compute U Dolt Pushing this button triggers the computation 6 55 ObliqueSlice The ObliqueSlice module lets you reconstruct arbitrarily oriented slices through 3D scalar fields of any type as well as through 3D color fields In the medical context such slices are also known as multi planar reconstructions MPR The module is derived from ArbitraryCut See the documentation of the base class for details about how position and orientation of a slice can be changed Like in the OrthoSlice module three different methods are supported to map scalar values to screen colors namely linear mapping monochrome mapping based on an adaptive histogram equalization technique as well as pseudo coloring Connections Data required The scalar or color field to be visualized Colormap optio
121. annel conversion dialog is popped up This dialog is also is also described the TIFF section 8 15 STL STL is a CAD format for Rapid Prototyping It is a faceted surface representation i e a list of the triangular surfaces with no adjacency information Currently the ASCII version of the format is supported for writing Amira objects of type Surface 8 16 Stacked Slices This file format allows to read a stack of individual image files with optional z values per slice The slice distance needn t be constant The images must be one channel images in an image format supported by Amira e g TIFF The reader operates on an ASCH description file which can be written with any editor Exemplary layout of a description file Amira Stacked Slices pathname usr data pictures proturel cit 10 0 FThts Ls a Comment pruCtLUTS Taca O00 praoturelo CIT 000 COLS tales pa 3040 end Amira Stacked Slices is an optional header which allows Amira to automatically determine the file format pathname is optional and can be included in case the pictures are not in the same directory as the description file A space or has to separate the tag pathname from the actual pathname Default is the subdirectory of the description file picturel tif 10 0 isthe name of the slice and its z value separated by a blank end defines the end of the description file With a after z values or the pathname comments can be included into the file 8
122. apping is not supported in hardware this might be quite slow As an alternative untextured splats may be used However in this case the scalar field is assumed to be constant in each tetrahedron To obtain such a piecewise constant function the vertex values of each tetrahedron are averaged As a consequence artifical discontinuities might be observed Connections Data required The tetrahedral scalar field to be visualized Ports Alpha Scale A global factor used to change the overall transparency of the individual splats Higher values produce denser clouds This value determines how the function value between the min and max values of port Range will be mapped to opacity and color If the gamma value is 1 a linear mapping will be used If the gamma value is smaller than the overall appearance of the cloud gets more opaque If the gamma value is bigger than 1 the cloud gets more transparent Range Range 239172 43 9744 160 CHAPTER 6 ALPHABETIC INDEX OF MODULES Data range Regions where the function value is below the min value will be completely transparent Likewise regions where the function value is above the max value will be opaque Interpolation amp Interpolation constant linear Lets you select the type of splats being used Constant enables untextured splats Linear enables textured splats The latter setting will be able to correctly display linearly varying scalar fields Commands setColor lt c
123. art up script e Frequently Asked Questions e System Requirements e Acknowledgements and Copyrights 5 1 Data Import Usually one of the first things Amira users want to know 1s how to import their own data into the system This section contains some advice intended to ease this task In the simplest case your data is already present in a standard file format supported by Amira To import such files simply use the File Load menu A list of all supported formats can be found in the index section of the user s guide Usually the system recognizes the format of a file automatically by analyzing the file header or the filename suffix If a supported format is detected the file browser indicates the format name Often 3D image volumes are stored slice by slice using standard 2D image formats such as TIFF or JPEG In case of medical images slices are commonly stored in ACR NEMA or DICOM format If you select multiple 2D slices simultaneously in the file browser all slices will automatically be combined into a single 3D data set Simultaneous selection is most easily achieved by first clicking the first slice and then shift clicking the last one If your data is not already present in a standard file format supported by Amira you will have to write your own converter or export filter For many data objects such as 3D images regular fields or tetrahedral grids Amira s native AmiraMesh format is most appropriate Using this format you can eve
124. ary condition ids with special meanings The meaning of an id depends on the type of simulation to be performed on the grid E field or temperature simulation e predefined boundary condition ids for E field simulation 102 CHAPTER 6 ALPHABETIC INDEX OF MODULES id 1 outer boundary open boundary conditions id 11 59 antenna triangles metallic boundary conditions id 61 99 triangles of antenna junctions e predefined boundary condition ids for temperature simulation id 1 predefined temperature 37 C Dirichlet condition id 2 insulating surface Neumann condition id 3 boundary to water bolus Cauchy condition id 5 boundary to air Cauchy condition Connections Data required The tetrahedral grid to be visualized Ports Bound cond id deal E This port provides a menu where all boundary condition ids occuring in the input grid are listed Faces belonging to the selected id are displayed using a red highlighted wireframe in the viewer You may crop the faces by turning the viewer into interactive mode and move the green handles of the selection box Only the faces inside the bounding box can be added to the buffer Buffer a Buffer dd to Remove Clear Hide box The Buffer buttons give you some control of the internal face buffer of the BoundaryConditions module Only the faces present in the buffer are displayed according to the current drawing style The Add button adds the highlighted faces to the buffer
125. ater the distance to the initial position of the mouse click gets the more the contour grows The contour is designed to grow in areas with homogenious grey values and to stop where grey values change abruptely 1 e at image edges The tolerance slider in the option panel controls how sharp the image edge has to be in order to stop the contour from growing at each contour point The smaller the tolerance the sharper the image edge has to be If the tolerance is large the contour will even stop at weak edges After releasing the mouse button the area within the contour will be marked Before the computation the image is smoothed using a gaussian smoothing filter You can change the width of the filter within ranges of 1 no smoothing to 8 very broad smoothing The default value is 4 The menu bar The menu bar has four sub menus Edit This menu provides an undo entry which undoes the last operation Succesive invokation of undo is possible to undo several operations Note that for memory and performance reasons 3D operations can not be undone Therefore it is highly recommended to frequently save the label field The options entry brings up an additional dialog in which you can control the data window and the opacity of the selection View This menu lets you change the Layout of the image viewer area You can choose between either one single viewer or four viewers three slice viewers one 3D viewer Details on these two arrangements are d
126. aterials in the image viewer the material you have clicked on the present appearance is marked The possible appearances are e Invisible The material is not visible e Contour The segments are enclodes by lines Hatched The segments are enclosed by lines and shown hatched e Dotted The segments are enclosed by lines and filled with dots e Light Dots The segments are enclosed by lines and filled with less dots e Locate This command sets all viewers to the slice with the largest region of this material This is especially useful to navigate in large data sets with many materials e Delete If you choose Delete the region you have clicked on will be deleted assigning all of its voxels to the first material in the list typically the background e Rename With this option you can change the name of a material A text cursor appears and lets you edit the name as easily as any other text field e Edit color This command brings up a color editor in which you can easily change the color of this material e Lock Unlock Material You can lock a material with this option A key will be displayed on the right hand side of each locked material If a material is locked no voxels can be subtracted from this region neither explicitly nor implictly by adding them to another material e New Material By selecting New Material from the popup menu a new entry is added to the material list with a randomly chosen color and a default name e g New
127. atient s and the applicator s geometry If necessary check if the chosen value is not too small This is the case if the power deposition pattern in the patient is independent of variations of the number of cubes The number of iterations should be chosen as at least 2500 for a size of 1 cm and at least 1500 for a size of 2 cm These iteration numbers prove to be sufficient for modelling the Sigma 60 applicator in the frequency range 80 120 MHz Furthermore the FDTD inherent resolution lies because of storage restrictions in the range of about 1 cm which is a value much bigger than the pixel resolution of the CT slices of about 1 mm Both the voxel based and the modified models are idealizations and cannot contain the full patient geometry information Keep in mind this important fact especially if the FDTD results are visualized over the CT background e g using the colorwash option The relative coarseness of FDTD lattice with respect to the real patient geometry requires averaging and interpolating procedures Thus solutions obtained may differ depending on the FDTD version used How to achieve a better field resolution within the patient s body and a better antenna modelling is still a subject of research 1 5 2 FDTD On Label Fields Once the CT volume has been labeled you can start an E field simulation From the popup menu of the green LabelField icon select the Antenna module This module defines the hyperthermia applicator Note Cu
128. ault settings compute contours between all the materials Connections Data required The label set to extract contours from Ports Orientation a Orientation O xf yt z Controls the direction used for contours computing The cutting planes will be orthogonal to this axis For example if z axis is selected all the contours will be contained in xy planes Options a Options M subwoxel accuracy There is only one check button which controls the use of subvoxel accuracy information 1f present Materials a Materials E Selects a material only contours separating this material from others will be computed By default all the materials and implicitly all the contours are considered 6 18 CONNECTED COMPONENT ANALYSIS 109 Action a Action E Dalt Triggers the computation 6 18 Connected Component Analysis This module searches for 6 connected regions in an image volume Regions are detected based on thresh olding A region is a set of adjacent voxels with a certain intensity This module is e g useful to count cells on a dark background Only input fields of type byte are supported Connections Data required Image dataset to be analyzed Ports Info a Info 0 components After hitting Dolt this port will display the number of detected regions the volume range and the average volume p ca O DN pi o ca lt amp Intensity Min el Mas 255 Voxels with values ou
129. ay On the other hand the port also provides an option menu specifying the way how seed points are distributed inside the seed box On default a homogeneous distribution will be used Alternatively seed points may be distributed according to the vector field s magnitude or according to the value of the distribution field if such a field is connected to the module The equalize option provides a mixture of homogeneous and proportional seed point distribution 6 26 Divergence The Divergence module computes the divergence of a vector field consisting of floats defined on a uniform grid The output is a uniform scalar field Connections Data required Vector field defined on a uniform grid UniformVectorField3 The vector components must be floats 6 27 DUPLICATE NODES 119 Ports This module has no ports 6 27 Duplicate Nodes This module takes a labeled tetrahedral grid as input and produces a new grid with all nodes on interior boundaries being duplicated Interior boundaries can be visualized using module GridBoundary They consist of all triangles incident on two tetrahedra with different labels Duplicated nodes are useful to represent discontinuities within a vector field e g an electric field on a tetrahedral patient model On an interior boundary such a field may have multiple values one for each incident material subvolume Connections Data required A tetrahedral grid without duplicated nodes Ports Acti
130. ay also determine some other threshold that separates exterior and interior as described in the tutorial on Scalar Field Visualization Choose the remove couch option from port Options Press the Dolt button of port Action By this procedure each voxel having a value lower than the threshold is assigned to Exterior and each voxels whose value is greater than or equal to the threshold is assigned to Interior This may however cause artifacts that are not part of the object but have voxel values above the threshold being assigned to the interior This can be suppressed by setting the remove couch option which assures that only the biggest coherent area will be labeled as the interior and all other voxels are assigned to the exterior After pressing the Dolt button a new data object is computed and its icon appears in the Object Pool The data object is denoted lobus Labels It is of type LabelField represents a cubic grid with the same dimen sions as lobus am and contains an interior or exterior label for each voxel according to the segmentation result 3 4 2 Refining Segmentation Results You can visualize and manually modify a LabelField by using Amira s image segmentation editor A more detailed description of this tool is contained in the User s Reference guide Here we use the image segmentation editor to smooth the data in order to get a nicer looking surface of the object e Select the lobus Labels icon and click on the icon in the
131. ay the loss of information caused by the resampling process will be minimized The GMC module can use the probability information to generate smoother surfaces 6 32 GETCURVATURE 123 Connections Data required LabelField from which the interfaces should be extracted Ports Options Options M subvosel accuracy 4 add border This port provides two toggles If sub voxel accuracy is on the probability information of the incom ing LabelField will be used to generate smoother surfaces If this option is off or if the LabelField does not contain probabilities no such smoothing is performed The second toggle add border ensures that the resulting surfaces will be closed even if some regions extend up to the boundary of the LabelField Closed surfaces are required if a tetrahedral grid is to be generated later on Border amp Border I adjust coords extra material This port will only be visible if add border has been selected It provides two toggle buttons labeled adjust coords and extra material It the first option is selected points belonging to triangles adjacent to boundary voxels will be moved exactly onto the nearest boundary face of the bounding box In this way the resulting surface appears to be sharply cut off at the boundaries The second toggle indicates that triangles adjacent to boundary voxels will be inserted into separate patches The outer region of these patches will be called Exterior2 If the toggle is of
132. b EE 3 Modifier Modi Combined Smoothing y D Parami nLoops E E Param threshold 1st loop Ja E Param threshold other loops Pra E Param4 save boundary triangles jo Figure 9 2 Tools for improving the quality of tetrahedral grids with the Grid Volume module If such a module is not already active an instance of it will be automatically created when the editor is invoked Tetrahedra can be distorted in different ways Slivers contain 4 nearly coplanar vertices forming a quadrangle Caps consist of a triangle and a 4th vertex just above it Needles consist of a triangle and a 4th vertex far away Wedges are characterized by one sharp edge Using the tools of the Select menu Index Selector This tool selects tetrahedra according to their index 1 Aspect Ratio Selector This tool selects tetrahedra according to their determinant d diameter ratio R or other dimensionless quality measures rl r2 Angle Selector This tool selects tetrahedra according to their minimal and maximal dihedral angles d D or solid angles s S For each edge of a tetrahedron the dihedral angle is defined as the angle between its adjacent faces The solid angles are related to the tetrahedron vertices they measure the part of the unit sphere which is occupied by the tetrahedron For an equilateral tetrahedron all dihedral angles are ca 70 deg all solid angles are ca 30 deg You can combine different selections e g the se
133. b is finished execution of the next job in the queue starts automatically thus all jobs in the queue will be executed successiveley by job run 4 1 9 File Dialog The File Dialog is the user interface component for importing and exporting data into resp from Amira It is used at several places in Amira most prominently by the Load Save Data As and Save Network items of the main window s File menu The dialog provides two modes of information a detail mode and a multi column mode In the detail mode which is active by default some file data are shown next to each filename namely the file size the file s last modification time and the file format You may sort the file list according to each of these properties by clicking on the particular column s header bar Subdirectories will always be displayed first In multi column mode only the file name is displayed You may switch between both modes using the tool buttons in the upper right part of the dialog window Most file formats supported by Amira will be recognized automatically either by analysing the file header or by looking at the file name suffix A list of all supported file formats is contained in the reference section of this manual You may manually set the format of a file by means of the dialog s popup menu see below 4 1 INTERFACE COMPONENTS 71 Output toie to printer A EA Browse Formal TIF I gisyscale Figure 4 7 The snapshot dialog allows
134. be ok But if you read data produced e g under Linux little Endian on an SGI big Endian you have to specify the correct byte order of the data to be read little Endian in this case e Index Order Order in which the data points are read The raw data format is a very powerful tool especially for quick access prototyping use However it may sometimes be tricky to figure out the parameters Some tools which may help are vi or od c to examine 210 CHAPTER 8 ALPHABETIC INDEX OF FILE FORMATS the header of files After loading click on the icon If the data range is obviously completely wrong then you have either specified a wrong data type or a wrong endianess or a to short header If most of the volume looks ok but is shifted in x direction then you probably have specified a wrong header If the data range looks ok but the data seems scrambled then you have specified wrong dimensions or a wrong index order 8 14 SGI RGB Image Format This is the SGI file format for RGB and greyscale images When writing an RGBA color field the alpha value will be discarded When reading RGB images full opacity is assumed 16 bit data values even though allowed by the SGI file format specification are not supported SGI RGB files are automatically identified by the filename extensions sgi rgb or bw Regarding the import and export of multiple slices the same remarks apply as for the TIFF image format When reading SGI RGB images the ch
135. be used to clip the graphical output of any other module Connections between data objects and processing modules shown as blue lines represent the flow of data You may connect or disconnect objects by picking and dragging a blue line between object icons As you might expect not all types of processing modules are applicable to all kinds of data objects If you click on an icon with the right mouse button a menu pops up that shows all types of modules that can be connected to that object Selecting one of them will automatically create an instance of that module type and connect it to the data object A new icon and a connecting line will appear in response This way you can set up a more or less complex network that represents the computational steps required to carry out a specific visualization task and is indeed used to trigger them If you look closer at an object s icon you will notice a tiny rectangle on its left If you click on it with the right mouse button a menu pops up that shows all connection ports of that object As mentioned above for most objects the required connections are automatically established on creation However in order to set up optional connections you must use the connection popup menu For example you may attach an optional scalar field to an Isosurface module in order to let its values on an existing isosurface be encoded by colors The colormap used for pseudo coloring is specified by another connection port O
136. between the original and the sheared z axis can be specified 158 CHAPTER 6 ALPHABETIC INDEX OF MODULES Connections Data required Connects to uniform scalar fields Info Info 224 311 59 mas shift 150 pixel The output field will be larger than the input field This port gives the details Specifies the angle between the input z axis and the sheared z axis Positive and negative values are allowed Dolt 3 Dolt E Dolt Triggers the computation 6 67 ShowContours This module computes and shows contours for a 3D label field on a 2D cutting plane The plane itself is defined by another module which must be connected to port Module Since the label field has integer coordinates and from the intersection with an arbitrary cutting plane result real coordinates the algorithm must make approximations This approach may lead to artifacts if the sampling density is too low The module computes contours between all the materials Connections Data required 3D label field for which contours are to be computed Module optional Module defining cutting plane used for contours computation Ports Parameters amp Parameters resolution 128 line width 2 The resolution value determines the resolution of the sampling raster used for computing contours The second input of this port determines the width of the contours in pixels 6 68 SmoothSurface This module performs a surface smoothing by shifting its vertices E
137. called HxSurface This class is documented in more detail in the index section of the user s guide For the moment we only mention that the class maintains connectivity information and that it may represent manifold as well as non manifold topologies 4 2 GENERAL CONCEPTS 75 The surface class provides a rich set of Tcl commands It is a good example of an Amira data class that does not simply store information but allows the user to query and manipulate the data by means of special purpose methods and interfaces 4 2 5 Vertex Set Another example of data abstraction and inheritance is the VertexSet class Many data objects in Amira are derived from this class e g landmark sets molecules surfaces or tetrahedral grids All these objects provide a list of points with x y and z coordinates Other modules which require a list of points as input only need to access the VertexSet base class but don t need to know the actual type of the data object One such example of a generic module operating on VertexSet objects is the Vertex View module This module allows you to visualize vertex positions by drawing dots or little spheres at each point 4 2 6 Transformations Data objects in Amira can be modified using an arbitrary affine transformation For example this makes it possible to align two different data objects so that they roughly match each other Internally affine transformations are represented by a 4x4 transformation matrix I
138. cation editor are sucessively reduced to points The shape of the original surface is preserved by minimizing a certain error criterium Special care is taken to prevent the triangles of the simplified surface from intersecting each other However in some cases intersections can still occur Therefore the resulting surface should be checked for intersections using the surface editor Ports Simplify This port provides two text fields for controlling some parameters of the simplification process Field faces determines the desired number of triangles of the simplified surface You may simplify the surface in multiple steps However somewhat more accurate results are obtained if the simplification is performed in a single step When the simplification process is finished a check is made whether the surface contains coplanar triangles Such triangles are removed automatically Therefore the total number of triangles of the reduced surface will usually be somewhat less than the value specified in faces The second field max dist defines a maximum edge length for the triangles of the simplified surface Collapsing edges with a length exceeding this value will occur less likely Usually the default value of 3 cm should be suitable but you can try to modify this value if the reduced surface still contains intersections Options If the toggle preserve slice structure is set edges of exterior triangles of the surface are treated in a special way s
139. ces are referenced by indices starting from 1 not from 0 The following example describes the surfaces of three connected tetrahedra which are assigned to three dif ferent regions Some of the definitions are optional Really necessary are only the list of vertex coordinates as well as the definition of the patches Boundary curves and surfaces may be reconstructed from this HyperSurface ASCII Vertices OO CO CO CO oO OOF OO AD OO CO CO OC oO O O O O AHO DOD O OOOO o NBranchingPoints 2 NVerticesOnCurves 2 BoundaryCurves 3 Vertices 3 DA e Vertices 2 la 2 Vertices 3 Ll E E Patches 5 InnerRegion Materiall OuterRegion OUTSIDE BranchingPoints 0 BoundaryCurves 2 b 2 Triangles 3 Se LS E D 2 2 3 e InnerRegion Material2 OuterRegion OUTSIDE BranchingPoincs 0 BoundaryCurves 2 i Triangles 2 3 1 4 2 3 4 InnerRegion Material3 8 6 ICOL 207 OuterRegion OUTSIDE BranchingPoints 0 BoundaryCurves 2 mo ad Triangles 3 4 1 6 2 4 6 de 2 6 InnerRegion Materiall OuterRegion Material2 BranchingPoints 0 BoundaryCurves 2 2 Ad Triangles 1 Sa LL oz InnerRegion Material2 OuterRegion Material3 BranchingPoints 0 BoundaryCurves 2 a ee Triangles 1 1 2 4 Surfaces 3 Region Materiall Patches 2 1 4 EA Region Material2 Patches 3 Zz do 3 y4 Region Material3 Patches 2 Sr 8 6 Icol This is a simple ASCII file format coming in two variants indexed and non indexed to
140. cess e Screen Door Transparent surfaces are approximated using a stipple pattern e Add Additive alpha blending e Add Delay Additive alpha blending with two rendering passes Opaque objects come first and transpar ent objects come second e Add Sorted Like Add Delay but transparent objects are sorted by distances of bounding box centers from the camera and are rendered in back to front order e Blend Multiplicative alpha blending e Blend Delay Multiplicative alpha blending with two rendering passes Opaque objects come first and transparent objects come second e Blend Sorted Like Blend Delay but transparent objects are sorted by distances of bounding box centers from the camera and are rendered in back to front order Lights The Lights menu lets you activate different light settings for the 3D viewer By default the viewer simply uses a single headlight 1 e a directional light pointing in the same direction as the camera is looking This setting may be restored using the Standard option Two more options Blue Red and Fancy let you activate other light settings At any time additional lights can be created via the Create light option Except for the viewer s default headlight all lights are represented by little blue icons in the Object Pool just like ordinary data objects or modules Any hidden light icons are listed at the end of the Lights menu and not in the Edit Show submenu In order to make all hidden ligh
141. choose the mip option of port Mode Internally the voltex module makes heavy use of OpenGL texture mapping Both textures modes 2D and 3D are implemented 3D textures yield slightly better results However this mode is only supported on high end graphics workstations such as SGI High or Maximum Impact SGI Octane SSI MXI or MXE SGI Infinite Reality HP fx 4 and fx 6 In particular it is currently not supported under Microsoft Windows The 3D texture mode requires you to adjust the number of slices cut through the image volume The higher this number the better the results are Alternatively 2D textures can be used for volume rendering In this case slices perpendicular to the major axes are used You may observe how the slice orientation changes if you slowly rotate the data set The 2D texture mode is well suited for mid range graphics workstations with hardware accelerated texture mapping If your computer does not support hardware texture mapping at all you should use visualization techniques other than volume rendering e Set the em ab button of port Mode e If you are using 3D texture mode choose about 200 slices 3 3 VISUALIZATION OF VECTOR FIELDS 43 Figure 3 11 The Voltex module can be used to generate maxmimum intensity projections as well as volume renderings based on an emission absoprtion model In both cases 2D or 3D texture mapping techniques can be applied applied e Click with the right mouse button on port Colormap
142. concept allowing the user to select triangles by means of an Open Inventor tab box dragger Only triangles added to the internal buffer will be displayed Thus complex surfaces may be decomposed into smaller pieces e An arbitrary 3D scalar field may be visualized on top of the triangular surface by means of pseudo coloring Pseudo coloring may be achieved via Gouraud shading mapped vertex colors will be interpo lated or more accurately via texture mapping vertex values will be interpolated linearly and mapped to color afterwards e The set of triangles currently being visible can be converted automatically into a Surface object This is useful for example in order to post process isosurfaces or to extract parts from a bigger surface e Common Tcl commands allow to control many parameters of modules derived from ViewBase This includes line width outline color highlight color specular color shininess alpha mode normal binding and more Connections Color Field Arbitrary scalar field to be visualized via pseudo coloring The color field will be evaluated at the surface s vertex positions and the vertex color will be set approriately Colormap Colormap used for pseudo coloring To connect the port to a colormap use the popup menu under the right mouse button To change the port s default color click it with the left mouse button See also Colormap Ports Draw Style a Draw Style outined more options This port dete
143. contain the labels but also the probabilities for each voxel You can leave the image segmentation editor by clicking on the pencil icon again 1 4 Grid Generation You may skip this section if you want to perform an E Field simulation on a LabelField using the FDTD voxel method upper branch in Figure figure 1 1 A tetrahedral patient model is needed for most of the numerical simulation methods included in HyperPlan To generate such a model from the results of segmentation you have to carry out the three steps described in the sequel 1 4 1 Extracting Surfaces from Label Fields In the first step the segmentation results are converted into surfaces separating the different tissue types The surfaces are composed of triangular surface patches each separating two different compartments In HyperPlan a method called generalized marching cubes GMC 1s used for surface generation It is a generalization of the marching cubes algorithm which is well known in computer graphics Load a LabelField 1 e the result of a segmentation operation into HyperPlan If the LabelField has x and y dimensions 256 or larger it is recommended to resample it to a lower resolution otherwise the number of resulting surface triangles will be very large Select the Resample module from the popup menu of the LabelField If the Resample module is attached to a LabelField the different parameter ports are used than in the case of ordinary image data You can choose in
144. ct of resampling by attaching an OrthoSlice module to the CT Data Tip you can pick the connection line of OrthoSlice and attach it to either of the two CT data sets Once you have loaded a CT data set for a new patient into HyperPlan and resampled it to 256 x 256 pixels per slice it is a good idea to save the resampled image volume to file To do so select the resampled volume by clicking on it Then choose Save Data As from the file menu and type in a new name in the file browser For convenience the file type should be ct data 1 3 2 Labeling CT Data After the CT images of a patient have been read next different tissue types have to be identified in these images This task is called image segmentation To simulate the electromagnetic fields inside the patient s body at least fat tissue muscles and bones have to be separated The LabelVoxel module provides a simple thresholding algorithm which can be used to perform this separation It is contained in the Compute submenu of the CT data icon s popup menu The Label Voxel module lets you select at least three different thresholds which define the boundary between exterior and fat fat and muscle and muscle and bone respectively To verify these boundaries you might have a look at the Hounsfield histogram press button Histo In the histogram two peaks should be clearly visible one for fat and one for muscle You should choose the threshold separating these tissue types in the middle bet
145. cted into the xy xz or yz coordinate plane The incoming data object must be derived from a vertex set cf Section 4 2 5 Note that the Delaunay algorithm may take some time especially for large data sets If the input is not of planar topology like e g a sphere the result will probably not be useful If multiple 3D vertices project to the same 2D vertex the result is undefined In the latter case it might be help to issue a jitterPoints 0 001 0 001 0 001 command on the command line Connections Data required The vertex set to be triangulated Ports Projection Plane a Projection Plane xy xz pz Lets you select whether the triangulation should be computed in the xy xz or yz coordinate plane You may use the axis module in order to find out which plane is most appropriate for your data Action a Action Doit Starts computation 6 24 DisplayColormap This module allows you to position a colormap icon onto the 3D viewer This is useful e g to produce snapshots that shall contain an explanation of what specific colors mean Note that although colormaps 116 CHAPTER 6 ALPHABETIC INDEX OF MODULES are ordinary data objects in Amira they often are hidden by default Use the Edit Show menu of the main window to bring their icons up Connections Data required The colormap to be displayed Ports Options E Options Pf custom test i vertical 4 relative size This port provides the following thr
146. d A tetrahedral grid has to be connected to this port Module optional An empty plane is loaded automatically Ports Lines amp Lines Al Toggles whether all or only material boundaries are shown Line Width amp Line width ji The linewidth of the boundary lines Selection a Selection Clear Exterior With the menu you can select the material which will be cutted on the cutting plane Subsequent selections are added to the list of selected materials With the Clear button the list can be resetted Commands setColor lt r gt lt g gt lt b gt Sets the color of the intersection lines 6 42 Isolines This module computes isolines for an arbitary 3D scalar field on a 2D cutting plane The plane itself is defined by another module which must be connected to port Module Isolines are computed using two 132 CHAPTER 6 ALPHABETIC INDEX OF MODULES different algorithms depending on the type of the incoming scalar field If the scalar field is defined on a tetrahedral grid then all tetrahedra intersecting the plane are determined first The straight isoline segments are generated for these tetrahedra according to the requested threshold values If the incoming scalar field is not a tetrahedral one then the field is sampled on a regular 2D raster first Each rectangular cell of the raster is then checked for isolines Note that this approach may lead to artifacts if the sampling density is too low To execute a
147. d InputC optional Input data object of type Scalar Field Ports Expr amp Expr BO Here you can type in an expression for the computation of the resulting object ResultType ResultType input regular With this radio box the type of the resulting object can be set either to the type of the object connected to port InputA or to a regular scalar field E Resolution 64 Ed E re P 5 If port Result Type is set to regular the resolution of the regular field to be generated is set to the values given here MinBox 3 MinBox 1 foo Po Port to set the minimum x y z coordinates of a bounding box around the output data object if one or more input data objects are connected the bounding box of the first input data object is also taken as output bounding box MaxBox amp HM axB ox Port to set maximum x y z coordinates of the bounding box around the output data object Action E Action I Dot Pushing this button triggers the computation 6 5 Axis The Axis module displays a coordinate frame If the module is attached to an input data object the co ordinate frame is adapted to the bounding box of the input object Otherwise global axes centered at the origin of the world coordinate system are displayed For convenience the View menu of the main window contains a toggle button labelled GlobalAxis Activating this toggle automatically creates an Axis module in the object pool 100 CHAP
148. d this island remains untouched Note that the percent value must be between 0 0 and 1 0 With the Mode buttons you can control whether the filter works in the current slice in all slices or in the 3D volume The difference between the two latter cases is that in 3D mode the filter searches for true 3D connected regions Note that a long thin structure like a blood vessel can be a very small region in each slice but has a rather large volume in 3D This filter is invoked by pressing Apply e Smooth This is a modified Gauss filter which smoothes the region boundaries therefore the labeling is slightly changed In 3D mode additionally probabilities of voxels belonging to regions are computed and as signed to voxels the probability is one for voxels in the interior of a region and decreases towards the region boundary voxels near region boundaries are also assigned probabilities with respect to neighbor ing regions The probability information is used in other modules to make region boundaries appear smooth e g in the GMC module otherwise such may be displayed as zigzag lines The Size option is for entering the size of the filter mask which is a square with dimensions Size x Size The smoothing effect increases with the mask size but computation time is higher for bigger masks The 2D button lets you start the smoothing operation on the present slice the 3D button lets you start a 3D smoothing on the whole data volume e Snakes
149. d click a last time The contour is then closed and filled automatically When autoTrace is enabled this is the default the line segments are fitted to image edges Click with the left mouse button to define a starting point Dragging the mouse after releasing the button a contour curve automatically fitted to the closest image edge is drawn Further mouse clicks mark fixed points on the contour Contour parts drawn before the latest mouse click remain in place Close the contour by clicking with the middle mouse button e Magic Wand By clicking with the left mouse button on a voxel you get the largest connected area that contains this voxel and all voxels whose data values lie within a range defined by the one of the selected voxel and the tolerance value set in the option panel Normally the magic wand works on the present slice only but if the 3D toggle button on the right of the Selection tools is on the adjacency of voxels is tested in the 3D image data volume The same material only toggle restricts the search to voxels which currently belong to the same material 228 CHAPTER 9 ALPHABETIC INDEX OF EDITORS as the start voxel If e g a voxel currently belonging to Exterior is used as seed point voxels which are allready assigned to different materials will not be selected Blowtool By clicking with the left mouse button on a voxel and dragging the mouse without releasing the button an initially circle formed contour blows up The gre
150. d for isosurface computation The slider is automatically adjusted to cover the whole range of data values For CT data use a value of 200 to extract the skin surface or a value of about 150 to extract the bone structures Options E Options M compact cubes W downsample If the compact cubes toggle is set up to 50 less triangles will be produced but it results in a slightly shifted surface This port further allows you to enable downsampling see below Sample Factor AYerage JE y 2 2 2 6 45 ISOSURFACE TETRAHEDRA 135 This port only appears if downsampling is enabled It allows you to specify a sample factor for each of the three main axes The factors determine how many of the original grid points in each direction will be merged into one Action amp Action E Dalt Press the Dolt button of this port to start the computation of the isosurface 6 45 Isosurface Tetrahedra This module computes an isosurface for a scalar field defined on a three dimensional tetrahedral grid The triangulation inside a tetrahedron exactly matches a linearly interpolated field Connections Data required The scalar field defined on a tetrahedral grid ColorField optional See port ColorField in section Isosurface Hexahedra Colormap optional See port Colormap in section sosurface Hexahedra Ports J PR m lt amp Draw Style shaded more options The draw style port 1s inherit
151. d in the resulting image Colormap 3 Colomap 2 MU Ap Q gt N O O O oS pi h qe Y OQ Y 3 A pl N UN O e O A O S 3 Slice Number amp Slice Humber See This slider allows you to select different slices The slices may also be picked and dragged directly in the 3D viewer Transparency a Transparency None Binan Linear This radio box port determines the transparency of the displayed slice None means that the slices are fully opaque Binary means that black parts are fully transparent while other parts are opaque Finally linear means that opacity is proportional to luminance 6 58 PlanarLIC This module intersects an arbitrary 3D vector field and visualizes its directional structure in the cutting plane using a technique called line integral convolution LIC The LIC algorithm works by convolving a random noise image along the projected field lines of the incoming vector field using a piecewise linear hat filter The synthesized texture clearly reveals the directional structure of the vector field inside the cutting plane As long as no valid LIC texture has been computed a default checkerboard pattern is displayed instead 146 CHAPTER 6 ALPHABETIC INDEX OF MODULES PlanarLIC is derived from ArbitraryCut See the documentation of this module for details on how to adjust the position and orientation of the cutting plane Click here in order to execute a sc
152. d points 9 9 Parameter Editor The Parameter Editor lets you view and modify the parameter list associated with a data object A parameter is a name value pair which contains some extra information related to the data Some parameters have a special meaning within Amira cf Section 4 2 7 of the user s guide Note that there are many standard file formats which do not support parameter information to be written If in doubt use Amira s native AmiraMesh format This format does write parameters 9 10 Simplification Editor E This editor can be used to reduce the number of triangles of a surface In particular the output of the GMC module has to be processed in this way before a tetrahedral patient model can be be generated Surface simplification is done by means of an edge collapsing algorithm Edges of the original surface 234 CHAPTER 9 ALPHABETIC INDEX OF EDITORS feel Parameter Dialog xl Parameters BoundingB ox 0 392157 199 608 0 392157 199 608 0 393678 136 606 Content 1282126887 byte uniform coordinates Filename D HOME befgrafs Armra 0D0 data tutorials lobus am z LoadEmd load O HOME befgrafsAriira 000 data tutorials lobus am Conard T ype uniform Surface 34830 ponts 12531 faces 49 patches O contours O edges a Simplify faces 18000 max dist 3 a Options V preserve slice structure fast a Acton Simplity Fis Coplanars Flip Edges Figure 9 7 User interface of surface simplifi
153. data icon representing the patient model The popup menu is activated using the right mouse button Press button Buffer Add in order to see the entire model 2 Select the Antenna module from the model s popup menu A geometric representation of the applicator appears in the 3D viewer Select the Antenna icon You may change parameters like position and inclination angle of the applicator The relative position of the applicator is specified in centimeters At port Applicator you can select the Sigma 40 the Sigma60 or the Sigma Eye applicator Simulation of all is supported by the FE method 3 Select module BolusGrid from the antenna s popup menu Click on the BolusGrid icon Parameter Offset lets you control how the bolus surface bends inwards to fit to the patient s body Press button Compute If the tetrahedral patient model contains duplicated points an error message will be issued Tetrahedral grids containing duplicated points are only needed if E field calculation is being performed using the FDTD method The error message will include a hint how to remove the duplicated points Once you have removed them press button Compute again After a few seconds a new green icon will appear It represents a data object containing the surface of the water bolus adapted to the patient model and two spherical surfaces enclosing both the patient model and the water bolus The spherical surfaces describe the outer boundary of the whole grid required
154. derlying surface data Ports Index 3 Index 1 al AK Choose index of contour to display If 1 is choosen all contours will be shown 6 20 ContrastControl The ContrastControl module Contrast in short is an extension to the OrthoSlice module and it is par ticularly useful for the grey or color value analysis of scalar fields like medical image data as well as a preliminary stage for image segmentation It allows a fast and intuitive adjustment of the transfer function mapping scalar values stored with the image data to those values used for visualization With the help of ContrastControl the linear mapping of the data values to a subset of scalar values or indices to color values defined by a Colormap can be modified The term windowing 1s often used within this context The window defines a possibly narrowed view to the data s scalar values for enhancing the contrast of certain structures within the image data The width of the window defines the range of data values between a lower and an upper threshold which shall be mapped to a range of values specified by the height of the window In terms of gray value mapping a subset of thousands of possible data values can be mapped to 1 e 256 gray values linearly distributed on a ramp varying from black 0 to white 255 Black values are represented by the lower border of the window and white values by the upper border The center of the window might be located at any value of th
155. dialog is popped up This dialog is also is also described the TIFF section 8 9 Leica Microscope 3D TIFF This reader is able to read 3D TIFF files containing a whole stack of 2D images In particular the 3D TIFF format is used by newer Leica laser scanning microscopes In addition to the image data itself special parameters like pixel size or slice distances may be stored in a 3D TIFF file If such information is found it will be interpreted in order to create a uniform scalar field of the proper type However if no bounding box information is encountered the channel conversion dialog described in the 2D TIFF section will be popped up 8 10 Leica Microscope Slice Series This is the file format used by the older Leica laser scanning microscopes It consists of an info file as well as several raw or TIFF slices which all must reside in the same directory In order to read these files select only the info file Parameters like pixelsize or slice distance are read from the info file If the file contains colormaps they will be read too 8 11 PNG Image Format PNG stands for Portable Network Graphics The format is mainly used for internet applications Usually image data is stored in compressed form using a lossless compression algorithm The format is able to store an alpha channel besides the ordinary color channels PNG files are automatically identified by the file name extensions png Regarding the import and export of multiple sl
156. direction with the y axis pointing upwards Any other orientation may be specified as a rotation relative to the default direction The rotation is specified by a rotation axis x y z followed by a rotation angle a in radians viewer lt number gt setCameraFocalDistance Defines the camera s focal distance The focal distance is used to compute the center around which the scene is rotated in interactive viewing mode viewer lt number gt setAutoRedraw lt state gt If state is O the auto redraw mode is switched off In this case the image displayed in the viewer window will not be updated unless a redraw command is sent If state is 1 the auto redraw mode is switched on again In a script it might be useful to disable the auto redraw mode temporarily viewer lt number gt redraw This command forces the current scene to be redrawn An explicit redraw is only necessary if the auto redraw mode has been disabled viewer lt number gt rotate lt degrees gt Rotate the camera around the current up direction viewer lt number gt rotateVD lt degrees gt Rotate the camera around the current view direction This does the same as the rotate button in the user interface viewer lt number gt decoration lt state gt The decoration is an extended window frame that serves as a user interface It contains buttons and thumb wheels for adjusting the view or switching between interaction and viewing mode The decoration command can be
157. dow Therefore the toggle button in the working area with the Window Show label must be activated The horizontal extent of the window graph specifies the image data range from the lowest to the highest value The linear ramp indicates the mapping function where the area below or above the ramp represents the currently chosen mapping window Connections Module required Connection to the OrthoSlice module Data required Connection to the scalar field is automatically established via the OrthoSlice module Ports E 5 O pel a pao E E 5 ga a Linear mapping 1023 1636 This port displays information on the image data range In verbose mode the current data window will be displayed too Center Center a 154 837 The window center can be positioned between the minimum and maximum value of the image data range The increment value for slider movement is 1 percent of the image data range More accurate values can be specified via the numeric input field Width amp Width Pere The window width can be adjusted between O and the total image data range The increment value for slider movement is percent of the image data range More accurate values can be specified via the numeric input field Window a Window M Show This port enables or disables the display of a graphical representation of the linear transfer function within the viewer If 1t is enabled an additional port appears which al
158. e E field calulation is finished and HyperPlan is still running the EFieldGrid and EFieldVals files are automatically loaded 1 6 Temperature Simulation This section describes how to perform a temperature simulation on a tetrahedral patient model It requires that an E Field simulation already has been performed either using the FDTD method as described in Section 1 5 3 or using the FE method as described in Section 1 5 4 Like for the electromagnetic fields a set of independent temperature channels is computed From these channels the actual temperature distribution for any set of antenna amplitudes and phases can be obtained by superposition very quickly 1 First you have to load a tetrahedral patient model as well as the corresponding E field values into Hy perPlan If the FDTD method was used for E field calculation the patient models are called EField GridFD while the files containing the E field values have a suffix EFieldValsED If the FE method was used the suffixes are EFieldGridFE and EFieldValsFE respectively 2 From the popup menu of the EFieldVals icon select the module called Static Heat In this module you can enter the names of the files for the temperature grid and the temperature channel data which are going to be computed The temperature grid is very similar to the initial electromagnetic coarse grid However it does not contain any duplicated vertices nor does it contain information about grid edges We recommend to use
159. e all voxels labeled with 4 belong to material Something Optionally label fields may contain probability information or weights as shown in the example above These weights denote the degree of confidence of the labeling This information is used by the GMC module when extracting boundary surfaces Landmarks for registration The data type Landmark Set is useful for registration and alignment of multiple 3D image data sets It allows you to store multiple sets of corresponding marker positions The data type can also be used to represent a simple list of 3D points in Amira In this case you would only specify a single set of markers Consider the following example AmiraMesh ASCII 1 0 define Markers 3 Parameters ContentType Landmarkset NumSets 2 Markers Flioat 3 Coordinates I Markers float 3 Coordinates2 2 1 99 e2 40 SODIO ITs ad 1264 6494 PA NA Sa 33s Shs IDOL LS 15 14 T5 La Poa AN Og On a CLOG Io Se SAO SZ JURA Zoe SL Lg S241 AUTO TE LI ORTA 202 CHAPTER 8 ALPHABETIC INDEX OF FILE FORMATS In this example first the number of markers or points is defined to be 3 In the parameter section of the AmiraMesh file the content type is specified as well as the number of marker sets The marker coordinates of the first set are denoted Coordinates xyz values stored as float 3 Likewise the marker coor dinates of the second set are denoted Coordinat
160. e buttons shows the current zoom factor E g a zoom of 2 1 means that 2 pixels on the screen correspond to one pixel of the original data set magnification while 1 4 would mean that four pixel of the data set correspond to one pixel on the screen If the pixel size is not the same in all dimensions the zoom factor belongs to the horizontal direction only to maintain the correct aspect ratio of the voxels 9 5 IMAGE SEGMENTATION EDITOR 221 Using the tools of the Selection command area Beside the Selection buttons there is a 3D toggle button which extends an action to all slices 1f it is activated Otherwise the present slice in the active viewer is affected e Picker This tool marks a connected area within one material If the 3D toggle button on the right is activated the connectivity check is also made in the third dimension marking affected voxels in all slices e Clear C This button lets you clear the current markings If the 3D toggle button is activated markings in all slices are cleared e Add This button adds all selected voxels to the active material Voxels that are currently assigned to a locked material are not affected If the Shift key is held down while clicking the voxels remain selected e Subtract This button lets you subtract all selected voxels from the active material if this one is not locked Tools for marking an image The various marking Tools offer you the opportunity to define areas in the pres
161. e difference algorithm and stores the result in a given file Since an E field simulation takes several hours of computing time the calculation is performed as a batch job The status of the job queue can be controled in the Job Dialog The results of E Field simulation can be visualized later on See section 1 5 1 for an overview on performing E Field simulations using the finite difference method The FDTD module works on both voxel grids FDTD Voxel Solver as well as on tetrahedral grids Modified FDTD Solver It must be attached to an Antenna module which in turn is connected to the voxel grid resp tetrahedral grid Currently only the BSD Sigma 60 applicator is supported by this module Note The maximal possible number of cubes Yee cells is 82 in x and y directions and 106 in z direction The number of cubes should be chosen such that 5 10 cells of background medium lie between the appli cator patient bounding box and the boundary of the FDTD lattice 1 e the number of cubes should be set to about 80 for a cube size of 1 cm and about 48 for a size of 2 cm The program will stop if the chosen number of cubes is too small to cover the patient s and the applicator s geometry The number of iterations should be chosen as at least 2500 for size of 1 cm and at least 1500 for a size of 2 cm These iteration numbers proved to be sufficient for modelling the BSD Sigma 60 applicator in the frequency range 80 120 MHz Connections Data Connect
162. e draggers you control the size of the subset of the data volume which has to be preserved but the location of it in the total data volume is set by moving the box around to the desired location Cropping an image by setting values explicitly in the text fields The text fields in the cropping area of the editor show the indices of the slices that have to be preserved for every dimension You can easily define a subset by setting a range of indices explicitly in the text fields of an axis this defines the size as well as the location of the data subset Notice that a slice index refers to an axis that is perpendicular to the slice Adding new slices Adding new slices 1s only possible by setting an index that does not fall into the range given by the minimum and maximum presently shown in the Image Crop panel thus a negative index must be specified if the minimum is zero Use the Min or Max text field for the required axis text field to enter a new slice index A warning dialog pops up whether you really want to add new slices and the slices are added on your confirmation to the volume at the specific end and according to the axis selected The new slices contain the data of the last slice in this direction e g if you add two slices before the slice with index O along the X axis they contain exactly the same data as the slice with index 0 232 CHAPTER 9 ALPHABETIC INDEX OF EDITORS LandmarkSet 3 markers 2 sets no types no onentations
163. e image more visible 3D Gauss Filter The Gauss filter smooths or blurs an image by performing a convolution operation with a Gaussian filter kernel The text fields labeled kernel size allow you to change the size of the convolution kernel in each dimension A value of 3 denotes a 3x3 kernel Odd values are required The text fields labeled sigma allow you to adjust the width of the Gauss function relative to the kernel size 3D Lanzcos Filter The Lanzcos filter can be used to sharpen images It performs a convolution with a Lanzcos kernel sin 7x sin 272 277 x7 flz la lt 2 The kernel size in each dimension can be adjusted using the parameter inputs kernel size A value of 3 denotes a 3x3 kernel Odd values are required 9 4 Grid Editor The Grid Editor allows you to analyze the quality of a tetrahedral grid according to different quality mea sures and to semi automatically improve the grid quality To do this push the edit button of a selected tetrahedral grid see the icon above Then some additional button controls will appear in Amira s Working Area The user interface is depicted in Figure 9 2 In case you select some other Selector or Modifier other ports might be shown The editor works in conjunction 9 4 GRID EDITOR 223 Es Pa Number of Nodes 13788 no duplicated Number of Triangles 150020 Number of Tetrahedrons 73532 Material Ds 0 10 E Selector Select Edge Quality gt a e qu q
164. e image data thus the entire window can be shifted to various points for data evaluation window center 255 y windows width E 1000 image data range 3095 The window s center and width can be modified with the two sliders in the working area of the Contrast module These values can either be adjusted by shifting the sliders to the left or right varying the values by a certain percentage of the image data range or they can be specified numerically via the appropriate entry fields For a fast modification of the window s center and width experienced users can directly use the mouse After putting the viewer into interaction mode indicated by an arrow shaped cursor the contrast can be adjusted via the left mouse button while the shift button 1s pressed Moving the mouse to the left or right moves the center of the window accordingly Up and down movements increase or decrease the width of 6 20 CONTRASTCONTROL 111 the window A vertical line that means lower and upper threshold are identical respectively the window width equals zero indicates a binary mapping of the image data values All values below the window s center will be mapped to black and all other values will be mapped to white Moving the mouse further down will invert the mapping thus exchanging black and white values For an overview of the current mapping a graphical representation of the mapping function can be displayed within the viewer see PortWin
165. e names of the materials the number of triangles they consist of the surface area of those triangles and the volume of the materials The choice of patches results in a spreadsheet showing the patchnumber the materials they form part of the number of triangles and the surface area of the patch Action amp Action E Dalt description 6 10 CastField This is a computational module that allows you to change the primitive data type of a regular 3D scalar field or of an RGBA color field A new scalar field will be created having the same dimensions and the same coordinates as the incoming one but the data values will be shifted scaled and casted to a new data type As an additional feature CastField is also able to convert a uniform scalar field of bytes into a label field which is commonly used to store segmentation results in Amira For each value or label occuring in the incoming field a corresponding material will be created Material colors may be defined via an optional colormap Connections Data required The scalar field or color field to be converted Colormap optional Optional colormap specifying material colors if a uniform scalar field of bytes is to be converted into a label field Only visible if LabelField has been selected for output 104 CHAPTER 6 ALPHABETIC INDEX OF MODULES Ports Info S Info byte 0 255 gt int 0 255 Shows how the input data will be mapped during conversion I
166. e or four color sliders which give you the opportunity to modify the values of the colormap cell with the focus on it for all color channels You see four or three sliders depending on whether Show Alpha is set or not The first three sliders correspond to the color model s channels and the fourth lets you modify the alpha value On the left side of each slider you see the name of the corresponding color channel e g Red Hue etc On the right side there is text entry which shows the actual value of the color channel for the color cell with the focus Then in the middle you see the true slider which is a rectangle with a color course depending on the model e g in case of a red slider a course starting with black on the left no additive red value and going on to bright red on the right side adding the full spectrum of red color Attached to the rectangle is a small triangle which lets you manipulate the value by dragging it to the left or to the right see How to modify a colormap F Control Buttons These three buttons let you choose whether the changes to the colormap should be kept or not By pressing the OK button the changes made with the editor are written back to the colormap object that you are working on This action also causes the editor to exit If you just want to write back the changes without exiting e g if you want to see how your changes take effect just press the Apply button If Apply is done in the
167. e resolution of the incoming data field to be resampled The other ports depend on whether the input field contains ordinary numbers or labels as used in image segmentation c f LabelField For non labeled data fields you see the Filter and the Resolution port In case of a labeled data field you see the Average port In both cases the Do t button completes the port list Depending on the existence of labeled data the resampling operation is performed differently Resampling non labeled data fields For non labeled input data two ports denoted Filter and Resolution will be shown Filter provides an option menu allowing you to specify the filter kernel for the resampling operation Usu ally the default kernel Triangle yields sufficiently good results for both minifications and magnifications The following filters are supported e Box simple replication of scalar values shows considerably tiling or jaggies e Triangle computationally simple still sharp transition lines e Bell smoothing filter e B Spline no sharp transitions but its width causes excessive blurring e Lanczos excessive ringing effect e Mitchell no sharp transitions good compromise between ringing and blurring e Minimum useful for down sampling preserves tiny dark features on a bright background e Maximum useful for down sampling preserves tiny bright features on a dark background The Minimum and Maximum filters can only be used to downsample n
168. e same things as when working with an editor i e click in the text field to activate the cursor erase the old value and write a new value with the keyboard and press Enter to submit your value This change will be visible in a corresponding position of the small triangle of the slider and in the color buttons and color chart as a changing of colors and a modified graph respectively Setting a value by dragging the small triangle You can see the modification interactively by dragging the small triangle all around the slider The values and displays will be refreshed while you drag the small triangle Modifying the focus cell this way lets you have an intuitive control of what new values will be the best for your needs Setting a value by clicking in the true slider s area Last but not least you can click on an arbitrary position in the color bar of the slider to set the new value This is a very inaccurate way to modify the value because you can neither set the exact value nor watch how the position will modify the surrounding colormap entries The values and displays are refreshed in the same way as described in the previous sections 9 3 Digital Image Filters 3 This editor allows you to apply certain digital image filters to 3D image data sets such as smoothing unsharp masking or morphological operations Some filters directly operate in 3D while others are applied 9 3 DIGITAL IMAGE FILTERS 221 Info 128 126 x 87 bytes 2
169. e size of the mask can be adjusted via the input field kernel size A value of 3 denotes a 3x3 mask 222 CHAPTER 9 ALPHABETIC INDEX OF EDITORS If applied to a binary label field the minimum filter implements a so called erosion operation It reduces the size of a segmented region by removing pixels from its boundary 2D Maximum Filter The maximum filter replaces the value of a pixel by the largest value of neighboring pixels covered by a NxN mask The size of the mask can be adjusted via the input field kernel size A value of 3 denotes a 3x3 mask If applied to a binary label field the maximum filter implements a so called dilation operation It enlarges the size of a segmented region by adding pixels to its boundary Unsharp Masking This filter sharpens a stack of 2D images using an unsharp mask The unsharp mask is computed by a Gaussian filter of size kernel size The scaled difference of the orginal image and the blurred image is then added to the original Thereby the sharp features of the image get emphasized The scaling factor determining the amount of sharpness can be adjusted via an text input field 2D Histogram Filter This filter performs a so called contrast limited adaptive histogram equalization CLAHE on the data set The CLAHE algorithm partitions the images into contextual regions and applies the histogram equalization to each one This evens out the distribution of used grey values and thus makes hidden features of th
170. e the menu at port Action from Default to the name of the plan file Now the Superpose module computes the optimal temperature distribution You can visualize 1t by creating an sosurface module or a FieldCut module from the popup menu of the Superposed icon 1 8 All in one Simulation HyperPlan also provides a module for performing all simulation steps namely E Field Simulation Tem perature Simulation and Temperature Optimization at once using the Finite Element method For E Field Simulation adaptive mesh refinement is used The corresponding module is called Refined E Field Simual tion It can be attached to an extended grid For details of how to create such a grid see Section 1 5 4 Details about the Refined E Field Simualtion module are described in the Amira reference manual In prin ciple the module provides a combination of the input ports of the ordinary E Field Simulation module and the Static Heat module as described in Sections 1 5 4 and 1 6 In addition the number of refinement steps can be specified In most cases a single refinement step yields sufficiently good results In addition to the EFieldGrid and EFieldVals files a number of additional data files are written to the output directory These also includes temperature values and a plan file containing optimized antenna parameters Part Il Amira User s Guide 27 Chapter 2 Introduction Amira is a 3D visualization and modelling system It allows you to visualize sc
171. e used for encoding stationary electromagnetic wave pattern as required by some applications Usually complex vector fields are visualized by projecting them into the space of reals using different phase offsets The Vectors module even allows you to animate the phase offset In this way a nice impression of the oscillating wave pattern is obtained 4 2 3 Coordinates and Grids Amira currently supports two important grid types namely grids with hexahedral structure regular grids and unstructured tetrahedral grids Other types e g unstructured grids with hexahedral cells or block structured grids will be added in future releases of Amira Regular Grids A regular grid consists of a three dimensional array of nodes Each node may be addressed by an index triple i j k Regular grids are further distinguished according to the kind of coordinates being used The most simple case comprises uniform coordinates where all cells are assumed to be rectangular and axis aligned Moreover the grid spacing is constant along each axis A grid with stacked coordinates may be imagined as a stack of uniform 2D slices However the distance between neighbouring slices in z direction may vary In case of rectilinear coordinates the cells are still aligned to the axes but the grid spacing may vary from cell to cell Finally in case of curvilinear coordinates each node of the grid may have arbitrary coordinates Grids with curvilinear coordinates are often used
172. e window appears It is possible to build more complex user interfaces with script objects as shown in the second example 156 CHAPTER 6 ALPHABETIC INDEX OF MODULES Amira Script Object V0 1 Proc constructor 1 F 1 global this Sthis newPortIntSlider myValue Sthis myValue setLabel Value if 4 this isFirstCall 4 constructor set val this myValue getValue echo The value is Sval Here we use a number of special commands The global variable always contains the name of the script object which is currently executed This allows to access its special commands The command this asrirstcall returns true only the first time the script is executed typically when the script is loaded or when reset is hit In the example a TCL procedure called constructor is defined and called the first time the script is executed Within this procedure the script object is told to create a new port of type HxPortIntSlider which will appear in the user interface The port has the internal name my Value and its visible label is set to Value Finally the current value of the port is accessed using the command this myValue getValue Whenever the slider is moved the script will be called and the current value is printed Each time the script is called it is read from the disk this means that you do not need to reload the data if you have modified the script Connections Data optional Can be connected to any data object Can be
173. eae 8 2 AMIRA MESH FORMAT 199 Use float 3 in order to encode a vector field instead of a scalar field Likewise you may modify the field s primitive data type For example 3D images are commonly encoded using byte or short Instead of Intensity you may use any other name in the data definition statement The field s xy bounding box is given by the minimum and maximum x and y coordinates of the grid nodes or pixel centers not of the pixel boundaries Amira will always assume the width of a single pixel to be xmax xmin dims 0 1 For degenerated 3D data sets with one dimension being 1 choose equal minimum and maximum coordinates in that direction Fields with rectilinear coordinates A field with rectilinear coordinates still has axis aligned grid cells However the x y and z coordinates of the grid nodes are specified explicitely for each direction In order to encode a 3D scalar or vector field with rectilinear coordinates you have to define a 3D array called Lattice and 1D array called Coordinates The field s data values are stored at Lattice while the x y and z positions for each direction are stored at Coordinates in subsequent order The size of the Coordinates array must be equal to the sum of the sizes of Lattice in x y and z direction The coordinate type of the field is specified in the parameter section of the AmiraMesh file Here is an example AmiraMesh ASCII 1 0 define Lattice 2 2 3 define Coordinat
174. ect first order neighbor triangles or points The larger the value of nAverage the smoother the curvature data be ing obtained Note that averaging only applies to the scalar curvature values not to the directional curvature vectors which are computed when port output is set to max direction Output E Output 1 Curvature This menu controls the output of the curvature module If curvature is selected then a surface scalar field is generated containing the maximal principal curvature of a triangle or of a point If curvature is selected then the curvature values are inverted In this case the output values have the dimension of a length indicating the radius of a sphere locally fitting the surface If max direction is selected then a surface vector field is computed indicating the direction of maximum principal curvature The length of a directional vector is equal to the corrsponding curvature value Action a Action Dot Press this button to start computation 6 33 Gradient The Gradient module computes the gradient of a scalar field consisting of floats defined on a uniform grid The output is a uniform vector field The direction of the gradient vector depends on the setting of port Output If Force is selected the negative gradient vector is computed end 5 OF N Ox dy Oz 6 34 GRID BOUNDARY 125 Connections Data required Scalar field defined on a uniform grid UniformScalarField3 The scalar va
175. ector magnitude is so low that the arrow vanishes completely Colorize a Colorize Magnitude An option menu allowing to control how arrows are colored In order to see an effect a colormap must be connected to the module If Magnitude is chosen then the vector magnitude is used to lookup a color from the colormap If Normal component is chosen then color denotes the signed length of the vector component perpendicular to the cutting plane This length is positive if the vector points upwards or negative if the vector points downwards Finally if Parallel component is chosen then color denotes the length of the vector component tangential to the plane This length will always be greater or equal than zero Phase 3 Phase Ad This port will only be visible if a complex valued vector field is connected to the module It provides a phase slider controlling which part of the complex 3D vectors is visualized by the arrows A value of O degree corresponds to the real part while a value of 90 degrees corresponds to the imaginary part The display can be animated with respect to the phase by the cycle button this way polarization properties of the field can be revealed or wave phenomena become visible Commands setLineWidth lt value gt Allows to change the line width of the arrows By default arrows are drawn two pixels wide 6 86 Vertex View This module allows you to visualize arbitrary vertex sets Vertex sets occur as part of objec
176. ed Streamlines Proc IEEE Visualization 96 Oct Nov 1996 San Francisco pp 107 113 1996 6 25 DISPLAYISL 117 The module computes a large number of field lines by integrating the vector field starting from random seed points The lines are displayed using a special illumination technique which gives a much better spatial understanding of the fields structure than ordinary constant colored lines In order to execute a script demonstrating this module click here The functionality of DisplayISL can be extended by means of the SeedSurface module Connections Data required The vector field to be visualized Since a procedural data interface is used all types of vector fields are supported e g fields on regular or curvilinear grids as well as procedurally defined fields ColorField optional An optional scalar field which if present will be used for pseudo coloring Often it is useful to create a scalar field from the vector field using the Magnitude module AlphaField optional An optional scalar field which can be used to control the lines opacity locally Distribution optional An optional scalar field which can be used to control the distribution of seed points Colormap optional The colormap used to encode the color field Will only be visible if a color field is connected to this module Ports Colormap 3 Cooma OT af Optional colormap Num Lines Hum Lines o E Number of field lin
177. ed from class ViewBase For a description of this port see there A x 3 Cooma 0 af See port Colormap in section Isosurface Hexahedra Threshold Determines the value used for isosurface computation The slider is automatically adjusted to cover the whole range of data values If the threshold value is changed the computation of the new isosur face is immediately invoked Buffer a Buffer Add Remove Clear Show Hide Draw This port must be enabled explicitly with the command Isosurface showBuffer For a de tailed description see the Viewbase documentation 6 46 IvDisplay The vDisplay module renders an object containing Inventor geometry data 136 CHAPTER 6 ALPHABETIC INDEX OF MODULES Connections Data required Connect a data object of type vData to this port Ports Draw Style a Draw Style Shade This port provides a menu to select on of three draw styles to render the Inventor geometry 6 47 IvToSurface The vToSurface computational module parses the connected Inventor Scene Graph Inventor geometry data and converts it into the surface format This is done when you push the Dolt button A green icon named GeometrySurface representing the generated surface should appear If no data object is connected all geometry currently displayed in the first viewer is converted Duplicated points are removed during the conversion Duplicated points are points with a distance less t
178. ed to interaction mode e g by hitting ESC as described in its documentation The editor has different Edit modes which are described in the following e Add In this mode new landmarks are added by clicking onto a 3D geometry e g an Isosurface or an OrthoSlice Multiple clicks are required if the landmark set contains more than one point set e Move Markers can be moved in this mode by first clicking on the marker selecting it and then clicking to a new position e Transform In this mode markers can be moved using a dragger Click on one of the markers then use the dragger to manipulate it e Flip Flip geometry of marker Only makes sense if the marker type is not Point e Remove The marker you click on will be removed If more than one point set is present the marker will be removed from all sets 9 8 LINESET EDITOR 233 e Query After clicking on a marker its type and its xyz position are shown The marker type can be changed via an option menu The default marker type is a Point represented by a little sphere In addition a number of predefined medical marker types can be selected In contrast to point type markers medical markers have fixed predefined sizes world coordinates assumed to be given in centimeters See also documentation for Landmark Set 9 8 LineSet Editor This component allows you to edit linesets It operates by directly interacting with the 3D geometry in the viewer window cf Section 4 1 6 I
179. ee toggles e custom text Whether or not custom text should be displayed See below for details e vertical Vertical orientation instead of horizontal e relative size Change size of displayed colormap when viewer size changes az DN pi o e pi o a Position 80 y 40 Position of colormap in viewer relative to lower left corner If one of the numbers is negative it is interpreted relative to right upper border Size a Size length 200 thickness 0 1 Size in pixels or relative if option is selected and thickness of colorbar Custom Text a Custom Text O Low 0 5 Medium 1 High This is only available if custom text option is selected You may specify a space separeted list of values that shall be displayed In addition you may specify a text which is displayed instead of the number by using the character The example in the image above has been generated using this text 8 cold 50 hot which displays cold at value 8 and hot at the value 50 the colormap in this case ranges from 8 to 50 If one of the labels should contain blanks you have to enclose the text in double quotes e g 100 very hot 6 25 DisplayISL This module visualizes a 3D vector field using so called illuminated field lines This technique was first presented on the Visualization 96 conference More details are described in M Z ckler D Stalling H C Hege Interactive Visualization of 3D Vector Fields using Illuminat
180. ee we Bt 170 RISSUCSIAUIGUCS Arias Bw ek ea de Diet Genre Se eos ELE a 171 Tranele mal ca id de a e a lia ee oe a E es 172 VECLOLLIODE dar E a e A RA A aa 173 NECIOS ara aa aa Hien ee aad aR e e cen ee Sek A 174 8 CONTENTS OSO VEO VIEW ec A AAA AAA Es 175 OST ai AE EA 178 008 VOX ad Sek seh do de ee ds e A es Sede tle oe bee a A a ee 180 OSI NORE IVI Wea Sh am tre Pee es Gah ee ne ee RN 182 7 Alphabetic Index of Data Types 185 Rel Analytical Scalar Field asias ee Bec Se Sa Ba A hd ett 185 Taza A alytical Vector Field 2 a a nd eR Ws eh ae a ee A Es Bw EB SS Ae Go 186 doe ACOLOMMAD 4 ADE A Ee A A RA EOE SS 187 Tee JE ICI SOUS amp be Ge dees Se wen cds oe a Be BO lt i Bae a Sky oe we be a 188 WS Label Fed sardina ae 188 LOs Landmark Set de 2 ote aig e eh tt Bad a OM Bok aes bw at Sk 189 Tel EDES ss AAA AAA SS Ee OE ND SO 190 TS PAD xd dra ea amp ee A a eee Be es A amp EA aoe ore Be ee 190 TI SAR DISTADUCONS ra acs aa ad AA Ai 190 LO Spread SNEG s lt u ae da Bho ee la AS A 190 Tall SUIS 2 e Care A A AAA AA 190 Pike Temperature SEIS poi a GS a A A a ada we Be a a a 192 AS Ter ahedra LGA gt te Da A AA RA AA A A eS as 192 7 14 Tetrancdral Patient Models ata il cs Goer Gl a ra a Fk 193 IS Tomographic Imase Data x osora A eo SSE A a e F 193 FIO MECS e rl we amp E A A Bd es amp AA ore Be ee 193 8 Alphabetic Index of File Formats 195 SL ACRENEMAS DICOM ou 6 205 4 8 adie AAA A BO eo a ee Se RA 195 0 2 Ata Me
181. een two rendering methods by the radio buttons Gouraud and Texture See also PortRadioBox e Gouraud shaded faces have their colors assigned at their vertices The colors in between are linearly interpolated Therefore misleading colors occasionly may occur or colors may appear to be washed out along the edges of the faces e Texture mapping means an exact mapping of values to colors in this special case but with the drawback of increased computing time if you have no hardware supported for texture mapping on your machine Selection a Selection Ada Remove Al This port maintains a list of materials assigned for cutting With the selection menu one can select a single material The Add button adds a previously selected material to the list and the Remove button removes the current selected material 6 31 GMC This module computes a triangular approximation of the interfaces between different tissue types in a La belField with either uniform or stacked coordinates This is done by means of a generalized marching cubes algorithm which explains the letters GMC The resulting surfaces can be non manifold surfaces Depending on the resolution of the incoming LabelField the resulting triangular surface may have a huge amount of triangles Therefore the LabelField should be resampled to 128x128 pixels per slice During the resampling process the Resample module will create or update the probability information of the La belField This w
182. eld 3 and 4 channel 212 CHAPTER 8 ALPHABETIC INDEX OF FILE FORMATS input only e Channel 3 The third channel of the input is converted into a uniform scalar field 3 and 4 channel input only e Channel 4 The fourth channel of the input is converted into a uniform scalar field 4 channel input only e Color Field An RGBA color field is created 4 channel input or 1 channel input with additional col ormap If the first image file contains a colormap the map will be loaded as a separate object if Channel 1 is selected or it will be used to compute an RGBA color field if Color Field is selected Moreover the dialog allows you to adjust the bounding box of the resulting image data set The bounding box specifies the world coordinates of the center of the lower left front voxel min values and the center of the upper right back voxel max values For example if your input is 256 pixels wide and the size of each voxel is Imm then you may set xMin to 0 and xMax to 255 The bounding box of a data object may also be changed later using the ImageCrop Editor Chapter 9 Alphabetic Index of Editors 9 1 Color Dialog The Color Dialog provides an interface for selecting colors The dialog pops up whenever a single color shall be changed within Amira The Color Dialog therefore provides serveral different interface components a menu bar color sliders color cells a color picker and five buttons The menu allows the user to set a
183. elect a data set by clicking on the corresponding green data icon and look at the text line labeled Info In order to create a uniform data set from a stacked one you may use the arithmetic module Choose the regular option of the arithmetic module and adjust the resolution of the resulting uniform field as required Afterwards you will have to convert to data values of the resulting field back to 8 bit or 16 bit integers by using the cast field module 16 CHAPTER 1 HYPERTHERMIA PLANNING In ACR NEMA or DICOM usually each slice is stored in a separate file but HyperPlan requires the whole image volume to be loaded at once so you have to select multiple files in the file dialog This is done by clicking the first file and then shift clicking the last one The file type filter can help to specify the selection You may enter arbitrary wildcard patterns here Only files matching the pat tern will be displayed HyperPlan assumes that a file is a ACR NEMA or DICOM file if the file name suffix is ima ani dem or dc3 or if the file name matches a DICOM unique instance ID e g 1 3 12 2 1107 5 1 2 20395 19980429221554713 4 Files are automatically uncompressed if they were compressed by either gzip Unix and Windows or compress Unix only Sometimes CT data are stored in raw format Raw data files only contain the image data but no header information like pixel size or image spacing If the data files have a suffix raw or if no other format can be de
184. emitted by the hyperthermia applicator Auto Scale This toggle determines what will happen if the parameters for the single channels are changed If the toggle is off the scale factor is kept constant and the total power may change If a file containing antenna parameters is read and this file also contains a scale factor this scale factor is applied If the toggle is set the total power is kept constant and the scale factor may change The scale factors contained in antenna parameter files are ignored If module Superpose is applied to results from a finite element E field calculation there is a second toggle update power If this toggle is set the power value is recalculated each time the antenna parameters are changed If port Output is set to E Field antenna parameters can be changed much faster if the toggle is switched off Output Select between output of the superposed electric field and output of the corresponding SAR distribu tion Other Ports Antenna parameters for all channels of the hyperthermia applicator Power Amplitudes relative units and Phase Delays degree If the number of channels is 4 it is assumed that the applicator Sigma60 is simulated and the channels are labeled Left Bottom Right and Top Note The order of the 4 channels differs from the order on the BSD 2000 console 6 76 Superpose Temperature Distributions The module Superpose also computes the temperature distribution corresponding to a giv
185. en set of antenna parameters power amplitudes and phase delays if it is selected from the popup menu of a file containing a set of temperature distributions Such files are created by module Static Heat They must contain N N 1 temperature distributions for simulating an applicator with N independent channels Connections Temperature Data Set A set of temperature distributions as created by module Static Heat The data files usually have a suffix ThermVals Plan Data optional Same functionality as in module Superpose as applied to electric fields For more information see the Plan Data description Ports The number of parameter ports and their functionality differ slightly from module Superpose as ap plied to electric fields Action Same functionality as in module Superpose as applied to electric fields 166 CHAPTER 6 ALPHABETIC INDEX OF MODULES Scale Factor The power amplitudes for the single channels see below should only be used to do a relative weight ing between the channels Using this port you can define an additional over all scaling factor to be applied to all channels Note The scale factor cannot be changed if toggle Auto Scale is set Auto Scale If this toggle is off the port Scale Factor is active If a file containing antenna parameters is read and this file also contains a scale factor this scale factor 1s applied If the toggle is set the port Scale Factor is inactivated and the scale factors con
186. encyType This command returns the current transparency type as a number in the range 0 6 The meaning of this number is the same as in set TransparencyType viewer lt number gt fogRange lt min gt lt max gt Sets a range of attenuation for the fog affect that can be introduced into a viewer scene by the View menu The default range is 0 1 Values within this range correspond to distances of scene points from the camera such that points nearest to the camera have value zero and those farthest away have value one Restricting the range of attenuation means that attenuation will start at points where the specified minimum is attained and reach its maximum at points where the specified maximum is attained Maximum attenuation by fog is equivalent to invisibility thus all points beyond that maximum will appear as background 4 1 7 Console Window The Console window is the user interface to Amira s advanced controlling features It serves two purposes First it gives you some feedback on what is currently going on Such feedback messages include warnings 4 1 INTERFACE COMPONENTS 67 Amira console Aleading lermperabure ical Aeading physics ical Reading voberA ed cal Hesdng glow col Amra 2 7 bets 3 aich wind2 Ophmize i help fer getting started gt Figure 4 4 Amira s console window displays info messages and lets you enter Tcl commands error indications and notes on problems as well as information on res
187. ent slice for subsequent edit operations A tool is activated by clicking on its icon with the left mouse button Selected areas are colored red The operation of most of the tools can be modified by pressing the Ctrl or the Shift key Ctrl typically des elects instead of selecting voxels while Shift adds voxels to the selection The description of the individual tools gives details e Brush If this tool is activated you can mark an area by simply brushing voxels holding down the left or right mouse button A textfield in the option panel controls the size of your brush in screen pixels If the Ctrl Key is held down or if the middle mouse button is used pixels are deselected instead of beeing selected The right mouse button is a flood fill tool You can e g sourround a region in the image by drawing along its border and then click into the middle of the currently unselected interior part to fill it Again the Ctrl Key inverts the operation 1 e deselects connected parts of the selection e Lasso The lasso lets you define an area by generating a closed contour curve Usually you draw such a curve freehand with the the left mouse button pressed but it is also possible to fence an area with line segments by pressing Alt and clicking succesively to points with the left mouse button holding down the Alt key all the time Succesive points will be connected with straight line segments To finish interaction release the Alt key an
188. ently selected tool additional widgets show up in the options frame e Info Area Below the tool box some basic information like cursor position is displayed 9 5 IMAGE SEGMENTATION EDITOR 225 large Pegasi Edd Ed yee Semcon abel Files Hi H ous edulla ES Loise ajaj 21 Rjofsj ra ajasa Tonma se Paria 1227 EAN ALGA sor 764447 Grey value 125 Figure 9 3 The Image Segmentation Editor window e Menu Bar From the menu bar additional tools and filters can be accessed Menu entries with behind the name open an additional dialog window e Image Viewer s The biggest part of the window is covered by one or four image viewers which display slices through the image data a visualization of the labels and a current selection Basic principle for interactive segmentation The basic idea of interaction in the ISE 1s a to first select some voxels and then to assign them to the active material The simplest way of selecting pixels is to simply draw with the mouse when the Brush or the Lasso tool is active see below for details Selected pixels are displayed in red To add selected pixels to the active material click the button The active material is the material which is currently selected in the material list New materials can be added using the right mouse popup menu in the material list Every pixel can only be assigned to one material Note that even with the advanced tool
189. er into interaction mode and adjust the crop box using the green handles directly in the viewer window e Put the viewer into interaction mode e With the left mouse button pick one of the green handles attached to the crop volume Drag and transform the volume until the part of the data you are interested in is included e Press OK in the crop editor s dialog window The new dimensions of the data set are given in the working area If you want to work with this cropped data record in later sessions you should save 1t by choosing Save Data As from the File menu As you already might have noticed the crop editor also allows you to rescale the bounding box of the data set By changing the bounding box alone no voxels will be cropped You may also use the crop editor to enlarge the data set e g by entering a negative value for the k min number In this case the first slice of the data set will be duplicated as many times as necessary Also the bounding box will be updated automatically 3 2 6 Volume Rendering Volume Rendering is a visualization technique that gives a 3D impression of the whole data set without segmentation The underlying model is based on the emission and absorption of light that pertains to every voxel of the view volume The algorithm simulates the casting of light rays through the volume from pre set 42 CHAPTER 3 FIRST STEPS IN AMIRA Figure 3 10 The crop editor works on uniform scalar fields It allows you
190. er part of the job dialog the current list of jobs of a user is shown For each job a short description is displayed as well as the time when the job has been submitted and the current state of the job A job may be waiting for execution running finished or it may have been killed The job directory For each job a temporary directory is created containing any required input data scripts state information and log files On Unix systems this directory is created at the location specified by the environment variable TMPDIR If no such variable exists t mp is used On Windows systems the default temporary directory is used Typically this will be C TEMP Controlling the job queue A job s state may be manipulated using the action buttons shown above the job list In order to start the job queue select the first job waiting for execution and then press the Start button Note that only one job can be executed at a time In order to kill a running job select it in the job list and press the Kill button You may delete a job from the job queue using the Delete button When deleting a job the temporary job directory will be removed as well Information about a job Once you have selected a job in the job queue more detailed information about it will be displayed in the lower part of the dialog window notably the state of the job the temporary job directory the submit time the time when the job has been started the run time and the name o
191. er sequence For example the expression img matches all filenames with the suffix img The File Dialog s Popup Menu The file dialog provides a popup menu which may be activated by pressing the right mouse button over the file list Among others this menu lets you rename or delete files or directories provided you have the permission to do that Note that you may only delete empty directories Using the Format option of the popup menu you may manually set the format to be used when loading a file into Amira This option is useful if for some reason the wrong format has been detected automatically or if no format at all could be detected Note however that any format specification set manually will be overwritten when the directory is reread the next time 4 1 10 Snapshot Dialog The Snapshot Dialog provides the user interface of the viewer s snapshot facility You get the dialog by clicking on the camera icon in the left toolbar of the viewer You can either send the grabbed image directly to the printer or save it into a file in order to include it into other documents In the to printer mode you first have to select and configure a printer by pushing the Configure button In addition you may enter an arbitrary text string which is printed as an annotation text below the snapshot image In the to file mode type in a filename or use the File Dialog Browse button to choose the output file T2 CHAPTER 4 PROGRAM DESCR
192. erpolation at all and the sample values are taken at the controlpoints only getOrder Returns the order of the spline probe setOrder lt value gt Sets the order of the spline probe getPoint lt index gt Returns the coordinate of the requested controlpoint Index defaults to 0 SetPoint lt index gt lt x gt lt y gt lt z gt Sets the coordinates of controlpoint index Index defaults to 0 getSamplePoints Returns the coordinates of all points where samples are taken getSampledValues Returns all sampled values 6 23 DELAUNAY2D 115 setImmediate 0 1 Switches the immediate mode on or off i e data is shown while the probe line resp point is being moved setOrtho 0 1 Switches the orthogonal mode on or off i e all controlpoints of a probe line are moved in sync or not getNumPoints Returns the number of control points of a probe line In case of a point probe 1 is returned getLength Returns the length of the probe line O in case of a point probe appendPoint lt x gt lt y gt lt z gt Appends a controlpoint with the given coordinates insertPoint lt index gt lt x gt lt y gt lt z gt Inserts a controlpoint with the given coordinates as the index point removePoint lt index gt Removes the given controlpoint 6 23 Delaunay2D This module takes a set of 3D vertices and produces a Delaunay triangulated surface with 2D topology In order to do so the vertices are temporarily being proje
193. ers must always begin with the letter Similar the following lines define additional data to be stored in the arrays called Nodes and Tetra hedra The primitive data types must be one of byte short int float double or complex Vectors of primitive data types are allowed aggregate structs are not however The statement Field float Example Linear 8 defines a continuous scalar field with the name Example This field will be generated by linear interpolation from the data values Values defined on the nodes of the tetrahedral grid Other interpolation methods include Constant X and EdgeElem X After the marker 1 the coordinate values of the grid are stored Likewise the other data arrays are given after their corresponding markers In case of a BINARY file the line containing the marker is read up to the next new line character Then the specified number of bytes is read in binary format It is assumed that sizeof short is 2 sizeof int is 4 sizeof float 1s 4 sizeof double is 8 and sizeof complex is 8 Multidimensional arrays indexed via k 3 i are read with i running fastest Backward compatibilty For backward compatibility the following statements are considered to be equal nNodes 99 is equal to define Nodes 99 nTriangles 99isequaltodefine Triangles 99 nTetrahedra 99isequaltodefine Tetrahedra 99 nEdges 99isequalto define Edges 99 NodeData is equal to Nodes TriangleData is equal to Triangles TetrahedraData
194. es making sure they do not exceed 255 Alpha Weighted weights the different inputs according to their alpha values 1 e inputs with a large alpha value become more prominent in the resulting field If all connected source fields are scalar byte fields of the same dimensions the module offers two more options colormaps which does exactly the same as the procedures above yet implemented in a much more efficient way and RGB planes which interprets sourcel source2 and source3 as the R G and B values of the resultfield respectively Connections Data required A scalar or color field This one determines the size of the result field Source2 optional Another scalar or color field Source3 optional And yet another one Colormap1 optional The colormap for source field 1 Colormap2 optional The colormap for source field 2 Colormap3 optional The colormap for source field 3 Ports amp Colormap1 A E y Ss ay Colormap input port for source field1 Colormap2 Colormap input port for source field2 Colormap3 Colormap input port for source field3 Mode a Mode alpha weighted average add amp clamr This option menu lets you choose the combining algorithm The choices are geometrical average simple addition and a addition weighted in relation to the corresponding alpha values This port is only visible if Colormode is set to colormaps 106
195. es 7 This is 2 2 3 Parameters CoordType rectilinear Lattice float ScalarField 1 Coordinates 4 Elgat Xyz p Z 1 00 50 0 y IN MS E E 2 2 TZ 2 Ox dl x coordinates OED y coordinates 1 12 z coordinates Use float 3 in order to encode a vector field instead of a scalar field Likewise you may modify the field s primitive data type Instead of ScalarField you may use any other name in the data definition statement Fields with curvilinear coordinates A field with curvilinear coordinates consists of a regular array of grid cells Each grid node can be addressed by an index triple i j k The coordinates of the grid nodes are specified explicitely In order to encode a 3D scalar or vector field with curvilinear coordinates you have to define a 3D array called Lattice This array is used to store the field s data values as well as the grid nodes coordinates The coordinates must be given as a float 3 vector containing x y and z values The coordinate type of the field is specified in the parameter section of the AmiraMesh file Here is an example 200 CHAPTER 8 ALPHABETIC INDEX OF FILE FORMATS AmiraMesh ASCII 1 0 define Lattice 2 2 3 Parameters CoordType curvilinear Lattice float ScalarField 1 lattice Tloat 3 Coordinates k U2 1 2x2x3 scalar values 0 1 2 N PO NO PO N PO Q2 2x2x3 xyz coordinates FeO OE OF eo e oO OrRrODODOF ODO OF OC O N NN NF
196. es of the surface makeOnePatch Puts all triangles of the surface into a single patch cleanup Removes any additional data such as edges boundary contours or connectivity information from the surface getArea lt i gt Compute area of all surface patches incident on material i getVolume lt i gt Compute volume enclosed by material i setColor lt material gt lt color gt Defines the color of a material used in module Surface View The material may be specified by either a material name or by a material index The color may be specified by either an RGB triple in range 0 1 or by a common X11 color name e g red or blue setTransparency lt material gt lt t gt Defines the transparency of a material used in module Surface View when draw style is set to transpar ent The material may be specified by either a material name or by a material index The transparency value t must by a floating point number in range 0 1 add pOlnt Axe Aye gt Adds a new point to the surface The method returns the index of the new point 192 CHAPTER 7 ALPHABETIC INDEX OF DATA TYPES add triangle lt pl gt lt 02 gt lt p3 gt Adds a new triangle to the surface and returns its index The triangle will be inserted into the first patch of the surface If no patch yet exists one will be created refine Refines the surface by subdividing all edges After this operation the surface will contain four times the number of triangles
197. es to be displayed The technique typically gives the best results with a rather large number of lines e g 100 500 Note however that on systems with slow 3D graphics without texture hardware a large number of lines can slow down rendering speed significantly Length 3 Length Ad The length of the field lines or more precisely the number of atomic line segments in forward respectively backward direction The lines may stop earlier if a singularity 1 e zero magnitude is encountered or if the field s domain is left On default lines are traced the same distance in forward and backward direction You may use the command set Balance to change this behavior Opacity 3 Opacity a os Base opacity factor of the lines A value of 1 produces completely opaque lines while O results in fully transparent lines m a O D 5 Fade Factor I 3 0 37 118 CHAPTER 6 ALPHABETIC INDEX OF MODULES This port controls how fast opacity decreases along field lines if fade mode is enabled The first atomic line segment will be assigned the base opacity set in port Opacity The opacity of each successive segment will be multiplied by the value of this port This is useful in order to encode the directional sign of a vector field The vector field points in the direction of increasing transparency Alpha Window amp Alpha Window min o mas 100 This port will only be visible if fade mode 1s disabled and i
198. es2 If more sets are defined the coordinate values must be called Coordinates3 Coordinates4 and so on It is also possible to define additional data values for each marker such as MarkerTypes or Orienta tions How these values are interpreted in detail will be specified in a future release of Amira Line segments The data type Line Set is used to represent a generic set of indexed line segments 1 e line segments defined by an index into a vertex list Optionally an arbitrary number of scalar data values may be associated with each vertex In order to store line sets in an AmiraMesh file two 1D arrays have to be defined namely Lines used to store the indices and Vertices used to store the vertex coordinates as well as additional vertex data Here 1s an example AmiraMesh ASCII 1 0 define Lines 15 define Vertices 12 Parameters ContentType HxLineSet vertices lost tal Coordinates b al Vertices float Data 2 Lines ant ie ase 2 3 Q1 12 xyz coordinates 0 OO OO OCOrFR FF O O e e O WOOD O WO O O O O e e O FF OWoO OF OD CO N WoO rR ODO FF Or OC O DIA O G2 4 12 data values 1 1 1 1222 2 1 1 1 1 3 15 indices defining 3 line segments Os AD Ze Al AS O96 O el ll Lines are defined using vertex indices as shown above The index of the first vertex is 0 An index value of 8 3 BMP IMAGE FORMAT 203 1 indicates that a line segment should be terminated An arbitary number of
199. escribed above In the single viewer layout you can choose the Orientation of the viewer The Info line toggle lets you switch off the on line information displayed in the lower left part of the window Selection This menu provides a number of filters and operators which modify the current selection They are described below Menu entries with dots behind their name open an additional dialog LabelFilter These filters and operators directly modify the label field and not the selection Selection Filters Grow Shrink This filter does a morphological dilatation or erosion of the current selection The filter can be applied on the current slice in the active viewer or on the whole volume Invert This operator inverts the selection 1 e selected voxels are deselected while unselected voxels become seleceted The filter can be applied on the current slice in the active viewer or on the whole volume Threshold Select voxels by threshold segmentation In the additional dialog a minimal and a maximal image intensity can be specified By clicking on Apply all voxels falling into the interval are selected If the current material only option is activated only voxels assigned to the current material are selected If the 3D option is active the operation is performed in the whole volume otherwise it is done in the current slice of the active viewer Make Ellipse By pressing this button the outline of a selected area is replaced by
200. ese steps 1 Click on all the demo scripts in the Online User s Guide If the system crashes turn off hardware acceleration choose the extended button from the Windows display settings dialog and try again If this eliminates the problem there is a bug in your OpenGL driver Try to get a new driver from the web site of the manufacturer of your graphics board 2 Try using a different color depth in the Windows display settings dialog Try 16 24 or 32 bit 3 Load the lobus am data set and visualize it with a Voltex module Turn on the spin rotation turn it with the mouse in the viewer and release the mouse button while moving the mouse so that the object continues moving Let it run over night turn off the screen saver If the system has crashed or frozen the next morning you probably have a hardware problem If this does not help or if a reproducible error occurs on different computers then it might be a bug in the 5 6 SYSTEM REQUIREMENTS 89 Amira software itself Please report such bugs so that they can be eliminated in the next release 5 6 2 Microsoft Windows Amira runs on Intel or AMD based systems with Microsoft Windows 98 Windows NT NT4 Service Pack 4 or later and on Windows 2000 If you are using Windows 95 be sure that the Windows Socket 2 Update is installed on your computer Otherwise the system will complain that ws2_32 d11 is missing You may download the update from www microsoft com windows95 downloads
201. esenting these two combinations Options AGS Sliders ChA r ASV Siders CirhA Selecting RGB Sliders provides controls over RGB color space Selecting HSV sliders provides sliders to manipulate the HSV color space 213 214 CHAPTER 9 ALPHABETIC INDEX OF EDITORS la Color Dialog E Edit Options c PR res Coo ME oer o E IE o O OO A A Current Color Old Color Custom Colors BENE E OF Apply Reset Cancel Help Color Sliders The color sliders present the color range in hue saturation value HSV or red green blue RGB color spaces If the color to be changed has an alpha component an additional slider is automatically displayed Each slider controls one color component The color sliders are visible depending on the user selection in the Option Menu Each of the color sliders is accompanied with a text edit field to view the exact value of the current color component and to set 1ts numerical value The component values are always in the range from O to 1 Furthermore two arrow buttons can be used to move each slider respectively On the left side of each slider except the alpha slider an additional check button is displayed allowing the user to select one color component to control the appearance and functionality of the color picker Color Cells The color cells are subdivided into three different groups One cell named Current Color displays the color depending on the current settings Each co
202. f 200 000 to 400 000 triangles Tetrahedral grids created from such surfaces are much too large to be suitable in subsequent simulation steps Thus the number of triangles must be reduced drastically This step is called surface simplification Click on the icon representing the surface to be simplified Then invoke the Surface Simplification Editor by pressing of the button displaying the mesh like icon The simplification algorithm included in HyperPlan repeatedly collapses surface edges to points essentially starting from the edge causing the least significant modification of the original surface The requested number of triangles can be entered in field faces In addition in the field max dist the maximal edge length in cm can be entered Simplification stops if either the desired number of faces is reached or no edge shorter then max dist exists anymore For hyperthermia simulation we recommend to set the number of triangles to O and to specify a maximum edge length of about 2 5cm to 3cm smaller numbers resulting in more triangles You may also choose whether to preserve the slice structure of the GMC surface or not by selecting the corresponding option toggle Preserving the slice structure only refers to the outer boundary of the patient model 1 e to all patches with outer region equal to Exterior If this option is set the patient model later can be combined with the hyperthermia applicator more easily so called bolus grid processing Ho
203. f an alpha field is connected to the module In this case the alpha field s values are mapped to opacity according to the range specified by this port At locations where the alpha field is equal or smaller than min field lines will be completely transparent Likewise at locations where the alpha field is equal or bigger than max field lines will be completely opaque g Y 5 Options fade I texture animate Fade Enables fading mode as described above Texture Controls illumination of lines If off constant colored lines are drawn flat shading Animate Activates particle like animation The animation speed may be controlled via the command setAnimationSpeed YN a y A amp Seed Box XfomBox TabBox Hide Clicking on XformBox or TabBox brings up a 3D dragger in the 3D Viewer This allows you to restrict the region of interest i e the region in which seed points are placed by interactively transforming the dragger Remember to switch the viewer into interaction mode by hitting ESC After changing the box you have to hit Dolt to trigger recalculation Distribute a Distribute Balt homogene On the one hand this port provides a Dolt button which is used to initiate distribution of seeds and recomputation of field lines Once the incoming vector field has changed or you have modified the number of field lines or the line s length you have to press Dolt in order to update the displ
204. f is taken for uncolored emission In RGBA mode colored images are generated by using all four channels of the colormap Colormap E E E E E E E E E E E E 180 Port to select a colormap Alpha scale amp Alpha scale i A global factor to change the overall transparency of the object independent of the data value Number of slices a Number of slices E DENE Only available in 3D texture mode The larger this number the better the image quality and the less the rendering performance Texture mode a Texture mode 2D 3D 2D texture mode requires some precomputation time but also works on machines which do not sup port hardware accelerated 3D texturing like e g SGI 02 3D mode needs less setup time and sometimes provides superior quality on high end machines 3D texture mapping 1s not available on the Windows platform 182 CHAPTER 6 ALPHABETIC INDEX OF MODULES Downsample a Downsample 2 y 2 z fi You can specify integer downsample factors to reduce the size of the data set on the fly E g down sampling by 2 in each direction would decrease the size of the data set by a factor of 8 This can dramatically improve rendering performance Update amp Update EDolt Click on this button in order to trigger computations necessary to display the volume Most parameter changes require hitting this button again 6 89 VoxelView This module can be attached to an OrthoSlice module It al
205. f no clipping occurs the input range covers all values between the minimum and maximum data value of the incoming scalar field This range will be mapped as indicated If clipping occurs the minimum or maximum value of the output range or both will be equal to the smallest respectively biggest value which can be represented by the selected output data type In this case the input range shows which values correspond to these limits Data values below the lower limit or above the upper limit will be clamped Output Datatype a Dutput Datatype signed int y Lets you select the primitive data type of the output field The item LabelField is special If this is selected the incoming scalar field is converted into a label field Scaling a Scaling cale 1 offset 0 Defines a linear transformation which is applied before the data values are clamped and casted to the output datatype The transformation is performed as follows output SCALE I1NnpuUCtOFFSET If you want to convert data with a range inmin inmax into arange outmin out max SCALE and OFFSET are determined like this SCALE outmax outmin in max inmin andOFFSET outmin SCALE inmin Options amp Options clean labels This port is only shown if you want to convert the incoming scalar field into a label field If option clean labels is set then the materials found in the input data set will be relabeled so that the first material is O the second
206. f no such extra material will be created Instead the boundary is assumed to be labeled with O which usually corresponds to Exterior Minimal edge length Minimal edge length o A non vanishing value indicates that short edges of the final GMC surface should be contracted in order to increase triangle quality as well as to decrease the number of triangles The value of the port indicates the minimal allowed edge length relative to the size of a unit grid cell On default values between 0 and 0 8 can be entered Typically a value of 0 4 already yields good results However note that intersections may be introduced during edge contraction If you want to avoid this try to use the simplification editor The editor applies some special strategies in order ensure topological consistency Action amp Acton Triangulate This port has a single button Triangulate which 1s used to start surface extraction Depending on the size of the LabelField the algorithm requires up to a minute to finish 6 32 GetCurvature This module computes curvature information for a discrete triangular surface of type HxSurface Either the maximum principal curvature value the reciprocal curvature value or the direction of maximum principal curvature can be computed The algorithm works by approximating the surface locally by a quadric form The eigenvalues and eigenvectors of the quadric form correspond to the principal curvature values and to the directions
207. f the command to be executed Any console output of a running job will be redirected to a log file located in the temporary job directory Once such a log file exists and has non zero size you may inspect it by pushing the View output button 70 CHAPTER 4 PROGRAM DESCRIPTION ey er Ds MOMEAodnemes2000 dalandonals gt El cl ae EE 0210 00 12 41 05 e 1425623 01 2800 17 5245 AmraMesh bobus grid am 302277 03 0900 124214 AmraMesh lobe Labels am 570778 0142800 175245 AmraMesh lobe landmark am 210 01 2300 17 5245 AnmraMezh bobus am 1081651 01 2300 17 5244 AnmraMezh Hing am 2583236 01 2800 17 5447 ArmraMezh HARI De B97 70 01 2800 17 5445 Open Invertor Fie hpa e a HeSutace binay sul Hi5utface apen surf Open inventos re Wawetroent cj 45 UCD ase inp AVS UCD binary inp DAF cha FLUENT UNS msh Hypermesh asci Frasca STL asen 581 Figure 4 6 Amira s file dialog Commands job submit cmd info tmpdir Submits a new job to the job queue command specifies the command to be executed info specifies the info string displayed in the job dialog tmpdir specifies the temporary job directory If this argument is omitted a temporary job directory is created by Amira itself In any case the directory will be automatically deleted when the job is removed from the job queue Example job submit clock exe Test job JO run Starts the first job in job queue pending for execution When a jo
208. ferent draw styles are provided filled lines and points Due to the regular structure of the voxel data only three different face orientations occur Thus only three different colors will be used to render the voxel regions Action E Acton Clear Provides a button to hide all selected 3D regions 184 CHAPTER 6 ALPHABETIC INDEX OF MODULES Chapter 7 Alphabetic Index of Data Types 7 1 Analytical Scalar Field This data class represents a user defined 3D scalar field based on a regular grid It provides a port Expression by which an arithmetic expression depending on uniform cartesian coordinates x y z can be entered that defines the value for each point of the unit cube The range of values with respect to this default domain is indicated as Component Range A data object of type HxAnnaSccalarField3 has two additional input ports that can be connected to other data objects representing scalar fields on a regular grid e g to image data objects The predefined variables a and b are available for referencing such connected data objects in the arithmetic expression this way a scalar field depending on other regular scalar fields can be defined Whenever an expression evaluation is triggered to compute the value for a point x y z the variables a and or b will be be substituted by the corresponding input values at the same point x y z For instance the value at a single point may be obtained by attaching a PointProbe module to the
209. field may be either of type HxScalarField3 or of type HxSurfaceScalarField In addtion to scalar surface fields also 3 and 4 component surface fields are supported In this case the field components are directly interpreted as RGB or RGBA values The values should range from 0 to 1 Colormap optional The Colormap is used to visualize the data values of a scalar field connected to port ColorField Ports Draw Style a Draw Style outined more optione This port is inherited from the ViewBase class and therefore the description will be found there Colormap Coloma 0 LS a This port becomes visible only if a scalar field has been connected to the ColorField port Buffer 5 Buffer Add Remove Clear Show Hide Draw This port lets you add and remove highlighted triangles being displayed in red wireframe to an internal buffer For a further description and for the functionality of each of the port buttons see amp Materials Exterior Exterior This port provides two option menus listing all regions defined in the surface By setting the menus 8 ae a gt y E a NN n 0 6 79 TETRA COMBINE 169 properly you can highlight all triangles separating two different regions Highlighted triangles are displayed in red wireframe You may restrict the set of highlighted triangles by means of an adjustable box Use port Buffer to add or remove highlighted triangles to the internal buffer Colormode Col
210. formation about the data set such as its size or its coordinate type is displayed in the working area The data will be loaded into the system Depending on its size this may take a few seconds The file is stored in Amira s native AmiraMesh format The file 1obus am contains 3D image data of a part of a fruit fly s brain namely an optical lobe obtained by confocal microscopy This means the data represents a series of parallel 2D image slices across a 3D volume Once it has been loaded the data set appears as a little green icon in the object pool In the following we call this data set lobus data seta e Click on the green data icon with the left mouse button to select it This causes some information about the data record to be displayed in the working area Figure 3 3 In our case we can read off the dimensions of the data set the primitive data type the coordinate type as well as the voxel size To deselect the icon click on an empty area in the object pool window You may also pick the icon with the left mouse button and drag it around in the object pool 3 1 2 Invoking Editors After selecting an object in addition to the textual information some buttons appear in the working area right next to the data object s name These buttons represent editors which can be used to interactively 36 CHAPTER 3 FIRST STEPS IN AMIRA Figure 3 4 In order to attach a module to a data set click on the green icon using the ri
211. functions X x y z Y x y z and Z x y z which can be specified by the user in the same way as a function for a HxAnnaScalarField3 data object The range of vector magnitudes defined as Euclidean vectors lengths is indicated as Magnitude A data object of type HxAnnaVectorField2 has three additional input ports named InputA InputB InputC that can be connected to other data objects representing scalar or vector fields on a regular grid There are some predefined variables for referencing such connected data objects in the arithmetic expressions namely a b c for scalar fields and ax ay az bx by bz cx cy cz for X y resp z components of vector fields This way a vector field depending on other regular scalar and or vector fields can be defined Whenever an evaluation of the three expressions is triggered to compute the vector associated to a point x y z each of the variables mentioned that occurs in them will be substituted by the corresponding input values at the same point x y z For instance the component values of a vector associated to a single point may be obtained by attaching a PointProbe module to the HxVectorField3 data object entering the point s cordinates by the Coord port of that module and setting the Vector toggle to all An expression consists of variables and mathematical and logical operators the syntax is basically the same as for C expressions The following variables are always defined e x the x coordi
212. g job of the queue starts running 7 It is a good idea to run simulations overnight You may quit HyperPlan while a job is running If you restart HyperPlan again select Jobs from HyperPlan s File menu to open the job dialog window again It will show the current state of the job queue More information is given in the reference documentation of the FDTD module 1 5 4 E Field Calculation Using the FE Method This section describes how to perform an E field calculation using the finite element method This method is the preferred one since it is more accurate than an FDTD simulation Also it can be used for the Sigma 40 and Sigma 2000 applicators not only for the Sigma 60 The whole task can be separated into two different parts namely in converting the patient model into a so called extended grid and in applying the simulation code itself 24 CHAPTER 1 HYPERTHERMIA PLANNING Creating an Extended Grid Before starting the E field calculation you must extend the tetrahedral patient model Grids have to be added representing the water bolus of the hyperthermia applicator and parts of the surrounding medium 1 e air If you want to perform several simulations with different relative positions of patient and applicator you must create such an extended grid for each simulation 1 Load a tetrahedral patient model filetype grid into HyperPlan To see the model in the 3D viewer select a Grid Volume module from the popup menu of the green
213. general it is not recommended that you use a remote display for demanding interactive 3D graphics applications like Amira However in principle you can redirect the output of the Unix version to a remote display For IRIX HP UX and SunOS the remote X server needs to support the GLX extension Call xdpyinfo to find out whether your computer has that extension installed Then simply set the DISPLAY variable and start Amira If heterogeneous platforms are involved problems with the overlay planes may occur If the viewer window remains black try using the Amira command line option no_overlays or set the environ ment variable AMITRA_NO_OVERLAYS Do I need to have root or administrator privileges in order to install the product No On Windows systems you can run the setup tool without having administrator privileges On Unix systems simply extract the provided tar file However on Sun and HP UX it is recommended that you set the default visual of the X server to 24 bit true color This may require root privileges In addition on some HP UX systems it is recommended that you increase certain kernel parameters like process data size or stack limit This requires root privileges as well What are the software and hardware requirements Software and hardware requirements are described in the user s guide in section System Require 5 5 FREQUENTLY ASKED QUESTIONS 83 11 12 13 14 15 ments What is the minimum configuration re
214. geometry in this format The vector field itself is stored in Amira s native AmiraMesh file format The data represents the flow around an airfoil computed on a regular grid with curvilinear coordinates By selecting the green data icon wing am you can find out that the number of grid nodes in x y z direction is 125 x 41 x 21 44 CHAPTER 3 FIRST STEPS IN AMIRA Figure 3 12 Open Inventor geometry of the airfoil 3 3 2 Line Integral Convolution Line Integral Convolution LIC is a method for visualizing 2D vector fields 1 e depicting the vector field direction for a suitably sampled subset of points in the 2D domain The direction is represented by local streamlines 1 e by curves whose tangent vectors coincide with those of the given vector field Local streamlines are computed such that all image pixels are covered The streamlines are projected onto a random noise input texture map of the same size as the vector field domain The projection step involves summations of texture pixel intensities along streamline paths by way of a convolution integral with a filter kernel This causes pixel intensities in the resulting image to be highly correlated along individual streamlines but statistically independent perpendicular to the latter Thus the directional structure of the vector field becomes clearly visible Here we use the 3D vector field that we have already loaded and visualize two dimensional slices Connect a PlanarLIC module to the
215. ges Input field factor determines the width of the grey value histogram which is of Gaussian type Higher numbers produce more contrast Options a Options filter length ell resolution 256 Parameter filter length specifies the one sided length of the triangular filter kernel used for line in tegral convolution The larger this value the more coherent the greyscale distribution along the field lines Often larger values are visually more attractive than smaller ones The second input determines the resolution of the LIC texture More precisely the width of a single texture cell is chosen to be equal to the length of the diagonal of the incoming vector field s bounding box divided by the value of the resolution field Action a Action E Dalt Starts computation of the surface LIC texture Computation may take a minute or more depending on texture resolution and on the number of triangles of the surface Commands setAmbientColor lt color gt Allows you to change the ambient color of the surface setDiffuseColor lt color gt Allows you to change the diffuse color of the surface setSpecularColor lt color gt Allows you to change the specular color of the surface setShininess lt value gt Allows you to change the shininess of the surface setCreaseAngle lt value gt Neighboring triangles will share a common vertex normal if the angle between their face normals is 168 CHAPTER 6 ALPHABETIC INDEX OF MODULES sm
216. get two files a temperature grid and a temperature channel file The filetypes are ThermGridFD and ThermValsFD or ThermGridFE and ThermValsFE re spectively Load both of these files into HyperPlan in order to compute the optimal antenna settings 2 Check if the patient model contains a region named Target Optimization will not work without a Target region 3 Select the Opt Temp module from the popup menu of the temperature channel file The optimization module will compute a plan file which contains the optimal amplitudes and phases of the radiowave antennas As with the other simulation modules you have to specify the name of the result file before the computation can be started HyperPlan suggests a name but be sure to check 1f this name is ok We recommend to use the filetype PlanFD or PlanFE respectively 4 If a simulation of the Sigma Eye applicator is to be performed you can set the number of available power generators 4 or 12 at the port Power Generators 5 Press the Submit button to start the optimization Usually temperature optimization takes only a few seconds Also it does not require much memory Therefore there is no need to leave HyperPlan before starting the batch queue 6 When optimization has been finished the resulting plan file is automatically loaded into HyperPlan If you want to visualize the optimal temperature distribution select the Superpose module from the popup menu of the ThermVals icon Chang
217. ght mouse button A popup menu appears containing all modules which can be used to process this particular type of data manipulate the data object in some way For example all data objects provide a parameter editor This editor can be used to edit arbitrary attributes associated with the data set e g filename original size or bounding box Another example is the transform editor which can be used to translate or rotate the data in world coordinates However at this point we don t want to go into details We just want to learn how to create and delete an editor T E Indoc 120x 128 x 87 bytes 22 254 undorm coeds Vowel Size 1 96053 x 1 56862 x 1 98395 e Invoke one of the editors by clicking on an editor icon e Close the editor by clicking again on the editor icon Further information about particular editors is provided in the user s reference manual 3 1 3 Visualizing Data Data objects like the lobus data can be visualized by attaching display modules to them Each icon in the object pool provides a popup menu from which matching modules 1 e modules that can operate on this specific kind of data can be selected To activate the popup menu e click with the right mouse button on the green data icon Choose the entry called BoundingBox After you release the mouse button a new BoundingBox module is created and is automatically connected to the data object The Bounding Box object is represented by a yellow icon in t
218. gs usr lib libGL so grep OpenGL Amira is sucessfully being used on systems with Creator 3D and Elite 3D graphics boards It runs on a simple Creator graphics boards as well However since no hardware texturing is available performance 1s limited 5 6 6 Linux Amira 2 2 runs on glibc 2 1 based Linux systems It has been tested on the following distributions RedHat 6 2 Suse 6 3 3D graphics hardware acceleration on Linux is a rather new and quickly evolving topic Amira is known to work with the 3D Accelerated X servers from XI graphics http www xig com with the XFreeS6 4 drivers from nVidia http www nvidia com for TNT and GeForce based cards and with SGI s drivers for their SGI 230 linux workstation In principle Amira should work with other hardware acceler ated OpenGL implementations as well The basic recipe to get hardware acceleration is to remove or rename the libraries libGL so x and libGLU so x in the Amira 1ib arch Linux Optimize directory so that the hardware accelerated libraries will be used instead Sometimes not all features are accelerated E g it is sometimes necessary to disable the stencil buffers by starting Amira with the option no stencils In any case Amira requires an X server resolution of at least 1024x768 and at least 15 bit of color depth Please note that if software rendering is used rendering performance may drop significantly especially for visualization techniques like volume rendering
219. han the diameter of the bounding box times the given Relative Tolerance factor Connections Data required Connect a data object of type vData to this port Ports Relative Tolerance E Relative Tolerance 12 005 Factor to determine duplicated points Options a Options create edges and connectivity If this toggle 1s set the triangle connectivity of the Surface data format is filled Action E Action I Dolt The surface is generated if the Dolt button is pressed 6 48 Label Voxel The LabelVoxel module provides a simple threshold segmentation algorithm applicable to CT or MR image data The method is also suitable for binary segmentation of other grey level images Up to five different regions separated by four different thresholds can be extracted For CT images the four regions Exterior Fat Muscle and Bone are predefined However the name of these regions as well as the corresponding thresholds may be reset by the user In order to find suitable thresholds an image histogram showing the absolute number of occurrences of voxel values and the current partitioning of the grey value range into the segments is provided In this 6 48 LABELVOXEL 137 histogram several peaks can be identified more or less clearly e g the ones for fat and muscle The corresponding threshold or segment boundary should be set at the minima between successive peaks The histogram window pops up by clicking on the Histo action b
220. he data of the original curve will be changed To do so you have to select the object in the Markerline Position 1 73205 x Horizontal Vertical Line Type 4 Width fi Color Oo Options F Use Annotation Figure 6 6 Editable markerline parameters 6 59 PLOT TOOL 151 list and then choose the Edit gt Copy pulldown menu After that choose Paste or Append in the menu and the object will be inserted at the current position position of the selected object resp the object will be placed behind the selected object With the New pulldown menu you can create new objects which will be inserted at the appropriate positions in the list of objects Printing The File pulldown menu of the main plot window provides a Snapshot item where you can send the plot directly to the default printer or save it as an image file Saving data The Save data item under the File menu lets you save the data of all curves in a file The date is stored in a proprietary format subject to change in the future Commands In the Amira environment Plot Tool commands have the following structure SthePlot command parameters or if the command applies to a plot object SthePlot objectname command parameters The following general commands are available getSize Returns the size of the plot window setSize lt width gt lt height gt Sets the size of the plot window hide Hides the plot window show Shows the plot window if it is
221. he labels themselves a LabelField may also contain weights indicating the degree of confi dence of the label assignment made for each voxel Such weights are calculated automatically when you choose option sub voxel accuracy in Label Voxel when you apply the smoothing filter of GI or when you resample a LabelField to a smaller resolution using the Resample module You can visualize a LabelField by attaching an OrthoSlice module to it If a LabelField contains weights the port Primary Array allows you to choose whether the labels or the probabilities are to be displayed Connections Master unused 7 6 LANDMARK SET 189 ImageData required Connection to the image data that the segmentation results refer to You cannot connect this port to an image object with dimensions different from that of the LabelField except the LabelField has been newly created via the Edit Create menu In this case the LabelField will be resized so that it matches the dimensions of the image object Ports Primary Array E Primary Labels An option menu which only appears if the LabelField contains weights In this case the menu lets you select whether the labels or the weights are the primary data array The primary data array is the default array visible to modules expecting an ordinary uniform scalar field like OrthoSlice or Arithmetic Commands hasMaterial lt name gt Returns true if the specified material is defined in the material section
222. he object pool and the connection is indicated by a blue line connecting the icons At the same time the graphics output generated by the BoundingBox module becomes visible in the 3D viewer Since the output is not very interesting in this case we will connect a second display module to the data set e Choose the entry called OrthoSlice from the popup menu of the lobus data set Now a 2D slice through the optical lobe is shown in the viewer window Initially a slice oriented per pendicular to the z direction and centered inside the image volume is displayed Slices are numbered O 3 1 GETTING STARTED 37 Figure 3 5 Visualization results are displayed in the 3D viewer window Parameters or ports of a module are displayed in the working area after you select the module 1 2 and so on The slice number as well as the orientation are parameters of the OrthoSlice module In order to change these parameters you must select the module Like for the green data icon this is done by clicking on the OrthoSlice icon with the left mouse button By the way in contrast to the BoundingBox the OrthoSlice icon is orange indicating that this module can be used for clipping e Select the OrthoSlice module Now you should see various buttons and sliders in the working area ordered in rows Each row represents a port allowing you to adjust one particular control parameter Usually the name of a port is printed at the beginning of a row For example
223. he plane as you please Connections Data required The labelled tetrahedral volume grid to be visualized Ports Orientation E Drientation Axial Coronal S agital This port provides three buttons to specify the slice orientation Axial slices are perpendicular to the z axis coronal slices are perpendicular to the y axis and sagittal slices are perpendicular to the x axis Options amp Options adjust view Po rotate P immediate If the adjust view toggle is set the camera of the main viewer 1s reset each time a new slice orientation is selected With the rotate toggle you can switch on the rotate handle for the cutting plane and off 6 36 GRID VOLUME 127 again If the immediate toggle is set the slice is updated every time you drag it with the mouse in the 3D viewer Otherwise only the bounding box of the cutting plane is moved and the update takes place when you release the mouse button Translate a Translate E OE This slider allows you to select different slices The slices may also be picked and dragged directly in the 3D viewer Selection amp Selection Ada Remove Al This port maintains a list of materials assigned for cutting With the selection menu one can select a single material The Add button adds a previously selected material to the list and the Remove button removes the currently selected material 6 36 Grid Volume The Grid Volume module is a powerful tool for visualizing l
224. hedral models adds some complexity to the hyperthermia planning procedure such models nevertheless offer the opportunity for accurate E field simulation and fast temperature computation The boundaries between different tissue compartments can be represented accurately using a small number of elements No artificial steps and rasterization effects occur as in cartesian grids Similar to a labeled volume a tetrahedral grid also contains a dictionary of different tissue types In addition to the tissue names the dictionary may also contain colors and default values for various simulation parameters For each patient model usually different versions are stored The generic patient models have a suffix grid If you want to perform an E field calculation on a tetrahedral grid using the FDTD method you need a modified grid containing duplicated points at the tissue boundaries suffix EFieldGridFD The duplicated nodes are required to represent E field discontinuities at the tissue boundaries Use module DuplicateNodes to create such a modified grid When you perform an E field calculation using the FE method another modification of the grid is stored as an output file suffix EFieldGridF E It is essentially the same as the original patient model however it additionally contains an edge list This is needed for the special field representation of the finite element method called Vector elements When you perform a temperature simulation an
225. hidden getObjects Displays a list of all plot objects currently in use update Processes the plot object and updates the display Snapshot lt filename gt Takes a snapshot and saves it under the given name The suffix of the filename determines the raster format used Available formats are TIFF tif tiff SGI RGB rgb JPEG jpg jpeg and PNM pgm ppm print lt filename gt Prints the plot window into a PostScript file vector based save lt filename gt Saves the data of all data based plot objects in a propriatary format load lt filename gt Loads data from the filename and stores it in a curve plot object 152 CHAPTER 6 ALPHABETIC INDEX OF MODULES The following commands apply to plot objects getMinMax Returns the minimum and maximum values of objects of type Curve Cartesian Axis Polaraxis setMinMax lt minX gt lt maxX gt lt minY gt lt maxY gt Sets the range of Cartesian Axis Polaraxis getArea Returns the plotting area of PlotArea objects setArea lt lowerleftX gt lt lowerleftY gt lt upperrightX gt lt upperrightY gt Sets the plotting area of a PlotArea object 6 60 Point Probe See Section Data Probing for details 6 61 PointWrap This algorithm performs a surface reconstruction from a set of unorganized points It models a probe sphere that is being dropped onto and then rolled over the set of points Every three points the sphere rests on during this
226. ices the same remarks apply as for the TIFF image format When reading PNG images the channel conversion dialog is popped up This dialog is also is also described the TIFF section 8 12 PNM Image Format This format includes the PPM PGM and PBM image formats These formats are used to store RGB color images greyscale images as well as black and white images respectively For each of the three formats there is a binary and an ASCII version Amira is able to read all six of them but will only write binary PPM and PGM files Black and white PBM images can only be read if the image width is a multiple of eight PNM files will be automatically identified by their file headers 8 13 RAW DATA 209 Data Type shot i Dimensions 512 512 1 Min Coords 0 fo 0 Max Coords 1 i 1 Header 0 bytes Endianess bigendian little endian Index Order x fastest 2 fastest OF Cancel Figure 8 1 Amira s raw data read dialog Regarding the import and export of multiple slices the same remarks apply as for the TIFF image format When reading PNM images the channel conversion dialog is popped up This dialog is also is also described the TIFF section 39 13 Raw Data Sometimes you may want to read data defined on uniform lattices in raw format 1 e plain three dimensional arrays of data Tomographic images might be given in this way and raw data is often the easiest format to produce with e g custom simulation programs
227. ield Simulation The data files usually have a suffix EFieldValsFE Ports Directory ThermGrid ThermVals The Static Heat Nonlinear module creates two output files a temperature grid ThermGrid anda file containing a temperature distribution ThermVals The temperature grid is very similar to the initial electromagnetic coarse grid However it does not contain any duplicated vertices nor does it contain information about the grid edges By this ports you can specify the names of the output files HyperPlan makes a suggestion for you but you can change it as you please It is recommended to use the suffixes ThermGridNL and ThermValsNL Action If you press the Parameters button an editor window appears where some global parameters for temperature simulation are presented Changes can be made by simply selecting an item and typing a new value The ok button in the editor window saves the changes If you press the Materials button you can change the thermal properties of the different tissue types If you want a tissue type different from Fat Muscle or Target to show nonlinear behaviour add the four parameters described above TLowForPerfusion THighForPerfusion PerfusionAtLow and PerfusionAtHigh to the parameter list of that tissue type After you have setup the simulation you can commit it by pressing the Submit button The job dialog window should appear showing you the status of the job queue If you press the Start button the fi
228. ientific data sets from various application areas e g medicine biology chemistry physics or engineering 3D objects can be represented as grids suitable for numerical simulations notably as triangular surface and volumetric tetrahedral grids Amira provides methods to generate such grids from voxel data representing an image volume and it includes a general purpose interactive 3D viewer Section 2 1 Overview provides a short overview of the fundamentals of Amira i e its object oriented design and the concept of data objects and modules Section 2 2 Features summarizes key features of Amira for example direct volume rendering image processing and surface simplification 2 1 Overview Amira is a modular and object oriented software system Its basic system components are modules and data objects Modules are used to visualize data objects or to perform some computational operations on them The components are represented by little icons in the object pool Icons are connected by lines indicating processing dependencies between the components 1 e which modules are to be applied to which data objects Data objects of specific types are created automatically from file input data when reading such or as ouput of module computations modules matching an existing data object are created as instances of particular module types via a context sensitive popup menu Networks can be created with a minimal amount of user interaction Parameters of
229. ific set of controllable parameters or options These are described in detail for each module in the index section of the reference manual Computational modules and visualization modules also provide a question mark button which lets you access the documentation of that module directly At the top of an object s control panel its name is displayed and a number of additional control buttons are provided All objects have one or more orange viewer buttons for each 3D viewer These buttons control whether any graphical output of an object is displayed in a particular viewer or not For example if you have two viewers and two isosurface modules you may want to display one isosurface in each viewer Display modules of slicing type orange ones provide a clip button Clicking this button will cause the graphical output of any other module to be clipped by that slice Clipping does not affect modules with hidden geometry or modules that are created after the clip button has been pressed Data objects provide a number of additional editor buttons Editors are used in order to modify the contents of a data object interactively For example you can perform manual segmentation of 3D image data by editing label fields using the image segmentation editor Some editors display their controls in the working area like all other objects while others use a separate dialog window that allows you to perform object manipulations As already mentioned specific input
230. ifier AmiraMesh Moreover if the tag ASCIT is given in this line all data arrays are stored in plain ascii text If the tag BINARY is given the data arrays are stored in IEEE big endian binary format Note that the header section of an AmiraMesh file is always given as ascii text The statement define Nodes 4 defines a one dimensional array of size 4 Later on this array can be referenced using the name Nodes Similarly a statement define Array 100 100 defines a two dimensional array of size 100 x 100 The actual kind of data stored per array element will be specified later on The optional section Parameters allows the user to define arbitrary additional parameters Each param eter consists of a name like Pi and a value like 3 1459 Values may be one or multiple integer or floating point numbers or a string Strings have to be quoted using a pair of characters The optional section Materials allows the user to define additional material information This is useful for finite element applications The material section consists of a comma separated list of parameters just as in the Parameters section The statement Nodes float 3 Coordinates 1 specifies that for each element of the array Nodes defined earlier three floating point numbers floats should be stored These data are given the 8 2 AMIRA MESH FORMAT 197 name Coordinates and a tag in this line and will appear below as a tagged block with the marker 1 Such data mark
231. ile formats Therefore it is likely that you can find a converter if your file format is not supported For image data Amira provides a powerful Raw Data interface which can handle most simple binary file formats with some additional manual work In order to implement custom I O methods the entensible version of Amira called AmiraDev is required How can I get access to my database Data I O is handled via files The developer version of course allows the user to add any database interface he she wants How can I reuse my work with Amira Can I compose modules You can save networks and you can save data objects that have been created or modified In order to build new modules you must use the developer version or write script objects in Tcl How can I print with Amira How can I take a snapshot of the viewer window In the viewer on the left hand side there is an icon showing a photo camera This allows you to write snapshots of the 3D scene to a file or to a printer If no printers show up in the list then probably they are not properly installed In the latter case you can still print to a PostScript file on disk and print 86 44 45 46 CHAPTER 5 TECHNICAL INFORMATION that file from a different computer You can also use the command line interface to make snapshots This is useful for generating anima tions via a Tcl script The syntax is viewer lt n gt snapshot lt filename gt where lt n gt denotes the vie
232. in fluid dynamics because they have a simple structure but still allow for accurate modeling of complex shapes like rotor blades or airfoils Tetrahedral Grids The TetraGrid class represents a volumetric grid composed of many tetrahedrons Such grids can generally be used to perform finite element simulations e g E field simulations A considerable amount of information is maintained in a TetraGrid For each vertex a 3D coordinate vector is stored For each tetrahedron the indices of its four vertices are stored as well as a number indicating the segment the tetrahedron belongs to as obtained by a segmentation procedure Beside this fundamental information a number of additional variables are stored in order for the grid being displayed quickly In particular all triangles or faces are stored separately together with six face indices for each tetrahedron In addition for each face pointers to the two tetrahedrons it belongs to are stored This way the neighborhood information can be obtained efficiently When simulating E fields using the finite element method the edges of a grid need to be stored explicitly because vector or Whitney elements are used These elements and its corresponding coefficients are defined on a per edge basis When a grid is selected information on the number of its vertices edges faces and tetrahedrons is displayed 4 2 4 Surface Data Amira provides a special purpose data class for representing triangular surfaces
233. ing the Windows version are based on Qt For the end user this guarantees that the set of features and the user interface will be compatible across all platforms 33 Is Amira dataflow oriented No Amira is not dataflow oriented Amira is object oriented Data objects are persistent in memory and represented in the user interface Data are accessed by the modules using the C interfaces of the data classes 34 How do modules communicate Modules are loaded into a common process space at runtime by using shared libraries This way they can communicate like C objects in a normal C program There is no overhead for module communication 5 5 FREQUENTLY ASKED QUESTIONS 85 35 What is the firing order of modules Most modules are fired in downstream order If you create a new module from the popup menu of an existing one the new module will be downstream Amira networks are typically much less complex than in dataflow oriented visualization systems Therefore the firing order is usually not of concern for the end user Data input output printing 36 37 38 39 40 41 42 43 What are the supported data formats input and output A list of supported file formats is contained in the index section of the user s guide How can use Amira to import export image formats other than the Amira image format Amira supports several standard image formats such as TIFF JPEG SGI RGB ACR NEMA or DICOM When Ami
234. ing visualization system Amira Contents I HyperPlan Documentation 1 Hyperthermia Planning II ST AOVSEYIEW ta sus Se en tes a ae RS ao Be ee oe E 12 Filename Convenvions s e ses is k einna tiaa a AA Bh Os LS Seo mentaciol 0 Aired Bt ke Arye o a si oo ee sica dns Lo Tmporino CleDala ova ia Ai EA ta Doe Tabere Cl Dates rta rod Pw AS AAA LS Manual Scomentati n osa a a a ARA e bA Gri Gencrali N s a a o e A a e AAA Ee Bhs 1 4 1 Extracting Surfaces from Label Fields o 142 Simpliyine SUIEACES o a a A e EA Se ate 143 Checking Surt ce Qualify epica a a cl S 144 Tetrahedron Generation 24047 bos eee ee eee he baaa LS BePicld Simulations e a ute do ae oh a ce he ce 2S ee hoe dee ee en eS o e 1 5 1 General Remarks About the FDTD Method 132 EDIDOn Label Fields 4 5 oia AA AA LS FDTD On Tet ane dal GdS aaa he kB A td e e 1 5 4 E Field Calculation Using the FE Method 16 Temperature Simulatioi s e i k oet asi a e E a RE es he dee ee hh ek es Ae L7 Temperature Optimization uk da baka ee ke ed e ed AA a A eS LS All in One Simulation 2 a tee SR SPA ORES SSE EY ee eo es Amira User s Guide Introduction Dil AQVGAIVIEWN SERA AS FS Bete ee eee Pa ee be bee ee ee ee Ze ARAU ia a Se tie ea ee ee ere ee ee a ios be es 221 Direct Volume Rendenns 2 4 06 ewig e oe ee wh ee KB SE 222 TSOU ICES n amp 5 6 AA ee BRE O ROSS SESS SS SS DO DEC MEAO ao ae
235. ion is only performed if it improves the quality of the tetrahedra involved Parameter threshold defines a threshold for tetrahedron quality If all adjacent tetrahedra have a quality better than threshold a face is not examined for flipping e Repair Bad Tetras This tool tries to repair slivers and caps For a sliver two opposite edges with obtuse dihedral angles are bisected If the distance between the new vertices is small compared to the sliver s mean edge length the edge connecting them is collapsed For a cap the triangle opposite to the vertex with largest solid angle is determined If that triangle is part of the outer boundary the tetrahedron is removed Otherwise it is examined if the cap can be removed by a face flip Parameter threshold defines a threshold for tetrahedron quality e Remove Inner Vertices This tool improves mesh quality by removing inner vertices If the number of tetrahedra adjacent to an inner vertex is 4 that vertex is removed This should always improve mesh quality If the number is 6 the vertex is removed if mesh quality is improved e Bisect Inner Edges This tool improves mesh quality by bisection of inner edges An inner edge is bisected if for its vertices different boundary conditions are defined After bisection apply Optimization or Laplace smoothing to improve the position of the new vertices e Combined Smoothing This tool combines edge and face flipping and optimization smoothing Parameter nLoo
236. ion to the Antenna module Ports Directory EField Vals These ports allow you to specify the directory and the file name under which the resulting E fields will be stored HyperPlan makes suggestions for you but you can change them as you please It is recommended to use the suffix EFieldValsFD in the filename Options In the first text field max iter you can type in the number of time steps for the FDTD calculation 6 30 FIELD CUT 121 For restrictions and recommendations see above In the second text field MHz you can define the frequency in Mhz It is best to choose a frequency between 80 and 120 Mhz Cubes Here you can type in the number of the cubic cells Yee cells in the directions x y and z For restrictions and recommendations see above Cube Size Here you can specify the size of the cubic FDTD cell so called Yee cell in centimeters For the FDTD Voxel Solver the size is restricted to the single or double distance between the CT slices If the modified FDTD on a tetrahedral grid is used the size can be set arbitrarily However it is recommended to use a size of 1 cm For restrictions and recommendations see above Action If you press the Materials button an editor window appears showing the material constants for the E field calculation Note The electrical parameters stored in HyperPlan s material database refer to a frequency of 90 MHz Changes can be made by simply selecting an item and typing a new v
237. ions commonly produced by other methods are avoided In addition the quality of the resulting mesh according to measures common in finite element analysis can be controlled For example triangles with long edges or triangles with bad aspect ratio can be suppressed 2 2 6 Generation of Tetrahedral Grids Amira allows you not only to generate surface models from your data but also to create true volumetric tetrahedral grids suitable for advanced 3D finite element simulations These grids are constructed using a flexible advancing front algorithm Again special care is taken to obtain meshes of high quality 1 e tetrahedra with bad aspect ratio are avoided Several different file formats are supported so that the grid can be exported to many standard simulation packages In the developer version additional file formats can easily be added by the user 32 CHAPTER 2 INTRODUCTION Chapter 3 First steps in Amira This chapter contains step by step tutorials illustrating the use of Amira The tutorials are almost indepen dent of each other so after reading the basics in the Getting Started section it is possible to follow each tutorial without knowing the others If you go through all tutorials you will get a good survey of Amira s basic features In all tutorials the steps to be performed by the user are marked by a dot If you only want to get a quick idea how to work with Amira you may skip the explanations between successive steps and
238. is 1 and so on If clean labels is not set then the resulting label field will contain exactly 256 materials and no check is performed if a material actually can be found Colormap 3 Colomap 0 TT Ap J O am e UN O O e jal O O pi z jal go e olor Channel a Color Channel Channel 0 Red This option menu will only be shown if an RGBA color field is to be converted It allows you to specify which channel of the color field should be regarded In addition to the four RGBA channels also Gray and Alpha Gray can be selected The gray channel is computed on the fly from the RGB values of the color field according to the NTSC formula 1 e I 3 R 59 G 11 B Action a Action Dolt Start data conversion 6 11 Clipping Plane The clipping plane module is an instance of the Arbitrary Cut module Refer to its documentation 6 12 COLORCOMBINE 105 6 12 ColorCombine This module combines up to three source fields into a HxUniformColorField3 The resulting field has the same dimensions as the field connected to sourcel Therefore it is imperative that there is a sourcel The CombineField connects to colorfields scalarfields and scalarfields with a colormap Relative scale of the input fields is determined by their bounding boxes The module supports three different ways of merging the input data Average is the simple geometrical average of the inputs Add amp Clamp adds the valu
239. is equal to Tetrahedra EdgeData is equal to Edges Other data objects Of course not only scalar fields defined on tetrahedral grids can be encoded using the Amiramesh format Many other data objects are supported as well In each case there are certain rules about what data arrays have to be written and how these arrays have to be named Below we describe how to encode the following data objects e Fields with uniform coordinates e Fields with stacked coordinates e Fields with rectilinear coordinates e Fields with curvilinear coordinates e Label fields for segmentation e Landmarks for registration e Line segments e Colormaps Fields with uniform coordinates In order to encode 3D scalar or vector fields defined on a uniform grid you first have to define a 3D Ami raMesh array called Lattice The field s data values are stored on this array The coordinate type of the field as well as the bounding box are specified in the parameter section of the AmiraMesh file This is illustrated in the following example AmiraMesh ASCII 1 0 Dimensions in x y and z direction define Lattice 2 2 2 198 CHAPTER 8 ALPHABETIC INDEX OF FILE FORMATS Parameters CoordIype uniform BoundingBox iS xmin xmax ymin ymax zmin zmax BOUnG Ene Box Q 00 de Or Y Lattice float ScalarField QI 1 ora wd A WO Sr a Use float 3 in order to encode a vector field instead of a scalar field Likewise you may modify the field s primit
240. is menu allows you to select one such variable which will be used to scale the diameter of the three dimensional tubes If no additional data values are present only Constant scaling will be available ScaleF actor a ScaleFactor A 0 1 Additional factor used to adjust the diameter of three dimensional tubes This factor has no effect if shape has been set to Lines ColorMode a ColorMode No Color If the line set object contains additional data values per vertex this menu allows you to select one such variable which will be used to lookup vertex colors If No Color has been selected the lines or tubes will be displayed in uniform default color This color may be changed using the command setLineColor Spheres Spheres No Spheres On default No Spheres is selected Changing this selection causes a sphere to be displayed at each line vertex If the line set object contains additional data values per vertex there will be one entry for each data variable Selecting such an entry causes the sphere radii to be scaled according to the selected variable SphereScale SphereScale A 01 Additional factor used to adjust the size of the spheres This factor has no effect if No Spheres is selected SphereColor 5 S phereColor No Color Like port Color Mode but affects the sphere colors instead of the line colors 140 CHAPTER 6 ALPHABETIC INDEX OF MODULES Colormap 3 Colomap 0 OT af Optional colormap
241. is shown Curvature information has been computed by a computational module and is stored as a separate data object In the mid right window the parameters of selected modules here Curvature and SurfaceView are shown The window at the bottom provides a Tcl command shell in several viewer windows or in a common one A built in transformation editor makes it easy to register data sets with respect to each other or to deal with different coordinate systems 2 2 1 Direct Volume Rendering One of the most intuitive and most powerful techniques for visualizing 3D image data is direct volume rendering Light emission and light absorption parameters are assigned to each point of the volume Sim ulating the transmission of light through the volume makes it possible to display your data from any view direction without constructing intermediate polygonal models By exploiting modern graphics hardware Amira is able to perform direct volume rendering almost in realtime even for data volumes of 40 megabytes and more Volume rendered images can be combined with any type of polygonal display This improves the usefulness of this technique significantly Moreover multiple data sets can be volume rendered simul taneously a unique feature of Amira Transfer functions with different characteristics required for direct volume rendering can either be generated automatically or edited interactively using an intuitive colormap editor 2 2 2 Isosurfaces Isosurf
242. ive data type For example 3D images are commonly encoded using byte or short Instead of ScalarField you may use any other name in the data definition statement The field s bounding box is given by the minimum and maximum x y and z coordinates of the grid nodes or voxel centers not of the voxel boundaries Amira will always assume the width of a single voxel to be xmax xmin dims 0 1 For degenerated 3D data sets with one dimension being 1 choose equal minimum and maximum coordinates in that direction Fields with stacked coordinates A field with stacked coordinates has uniform pixel spacing in x and y direction but slices may be arranged arbitrarily in z direction This type of coordinates is commonly used to encode 3D medical images with non uniform spacing In order to encode a 3D scalar or vector field with stacked coordinates you have to define a 3D array called Lattice and 1D array called Coordinates The field s data values are stored at Lattice while the slices z positions are stored at Coordinates The coordinate type of the field as well as the bounding box in xy are specified in the parameter section of the AmiraMesh file Here is an example AmiraMesh ASCII 1 0 define Lattice 2 2 3 define Coordinates 3 Parameters CoordType stacked BoundingBoxXY is xmin xmax ymin ymax BoundingBoxxy 01 0 1 Lattice byte Intensity l Coordinates float z 2 1 018 1 0 LLL Zo Can eZ 2 Car Chay
243. ive interpolation method is used e g trilinear interpolation on regular grids Finally the toggle labeled interpolate texture controls how the slice is texture mapped by the underlying OpenGL driver If the toggle is off nearest neighbor sampling is used Otherwise bilinear filtering is applied Overlay amp Overlay da This port determines how optionally attached ColorWash modules are mapped onto this slice 6 56 OptTemp The OptTemp module helps you to perform a temperature optimization for a tetrahedral patient model The optimization procedure attempts to heat the entire tumor to 43 C and to keep the temperature in healthy tissue below 42 C However in most cases these tasks cannot be fulfilled perfectly 1 e there may be some underheated parts of the tumor and some hot spots in healthy tissue For healthy tissue some absolute temperature limits are prescribed which may depend on the tissue type At the moment they are 44 C for most tissues and 42 C for some heat sensitive tissues like bladder and intestine Temperature optimization results in a set of power amplitudes and phase delays for the channels of the hyperthermia applicator which are stored in a file suffix Plan Use module Superpose to load this file and inspect the optimized temperature distribution and the corresponding SAR distribution 144 CHAPTER 6 ALPHABETIC INDEX OF MODULES Summarized briefly you have to perform the following steps for a temparatue
244. ixes EFieldGridFE and EFieldValsFE in the filenames Frequency Here you can enter the frequency in MHz of the electromagnetic waves Recommended values are 90 MHz for the Sigma 60 and 100 MHz for the BSD Sigma Eye applicator 120 CHAPTER 6 ALPHABETIC INDEX OF MODULES Precision This port is currently not used Options If toggle Save total field is set two additional files are created EFieldGrid and EFieldVals which contain the fields in the whole extended grid The filenames contain an additional suffix To tal This option is for testing purposes only Action If you press the Materials button an editor window appears where some important material constants for the E field calculation are presented Note the electrical parameters stored in HyperPlan s material database refer to a frequency of 90 MHz Changes can be made by simply selecting an item and typing a new value The ok button in the editor window saves the changes After you have setup the simulation you can commit it by pressing the Submit button If one of the specified output files did already exist a warning message is issued If you don t want to overwrite the file press Cancel and change the filename When the job has been submitted the job dialog window appears showing the status of the job queue If you press the Start button the first pending job of the queue starts running 6 29 FDTD The FDTD module calculates an electric field using a finit
245. just follow the instructions But in order to get a deeper understanding you should refer to the text Section 3 1 Getting started explains some very basic principles of Amira You will learn how to load a data set from a file and how to create a module in order to visualize it Section 3 2 Scalar field visualization demonstrates how to read and manipulate 3D image data You will learn how to display isosurfaces and how to apply direct volume rendering Section 3 3 is devoted to vector field visualization You will explore interesting visualization methods such as line integral convolution LIC and illuminated field lines Section 3 4 Grid generation demonstrates all the steps required to reconstruct a polygonal model from 3D image data The tutorial also shows how to convert a surface model into a volumetric tetrahedral grid suitable for finite element simulations Finally Section 3 5 explains how to warp two 3D objects into each other by defining landmarks Note If you want to visualize your own data please first refer to Section 5 1 This section contains some general hints on how to import data sets into Amira 3 1 Getting Started In this section you will learn how to Start the program load a demo data set into the system 1 2 3 invoke editors for editing the data 4 connect visualization modules to the data 5 interact with the 3D viewer The following text has the form of a short step by step tutorial E
246. k scripts In addition it gives you access to Amira s job dialog and allows you to quit the program In the following text all menu entries are discussed separately Load The Load button activates Amira s file dialog and lets you import data sets stored in a file Most file formats supported by Amira will be recognized automatically via the file header or the file name extension For each file the file dialog will display its format If you try to load a file for which the format couldn t be detected automatically an additional dialog pops up asking you to select the format manually You may also manually set the file format for any file by selecting the file activating the file dialog s popup menu using the right mouse button and then choosing the Format option A list of all supported file formats is contained in the reference manual Hints on how to import your own data sets are given in Section 5 1 If you select multiple files in the file dialog all of them will be loaded provided all of them are stored in the same format 2D images stored in separate files usually will be combined into a single 3D data object On the other hand there are some file formats which cause multiple data objects to be created Finally you can also import and execute Amira network scripts using the Load button 55 56 CHAPTER 4 PROGRAM DESCRIPTION Save Data The Save Data button allows you to save a single modified data object again using the
247. l button shows all components of the vector field as separate curves 114 CHAPTER 6 ALPHABETIC INDEX OF MODULES Points a Points xf 0 o 2 4 7959 options Here you can see resp type in the coordinates of all controlpoints the data probing module makes use of The options menu lets you toggle whether a dragger or a sphere is shown for the controlpoints You can also append insert or remove controlpoints if this module is a SplineProbe module Control Use Samples Distance With this radio buttons you can choose which of the following two ports are taken to compute the sample points This port is not shown for module PointProbe Samples This slider allows you to choose the numbers of samples along the probe line This port is not shown for module PointProbe Distance Distance This slider allows you to choose the distance between two consecutive sample points along the pro beline Show E al If the Show button 1s pressed a plot window appears where the sampled values are plotted against the length of the probe line Note There will be only one plot window regardless of how many Line Probe modules there are in your setup Every line probe is represented in that plot window by a curve bearing the name of the corresponding module Commands getInterpol Returns the currently used interpolation method setInterpol none linear spline Sets the interpolation method none means no int
248. l triangles corresponding to one tissue type Then the volume enclosed by that surface is filled with tetrahedra Select module TetraGen from the popup menu of the simplified and edited surface Tetrahedron generation typically takes 10 15 minutes CPU time It is performed as a batch job so that you can continue working with HyperPlan while the job is running The Region port allows you to specify whether tetrahedra should be generated for all tissue types or just for one selected tissue type The latter choice is needed for testing purposes only In port Grid you can enter the filename for the resulting tetrahedral grid We recommend the filetype grid If you press button Materials a special dialog window is invoked It allows you to define a desired mesh size in cm for each tissue type Normally the predefined values should work well Press button Run batch to submit the batch job If a file with the name as the specified grid already exists a warning message is issued If you don t want to overwrite the file press Cancel and change the filename Then press Run batch again Afterwards the job dialog window should appear showing you the status of the job queue If you press the Start button the first pending job of the queue starts running You can bring up the job dialog at any time by selecting Jobs from the File menu If tetrahedron generation succeeded the job is marked as being completed If HyperPlan is still running or is running ag
249. lar grids such as stacks of tomographic images The data are visualized by extracting an arbitrary axial frontal or sagittal slice out of the volume This slice is represented as a surface for which the heights of the vertices are mapped to the data using a tunable scale parameter Connections Data required The scalar or color field to be visualized Colormap optional The colormap used to map data values to colors Ports Orientation E Orientation Axial Coronal Sagittal This port provides three buttons for resetting the slice orientation Axial slices are perpendicular to the z axis coronal slices are perpendicular to the y axis and sagittal slices are perpendicular to the x axis Colormap 3 Cooma af Choose colormap for the visualization Slice Number amp Slice Humber See This slider allows you to select different slices Scale Scale I A 0 312 This slider allows you to select the desired scale for the data heights mapping This should be in the range 1 1 6 39 Histogram The Histogram module creates a value volume histogram for a scalar field defined on a tetrahedral grid e g a temperature volume histogram for a scalar field that represents a temperature distribution For this purpose it has to be attached to a Grid Volume module and a selection of tetrahedra specifying parts of the 130 CHAPTER 6 ALPHABETIC INDEX OF MODULES grid or the complete grid must be made there
250. le modules and you can save and load it like the original data You may want to compare the resampled data set with the original one using the OrthoSlice module You can simply pick the blue line indicating the data connection and drag it to a different data source Whenever the mouse pointer is over a valid source the connection line appears highlighted in yellow 3 2 4 Displaying an Isosurface For 3D image data sets isosurfaces are useful for providing an impression of the 3D shape of an object An isosurface encloses all parts of a volume that are brighter than some user defined threshold e Turn off the viewer toggle of the OrthoSlice module e Connect an sosurface module to the resampled data record and select it e Adjust the threshold port to 85 or a similar value 3 2 VISUALIZATION OF SCALAR FIELDS 41 Figure 3 9 Lobus data set visualized in 3D using an isosurface e Press the Do It button 3 2 5 Cropping the Data Cropping the data is useful if you are interested in only a part of the field A crop editor is provided for this purpose Its use is described below Remove the resampled data lobus Resampled Activate the display of the OrthoSlice module e Select the lobus am data icon e Click on the green cropping icon in the working area MW A new window pops up There are two ways to crop the data set You can either type the desired ranges of X y and z coordinates into the crop editor s window or put the view
251. lection d lt 10 amp amp D gt 140 detects slivers and the selection S gt 180 detects caps Edge Quality This tool selects tetrahedra according to their edge lengths Using the tools of the Modify menu Laplace Smoothing This tool improves mesh quality by moving inner vertices For each inner vertex the center of mass of the adjacent vertices is calculated The inner vertex is moved to that location if the quality of the adjacent tetrahedra is improved Otherwise the midpoint between the old location and the center of mass is examined Parameter nLoops defines the number of smoothing loops Optimization Smoothing This tool improves mesh quality by moving inner vertices For each inner vertex a new location 1s determined that optimizes the quality of the adjacent tetrahedra Parameter nLoops defines the number of 224 CHAPTER 9 ALPHABETIC INDEX OF EDITORS smoothing loops parameter threshold defines a threshold for tetrahedron quality which is applied starting with the second loop If all adjacent tetrahedra have a quality better than threshold the vertex position is not changed e Flip Edges and Faces This tool improves mesh quality by flipping edges and faces For each inner triangular face the adjacent tetrahedra are determined It is examined if the face is a boundary face and if the adjacent tetrahedra form a convex polyhedron Depending on this classification a suitable type of edge or face flipping is selected The flip operat
252. les between navigation mode and interaction mode The trackball of the last active ArbitraryCut can also be turned on and off by pressing the TAB key inside the viewer window Finally the immediate toggle determines whether derived modules and downstream modules receive an update signal while the plane is being translated or rotated or not This toggle might not always be visible Translate a Translate SS Aso This port lets you translate the plane along its normal direction Commands frame 0 1 This command lets you turn on or off the orange frame indicating the intersection of the plane with the bounding box of the data object connected to port Data getPlane Returns 9 numbers specifying the current plane settings The numbers comprise the x y and z coordinates of the plane s origin the u vector and the v vector setPlane lt origin uVec vVec gt Adjust position and orientation of the plane The command expects 9 number in the same format as returned by the get Plane command 6 4 Arithmetic The computational module Arithmetic does calculations on up to three input data objects according to a user defined arithmetic expression The result is written into a new data object named Result The calcula tions are triggered by a Doit button The arithmetic expression is evaluated either on appropriate points of the domain underlying the first input data object e g for points of a grid on which a scalar field is defined o
253. lgorithm to create smooth boundary surfaces c f the GMC module If no weights are present quite blocky surfaces occur Note that weights can also be defined using the smoothing filter of the Image Editor The second option remove couch may be used for medical CT images if parts of the couch the patient 1s lying on are falsely classified as muscle or bone In particular the biggest connected component of voxels not assigned to the first region 1 e Exterior will be detected Then all voxels not contained in this component will be assigned to Exterior Finally if option bubbles is set an algorithm similar to remove couch is applied in order to detect bubbles or lung tissue inside the patient Because of their low intensity values otherwise these regions would be assigned to Exterior Action amp Action Dolt Histo 138 CHAPTER 6 ALPHABETIC INDEX OF MODULES The Dolt button triggers the segmentation process The Histo button makes a window pop up showing a histogram for the input image data 6 49 LandmarkView This module displays a landmark set as small spheres or in case of medical markers shows a specific geometry Connections Data required The landmark set to be displayed Ports Point Set a Point Set Pine set You may select whether only the first only the second or all point sets are shown Lines a Lines Y show Display lines connecting corresponding points in the first and second set This
254. ll copies and that this notice is included verbatim in any distributions No written agreement license or royalty fee is required for any of the authorized uses Modifications to this software may be copyrighted by their au thors and need not follow the licensing terms described here provided that the new Fe terms are clearly indicated on the first page of each file where they apply IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY FOR DIRECT IN DIRECT SPECIAL INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF THIS 5 7 ACKNOWLEDGEMENTS AND COPYRIGHTS 91 SOFTWARE ITS DOCUMENTATION OR ANY DERIVATIVES THEREOF EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY FITNESS FOR A PARTICULAR PUR POSE AND NON INFRINGEMENT THIS SOFTWARE IS PROVIDED ON AN AS IS BASIS AND THE AUTHORS AND DISTRIBUTORS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE SUPPORT UPDATES ENHANCEMENTS OR MODIFICATIONS GOVERNMENT USE If you are acquiring this software on behalf of the U S government the Government shall have only Restricted Rights in the software and related docu mentation as defined in the Federal Acquisition Regulations FARs in Clause 52 227 19 c 2 If you are acquiring the software on behalf of the Department of Defense the soft
255. ll tetrahedra selected by that module On default the histogram 1s shown with a logarithmic scale to direct the focus on the tetrahedra with worst quality Connections Data required The tetrahedral volume 6 82 TISSUESTATISTICS 171 GridVolume required A Grid Volume module that selects the tetrahedra for which the quality 1s calculated Ports Quality Measure Quality Measure Dihedral Angle y This option menu lets you select between different quality measures e Diameter Ratio Ratio of diameters of circumscribed and inscribed sphere The optimal minimal value is 3 e Aspect Ratio Aspect ratio 3 diameter ratio The optimal maximal value is 1 e Dihedral Angle For each tetrahedron edge the dihedral angle is defined as the angle between its adjacent faces For an equilateral tetrahedron all dihedral angles are about 70 degrees e Solid Angle For each tetrahedron vertex the solid angle is defined as the part of the unit sphere which is occupied by the tetrahedron For an equilateral tetrahedron all solid angles are about 30 degrees e Edge Length If you choose this measure a histogram of edge lengths is created for all selected tetrahedra Select Angle E Select Angle Jal If the quality measure is dihedral or solid angle you can select whether a histogram is created for e all angles e the minimal angle e the maximal angle or e minimal and maximal angle of each tetrahedron Samples
256. loaded colormap that is currently visible is also deleted but all hidden objects are retained Database The Database button activates the Parameter Editor and allows you to manipulate Amira s global material database The material database contains various material parameters of which most are required for certain numerical simulations to be performed on segmented volumetric grids representing specific physical objects e g E field simulations on tetrahedral patient models in medical applications such that parameter values are fixed within segments but vary across segments notably object colors density heat capacity Each data object containg materials e g a label field or a tetrahedral grid may have its own copy of these values However if a value is not found locally it is looked up in the global material database The material database is stored in the file share materials database hm located in the Amira installation directory If you want to make permanent changes in the database you must edit this file Create The Create button lets you create modules or data objects that cannot be accessed via the popup menu of any other object For example it allows you to create a procedurally defined scalar field from scratch The icon of a newly created object will not be connected to any other object in the Object Pool In order to establish connections later on use the popup menu over the small rectangular connection area of the object s ic
257. lor manipulation is shown by this cell immediately The cell named Old Color displays the original color the dialog has been invoked with The old color does not change until current setting are applied by activating the Apply button The other cells labeled Custom Colors provide a user defined palette for storing colors The custom colors stay resident between successive color dialog pop ups The Drag and Drop mechanism is applied to store and restore colors The colors can be copied arbitrary between all cells except that a color could not be stored to the old color cell To drag and drop a color 1 move your mouse cursor on top of a color cell source 2 press down on the left mouse button and keep it pressed 3 move your mouse cursor on top of another cell destination 4 release the mouse button Buttons The four buttons named OK Apply Reset and Cancel are for quitting the dialog and applying the changes to the underlying color OK applying the changes without quitting Apply resetting the current color to the old color 1 e discarding last changes Reset and quitting the dialog without applying the changes Cancel The fifth button named Help is for displaying this documentation in the Amira help window Color Picker The Color Picker provides visual selection of a color Depending on the selected color component done by the toggle button on the left side of each slider the two other components of 9 2 COLORMAP ED
258. lormaps or vertex sets such as landmarks The format itself is very flexible In fact it can be used to save arbitrary multi dimensional arrays into a file In order to create an Amira data object from an AmiraMesh file the contents of the file are analysed and interpreted For example a tetrahedral grid is expected to have a one dimensional array Nodes containing entries of type float 3 called Coordinates as well as a one dimensional array Tetrahedra containing entries of type int 4 called Nodes If the Amiramesh file contains an entry ContentType in its parameter section the value of this parameter directly determines what kind of Amira data object is to be created A first example In order to describe the syntax of an AmiraMesh file we first give a short example This example describes a scalar field defined on a tetrahedral grid Concrete examples of how to encode other data objects are given below AmiraMesh ASCII 1 0 define Nodes 4 define Tetrahedra 1 195 196 CHAPTER 8 ALPHABETIC INDEX OF FILE FORMATS Parameters Info This is an AmiraMesh example Pa 31459 Materials Name Stone Color Use 10 3 Uy Name Water Color 0 Us 0 6 Nodes Eloat 3 Coordinates I Q Tetrahedra int 4 Nodes 4 Nodes float Values 8 Tetrahedra byte Materials 12 Field float Example Linear 8 Or OC O FY CTO O The first line of an AmiraMesh file should be a special comment including the ident
259. lows the specification of the graph s position The graph will be updated synchronously with the contrast adjustment Position a Position 155 5 This port is only visible when Window Show is enabled The input values are the X and Y position of the graph within the viewer The lower left corner of the viewer has the coordinates 0 0 Negative coordinates are relative to the right respectively upper border of the viewer 112 CHAPTER 6 ALPHABETIC INDEX OF MODULES Commands verboseMode 0 1 Setting verboseMode to a value not equal to zero leads to a permanent refresh of the current data window settings via the mapping port Due to the possibilities of changing the window settings quickly this leads to flickering results and furthermore reduces the interactive adjustment speed A value of 0 is the default showWindowGraph This is just a command line interface for the window port bringing the window graph up front hideWindowGraph This is the counterpart to show WindowGraph removing the window graph info Prints out a short info to the ContrastControl module setLineColor lt r gt lt g gt lt b gt Using setLineColor you can change the visual appearance of the window graph This is useful when the currently chosen background color interferes with the line color of the graph The RGB triple specifies how much a certain color component contributes to the resulting color These values are clipped to O and 1 setMouseSen
260. lows you to visualize contiguous 3D regions of a LabelField or of some other uniform scalar field with integer values The regions are selected by clicking onto the OrthoSlice with the middle mouse button Starting from the selected pixel a 3D flood fill process is performed Multiple regions can be selected by shift clicking multiple seeds On default the regions to be visualized are taken from the same input object the OrthoSlice module is attached to However optionally an independent scalar field may be connected to the VoxelView module For example an OrthoSlice module may be used to visualize a stack of CT images while a VoxelView attached to it is used to display segmented regions defined in a label field Connections Slice required The OrthoSlice module which provides the slice where seed points have to be selected using the middle mouse button Data optional Optional scalar field If set contiguous regions of this field will be displayed instead of regions of the field the OrthoSlice module is attached to Colormap optional The colormap used to color the 3D regions Ports Colormap 3 Cooma Ta Port to select a colormap Max Dist This port limits the region growing process At most the given number of slices are considered in upward or downward direction May be useful on slow machines in order to limit the number of triangles Draw Style amp Draw Style Filed 6 89 VOXELVIEW 183 Three dif
261. lues must be floats Ports Output amp Output Force If Force is selected the negative gradient vector is computed 6 34 Grid Boundary The Grid Boundary module is a tool for visualizing individual faces of a tetrahedral grid The faces may be colored according to an arbitrary scalar field As the name implies the module extracts boundaries between tetrahedra of different material type The particular materials to be shown can be selected manually In some cases two materials may have no common faces and nothing will be seen However selecting All as the first material parameter and any other material as the second will show the surface of the second material Visible faces are stored in an internal buffer similar to the GridVolume module Likewise the selection domain can be restricted interactively by adjusting a selection box Ctrl clicking on a face makes it invisible If the ColorField port is connected to a scalar field an additional colormap port becomes visible and the faces are drawn in pseudo color mode By default the colormap port is not connected to any colormap Therefore the grid appears in a constant color You can click with the right mouse button over the colormap to get a popup menu of all available colormaps When a colormap has been connected to the module the data values at the vertices of the selected triangles are mapped to their associated colors Connections Data required The tetrahedral grid to be visu
262. ly identified by the file name extensions bmp Regarding the import and export of multiple slices the same remarks apply as for the TIFF image format When reading BMP images the channel conversion dialog is popped up This dialog is also is also described the TIFF section 8 4 Encapsulated Postscript Amira is able to save snapshots as well as individual slices of a 3D image data set in Encapsulated Postscript format You may directly send EPS files to a Postscript printer or you may include these files in many 204 standard desktop publishing programs The EPS files produced by Amira contain bitmaps rather than vector information The import of EPS files is not supported 3 5 HxSurface Simplified version The surface format has been designed to represent triangular non manifold surfaces The triangles of such a surface are grouped in patches In addition information about so called boundary contours and branching points can be stored is a surface file However since this information can be recomputed automatically if required we discuss a simplified version of the format first Here is an example HyperSurface ASCII Parameters Info Materials color 0 03562 De 10 0 06 Name GMC 3 lt GoOlors Vek Owey 3 CHAPTER 8 ALPHABETIC INDEX OF FILE FORMATS case 13 COLORE Un 2 Lote Dio LOs name Green COLO Uso Ue Lo OOO Oy name Vertices 11 1 000000 0 666667 0 666667 0 500000 L0
263. matically In addition to data files script files can also be specified These scripts will be executed when the program starts The following options are supported e help Prints a short summary of command line options e version Prints the version string of Amira e no stencils Tells Amira not to ask for a stencil buffer in 1ts 3D graphics windows This option can be set to exploit hardware acceleration on some low end PC graphics boards e no_overlays Tells Amira not to use overlay planes in its 3D graphics windows Use this option if you experience problems when redirecting Amira on a remote display e no gul Starts up Amira without opening any windows This option is useful for executing a script in batch mode e logfile filename Causes any messages printed in the console window also to be written into the specified log file Useful especially in conjunction with the no gui option e depth_size number This option is only supported on Linux systems It specifies the preferred depth of the depth buffer The default on Linux systems 1s 16 bits e style windows motif cde This option sets the display style of Amira s Qt user inter face e debug This options applies to the developer version only It causes local packages to be executed in debug version By default optimized code will be used e cmd command host hostname port port Send Tcl command to a running Amira application Optionally the host na
264. mber speci fied with this slider Action Action Dolt The Dolt button triggers the computation 6 62 Refined E Field Simulation The Refined E Field Simulation module performs an E field calculation using the Finite Element method with adaptive grid refinement For this purpose 1t also performs a temperature calculation and a temperature optimization on each refinement level See the descriptions of modules E Field Simulation Static Heat and OptTemp for more details Before starting the E field calculation you must create an extended tetrahedral grid by combining a pa tient grid and a grid representing the exterior space This can be done using module Combine The grid representation of the exterior space itself 1s generated using modules Antenna and BolusGrid When you have created an extended grid load it into HyperPlan Then you can select the Refined E Field Simulation module from the grid s popup menu E field calculation will take ca 10 20 minutes CPU time per channel of the applicator on the starting grid For each refinement level calculation time will increase approximately by a factor 2 The calculation is performed as a batch job The status of the job queue can be controled in the Job Dialog Connections Data An extended tetrahedral grid Usually such a grid has the suffix ExtendedGrid Ports Directory EFieldGrid EF ield Vals Frequency Precision Options Same functionality as in module E Field Simulation
265. me and the port number can be specified You must type app listen in the console window of Amira before commands can be received 5 3 Environment Variables In order to execute Amira no special environment settings are required The Amira start script automatically detects in which directory Amira has been installed If necessary certain shell variables for example the shared library path or the X11 application resource path will be set for you Nevertheless some environment variables may be set in order to control certain features These variables 5 4 USER DEFINED START UP SCRIPT 79 are listed below and their effects are explained Environment variables may be set using setenv C shell or export Bourne shell e AMITRA_DATADIR A list of data directory names separated by semicolons on Windows systems and colons on Unix systems The first directory will be used as the default directory of the file dialog Other directories are quickly accessible via the file dialog s path list eo AMIRA_MESA If this variable is set it is assumed that OpenGL software rendering is used i e by means of the Mesa library In this case no limits to the size of texture memory are set The Voltex module does not apply a bricking technique e AMIRA_TEXMEM Specifies the amount of texture memory in megabytes If this variable is not set some heuristics are applied to determine the amount of texture memory available on a system However these heu
266. meter Editor 233 parameters of data objects 75 Plan Data 190 PlanarLIC 145 Plot Tool 147 PNG Image Format 208 PNM Image Format 208 Point Probe 152 PointWrap 152 Port 61 Raw Data 209 Refined E Field Simulation 153 regular grids 74 239 Resample 154 SAR Distributions 190 scalar fields 73 ScriptObject 155 SeedSurface 156 SGI RGB Image Format 210 Shear 157 ShowContours 158 Simplification Editor 233 SmoothSurface 158 Snapshot dialog box 71 Splats 159 Spline Probe 160 SpreadSheet 190 Stacked Slices 210 Standard View 160 start up script 79 Static Heat 161 Static Heat Nonlinear 162 STL 210 StreamSurface 163 Superpose Electric Fields 164 Superpose Temperature Distributions 165 Surface 74 190 Surface Editor 235 SurfaceLIC 166 Surface View 168 swap space 88 system requirements 88 HP UX 89 Linux 90 Silicon Graphics 89 SunOS 89 Windows 89 system stability 88 Temperature Sets 192 Tetra Combine 169 TetraGen 170 Tetrahedral Grid 74 192 Tetrahedral Patient Models 193 TetraQuality 170 TIFF Image Format 210 TissueStatistics 171 Tomographic Image Data 193 Transform Editor 237 TriangleQuality 172 vector fields 74 VectorProbe 173 Vectors 174 Vertex Sets 75 193 Vertex View 175 View menu 240 Axis 59 Background 58 Fading effect 59 Fog 58 Layout 58 Lights 58 ViewBase 178 Viewer 62 Animate Camera 63 Edit Background Color 63
267. mmand is used to show a possible 3D output of the object in certain viewer windows and to hide it in other viewers The bits in mask controls the viewers e g a mask value of 2 shows the output in viewer 1 and hides it in viewer 0 Object showIcon Shows a specific object as an icon in the Object Pool display area Object unclipGeom PlaneModule Undos the effect of the cl ipGeom command described above Object update Calls the internal update method of the object 4 1 INTERFACE COMPONENTS 69 E Job Dialog x E quave zib de Generate gid C op lobustestond Feb 167184859 finished Generate gid dr HOME eadmA8mra2000lobus gud Ma 3123232 finished Generate gid d HOME is adm A mra2000 lobus gud Mar 318 3302 waling Job Into Job status wailing dob directory C TEMP tetgen Es Submitted at Thu Mar 9 19 33 02 2000 Started at Run time Vrean output d HOME sadn Amira 000 bin achina plimgee amtra ere no_gui og le log belger bo Close Figure 4 5 The job dialog lets you start stop examine and delete batch jobs 4 1 8 Job Dialog Certain time consuming operations in Amira can be performed in batch mode For this purpose Amira provides a job queue where jobs like generation of a tetrahedral grid can be submitted You can inspect the current status of the job queue start and delete jobs from the queue by selecting Jobs from Amira s file menu This will bring up the Job Dialog In the upp
268. must be 8 or 16 1 channel images only e Images defined in YbCbR colorspace can not be read e Tiled images can not be read e Only scalar fields consisting of bytes can be saved The Channel Conversion Dialog When reading 2D image files a special dialog window will be popped up This dialog asks the user to specify how the 2D images should be converted into Amira data objects In addition the world coordinates of the resulting 3D data object can be adjusted The channel conversion dialog looks as depicted in Figure 8 2 First of all the dialog displays the number of files to be read the number of 2D slices in most cases equal to the number files the size of a 2D slice in pixels as well as the number of channels stored in the files An option menu lets you select whether a 1 component uniform scalar field should be created or a 4 component RGBA color field Depending on the type of input not all options may be active The meaning of the individual items is described below e Maximum The maximum value of the red green and blue channel is stored in a uniform scalar field 3 and 4 channel input only e Weighted Average A grayscale uniform scalar field 1s created according to the NTSC formula I 3 R 59 G 11 B 3 and 4 channel input only e Channel 1 The first channel of the input is converted into a uniform scalar field will always be active e Channel 2 The second channel of the input is converted into a uniform scalar fi
269. n be interactively added deleted or edited using the parameter editor Parameters are useful for example to store certain parameters of a simulation or of an experiment In this way the history of a data object can be followed There are certain parameters which are interpreted by several Amira modules The meaning of these pa rameters is summarized in the following list e Colormap name This specifies the name of the default colormap used to visualize the data Some modules automatically search the object pool for this colormap and for example use it for pseudocoloring e DataWindow minVal maxVal This indicates the preferred data range used for visualizing the data The OrthoSlice module automati cally maps values below minVal to black and values above maxVa1l to white e LoadCmd cmd This parameter is usually set by import filters when a data object is read It is used when saving the current network into a file and it allows to restore the object automatically Internal use only 76 CHAPTER 4 PROGRAM DESCRIPTION Note that there are many file formats which do not allow to store parameters Therefore information might get lost when you save the data set in such a format If in doubt use the Amira specific AmiraMesh format Chapter 5 Technical Information This chapter contains technical information about Amira which is not covered in the previous chapters e Data Import e Command Line Options e Environment Variables e Amira st
270. n indicate the two regions the patch is supposed to separate If you don t want to generate a tetrahedral grid from your surface you may omit these statements or you may choose both regions to be the same Finally the triangles of a patch are specified by indexing vertices defined in the vertex section Like in an AmiraMesh file indices start at 1 not at 0 Extended version In its extended version the surface format is able to store additional topological infor mation of a surface Before we discuss this in detail let us first make some definitions and introduce the underlying concepts e Region In finite element applications regions are usually called materials A region is defined by its surrounding surface which may consist of multiple patches Each region must have a unique name e Surface A surface is defined by the boundary of a 3D region and therefore must be closed This means that for example each edge must be connected to an even number of triangles In one half of the triangles the edge is referenced in forward orientation in the other half in backward orientation A surface may consist of multiple pieces so called patches In the file format the patches of a surface are given by a list of signed indices A negative index means that the patch has negative orientation in the current surface e Patch A part of a surface which separates exactly two differnt regions Patches are built from triangles The triangles are all oriented in
271. n order to do so the viewer has to be switched to interaction mode e g by hitting ESC as described in its documentation Points and lines can be selected by clicking on them in the viewer Selected points or lines will be highlighted in red Multiple actions can be performed by pushing one of the buttons in the Action port They are described below The Selected port informs you how many points and lines are selected at the moment In the Display port you may choose in which way the lineset is displayed By clicking on the toggles optionally all points endpoints and lines will be displayed in the viewer Only displayed geometry is selectable Default 1s endpoints and lines The Select port provides the following selection modes e All Clicking this button all lines will be selected e By Length Clicking this button an additional dialog pops up where you can enter the minimal and maximal numbers of points in lines that are to be selected Pushing OK performs the selection e Clear Pushing this button the current selection will be cleared The Action port provides the following actions e Connect Pushing this button two lines can be connected In order to do this exactly two points have to be selected otherwise this button will not be active e Delete Selected points and lines will be deleted from the lineset e Stretch Pushing this button all selected lines will be smoothed e Split Pushing this button all lines will be splitted at selecte
272. n particular a uniform scalar field remains a uniform scalar field even if it is rotated or sheared Display modules like OrthoSlice still can exploit the simple structure of the uniform field The possible transformation is automatically applied to any geometry shown in the 3D viewer In order to interactively manipulate the transformation matrix use the Transform Editor documentation is contained in the index section of the user s guide Be careful when saving transformed data sets Most file formats do not allow to store affine transformations In this case you have to apply the current transformation to the data This can be done using the Tcl command applyTransform In case of vertex set objects the transformation is applied to all vertices Old coordinates are replaced by new ones and the transformation matrix is reset to identity afterwards After a transformation has been applied to a data set it cannot be unset easily anymore If a transformation is applied to uniform fields e g to 3D image data the coordinate structure is not changed i e the field remains a uniform one Instead the data values are resampled 1 e the transformed field is evaluated at every vertex of the final regular grid The bounding box of the resulting grid is modified so that it completely encloses the transformed original box 4 2 7 Parameters For any data object an arbitrary number of additional parameters or attributes may be defined Parameters ca
273. n represent point sets or line segments for which there is hardly any other standard format The AmiraMesh documentation explains the file syntax in detail and contains examples of how to encode different data objects One important Amira data type triangular non manifold surfaces cannot be represented in a AmiraMesh file but has its own file format called HxSurface format Finally in case of images or regular fields with uniform coordinates you may also read binary raw data Note that for raw data the dimensions and the bounding box of the data volume must be entered manually in a dialog box which pops up after you have selected the file in the file browser 11 78 CHAPTER 5 TECHNICAL INFORMATION 5 2 Command Line Options This section describes the command line options understood by Amira In general on Unix systems Amira is started via the start script located in the subdirectory bin Usually this script will be linked to usr local bin amira or something similar Alternatively the user may define an alias amira pointing to bin start On Windows systems Amira is usually started via the start menu or via a desktop icon Nev ertheless the Amira executable may also be invoked directly by calling bin arch Win32 Optimize amira exe In this case the same command line options as on a Unix system are un derstood The syntax of Amira is as follows amira options files Data files specified in the command line will be loaded auto
274. n the Inventor man pages man SoDragger 3 SoTabBoxDragger 3 Display modules that are connected to a transformed data set will consider the transformation Also some but not all computational modules that take more than one input support transformations Most data file formats do not support transformations Therefore transformations are currently not saved along with the data However using the commands getTransform setTransform the transfor mation can be retreived as a homogeneous matrix For details see man SoTransform 3 Index Amira 79 ACR NEMA DICOM 195 affine transformations 75 Amira class structure 72 Amira data objects 29 Amira features direct volume rendering 30 1so surfaces 30 segmentation 31 surface reconstruction 31 Amira Mesh Format 195 Amira modules 29 Amira init 79 Analytical Scalar Field 185 Analytical Vector Field 186 Annotation 95 Antenna 95 Arbitrary Cut 96 Arithmetic 97 Axis 99 BMP Image Format 203 BolusGrid 100 Boundary Conditions 101 Bounding Box 102 bounding box 212 232 CalcAreaVolume 103 CastField 103 Clipping Plane 104 color depth 88 Color Dialog 213 ColorCombine 105 Colormap 187 Colormap Editor 215 Colorwash 106 CombineLandmarks 107 command format 67 command line options 78 ComponentField 107 Compute SAR 108 ComputeContours 108 Connected Component Analysis 109 ContourView 110 ContrastControl 110 238 coordinates 74 Curl
275. nal The colormap used to map data values to colors This port is ignored when linear or histogram equalized mapping is selected See also Colormap Ports Orientation Drientation Axial Coronal Sagittal This port provides three buttons for resetting the slice orientation Axial slices are perpendicular to the z axis frontal slices are perpendicular to the y axis and sagittal slices are perpendicular to the x axis Options amp Options adjust view Po rotate P immediate If the adjust view toggle is set the camera of the main viewer 1s reset each time a new slice orientation is selected With the rotate toggle you can switch the rotate handle for the cutting plane on and off If the immediate toggle is set the slice is updated every time you drag it with the mouse in the 3D viewer Otherwise only the bounding box of the cutting plane is moved and the update takes place when you release the mouse button Translate This slider allows you to select different slices The slices may also be picked and dragged directly in the 3D viewer 6 56 OPTTEMP 143 MappingType amp Mapping ype Colormap This option menu controls how scalar values are mapped to screen colors In case of a linear mapping a user defined data window is mapped linearly to black and white If historam is selected an adaptive histogram equlization technique is applied This method tries to show all features of the data even if a wide range of
276. nate of the current point e y the y coordinate of the current point e z the z coordinate of the current point If a scalar data object is connected to any of the ports InputA InputB InputC a corresponding variable for access to the data values is also defined namely e a the values of input object A e b the values of input object B e c the values of input object C If a vector data object is connected to any of the ports InputA InputB InputC corresponding component variables for access to the data values are also defined namely e ax ay az the xyz vector components of input object A e bx by bz the xyz vector components of input object B e cx cy cz the xyz vector components of input object C The same C style mathematical and logical operators as well as built in functions that are availabe for arithmetic expressions can be used here see HxArithmetic module description Connections InputA optional Optional scalar or vector field 7 3 COLORMAP 187 InputB optional Optional second scalar or vector field InputC optional Optional third scalar or vector field Ports A ax 5 Input field for arithmetic expression defining the x component field values Y a y 10 Input field for arithmetic expression defining the y component field values Z A Input field for arithmetic expression defining the z component field values 7 3 Colormap A Colormap is a sequence of arbitrar
277. nce you have selected an entry from the connection popup menu you can choose a new input object for that port In order to do so click on the input object s icon in the Object Pool The blue connection line will become yellow if the connection port can be connected to the chosen object In order to disconnect an input object click on the icon of the module the port belongs to Data objects possess a special connection port called Master This port refers to a computational module or editor the data object is attached to It indicates that the computational module or editor controls the data object 1 e that 1t may modify its contents Each object has an associated control panel containing buttons and sliders for setting or changing additional 62 CHAPTER 4 PROGRAM DESCRIPTION parameters of the object The control panel becomes visible once the object has been selected i e by clicking on its icon with the right mouse button In order to select multiple objects you must shift click the corresponding icons Clicking on the icon of a selected object deselects it again Clicking somewhere on the background of the Object Pool causes all selected objects to be deselected An icon may be dragged around in the Object Pool by clicking on it and moving the mouse pointer while holding down the mouse button Working Area Once an object has been selected its input controls will be displayed in the Working Area below the Object Pool Each object has a spec
278. ne to which the information as to which processing module is applicable to which data object is hooked Its classes reflect the mathematical structure of the object models supported by Amira For example scalar fields and vector fields are such structures and derived from a common field class which represents a mapping R R Deriving a sub class from this base class requires a value to be specified for n At the same time fields defined on cartesian grids are distinguished from fields defined on tetrahedral grids 1 e this distinction 1s part of the classification scheme that gives rise to branches in the data class subtree In the next section of this chapter you will learn more about the data class hierarchy In the second section we discuss how some data types frequently used for various visualization tasks fit into 1t Internally all class names begin with a prefix Hx However you don t have to remember these names unless you want to use the command shell to create objects For example a bounding box is usually created by choosing the BoundingBox item from the popup menu of a data object that 1s to be visualized but you may also create 1t by typing create HxBoundingBox in the command window 4 2 2 Scalar Field and Vector Fields The most important fields in Amira are three dimensional ones These fields are defined on a certain domain C R A field can be evaluated at any point inside its domain If the field is defined on a disc
279. nes as well provided the OpenGL runtime environment has been installed In any case we recommend to install the texture acceleration option for your graphics system hardware texture mapping especially 1f you intend to work with large 3D image data sets Important By default some HP workstations are configured with a data size limit of 64 MB for each process In order to load reasonable data sets you should increase this value to 1 GB and the stack size to 128 MB Do this by modifying the values in sam Kernel Configuration maxdsiz 0x80000000 ssiz 0x8000000 tssiz 0x8000000 The graphics patches PHSS_17160 10 20 3D Common Runtime patch and PHSS_17166 10 20 OpenGL 1 1 Runtime patch or later should be installed on your system otherwise X Errors and program crashes can occur You may download these patches from a HP support server e g from http europe support external hp comor http us Support external hp com Finally Amira requires version 1 21 of usr lib libCsup sl to be installed on the system Otherwise an unre solved symbol error will occur If you have an older version of this library please install patch PHSS_17872 or some later replacement 5 6 5 SunOS Amira runs on Sun workstations with SunOS 5 7 Note that 1 2 OpenGL 1 1 1 106022 05 for Solaris or some newer version of OpenGL must be installed on the system You may check the version using the following shell command 90 CHAPTER 5 TECHNICAL INFORMATION strin
280. ng to but will not be changed if the relative incidence of that tissue is below the given percentage There are three ways of applying the filter slice refers to the 2D version of the filter which is applied to the currently selected slice only all slices means application of the 2D filter to all slices and 3D volume 1s for the 3D filter We recommend to use the second variant all slices e Fill Holes This filter fills holes in the interior of the currently selected tissue type It should be applied to Bone in order to remove marrow regions falsely assigned to muscle or fat Select Bone in the material list then choose Fill Holes and all slices from the Label Filter menu of the segmentation editor Now you are ready to start manual segmentation For this task you generally proceed as follows First select an arbitrary area in a slice Selected pixels are highlighted in red in the 2D window Then change the labeling for the selected pixels either by adding them to the currently selected region button or key a or by subtracting them from this region button or key s In the latter case pixels are assigned to an automatically determined background region There are different ways to perform a selection simply clicking on a segment using a lasso tool a brush or a picker The functionality of the selection tools is very similar to pixel oriented painting programs For a detailed description refer to the Amira reference man
281. ng to select different pseudo color modes If item none is selected the LIC texture will be displayed in greyscale only If magnitude is selected each pixel of the LIC texture will be colored according to vector magnitude at this point If normal component is selected then color denotes the signed length of the vector component perpendicular to the cutting plane This length will be positive if the vector points upwards or negative if the vector points downwards If parallel component 1s selected then color denotes the length of the vector component tangential to the plane This length will always be greater or equal than zero Finally if color field is selected and if a scalar field is connected to port ColorField the external scalar field will be used for pseudo coloring Colormap 3 Cooma TT Ap Port to select a colormap 6 59 PLOT TOOL 147 Lic a Lic filter length el resolution 100 The input denoted filter length controls the one sided length of the filter kernel used for line integral convolution The larger this value is the more coherent is the greyscale distribution along the field lines Often larger values are visually more attractive than smaller ones A value of 0 lets you see an isotropic noise pattern without any directional information The second input of this port determines the resolution of an intermediate sampling raster used to compute field lines Fine details of the vector field might be missed if the sampling resol
282. ngth a a The length of the field lines or more precisely the number of atomic line segments in forward respectively backward direction The lines may stop earlier if a singularity 1 e zero magnitude is encountered or if the field s domain is left ez z A o Balance 322 0 On default field lines are equally long in forward and backward direction corresponding to a balance value of 0 This port allows you to change this behavior A value of 1 indicates that field lines should extend in backward direction only while a value of indicates that field lines should extend in forward direction only Distribute amp Distribute Do lt At vertices On the one hand this port provides a Dolt button which is used to initiate distribution of seeds and recomputation of field lines Once the incoming vector field has changed or you have modified the number of field lines or the line s length you have to press Dolt in order to update the display On the other hand the port also provides an option menu specifying the seed distribution mode If at vertices is chosen a field line is started at each vertex of the surface If on surface is chosen a user defined number of field lines will be uniformly distributed across the surface 6 66 Shear This module shears a uniform scalar field by shifting each xy slice in y direction The shift is proportional to the z coordinate of the slice resulting in a shear operation The angle
283. nline Help Amira user s documentation is available online You can access it via the User s Guide entry of the main window s Help menu The user s guide contains some introductory chapters as well as a reference part containing documentation for specific modules data types editors file formats and other components You may access the documentation of any such object via a separate index page accesible from the home page of the online help browser Amira modules also provide a question mark button in the working area Pressing this button directly pops up the help browser for the particular module Going through the online documents is similar to text handling within any other hypertext browser In fact the documentation is stored in HTML format and can be read with a standard web browser as well Some specially marked colored and underlined text items allow you to jump quickly to related or referenced top ics where blue items point to unread sections and red items to already viewed sections Use the Backward and Forward buttons to scroll in the document history and Home to move to the first page Searching the online documentation The online help browser provides a very simple interface for a full text search For example if you are looking for information about the surface editor type these two words into the text field in the upper part of the help window Then press the search button in order to perform the search
284. nnections Data required The input surface file suffix surf ExteriorSurface optional Additional outer bounding surface Not needed in most applications Ports Region E Region E The menu of this port allows you to specify whether tetrahedra should be generated for all regions or just for one selected region The latter choice is needed for testing purposes only Grid amp Grid KERNEL main GeometySurface ord Here you can define the filename for the resulting tetrahedral grid We recommend to include a suffix grid into the filename Action amp Action Materias Aun batch Aun now If you press the Materials button an editor window appears It allows you to define a desired mesh size in cm for each region Normally the predefined values should work well After you have set up the simulation you can commit it by pressing the Run button If the file specified at port Grid did already exist a warning message 1s issued If you do not want to overwrite the file press Cancel and change the filename When the job has been submitted the job dialog window appears showing the status of the job queue If you press the Start button the first pending job of the queue starts running 6 81 TetraQuality The TetraQuality module creates a histogram of qualities for tetrahedral volume grids e g tetrahedral patient models For this purpose it has to be attached to a Grid Volume module Quality is calculated for a
285. nnotation parameters it at the new position Editing legend parameters legend Position 05 0 85 Delta 0 05 RowCol g Options _ Frame Color Figure 6 5 Editable legend parameters The position denotes the coordinates of the first legend item Positions of legends are always normalized coordinates The delta parameter applies only to the vertical y coordinate The RowCol parameter de termines how many rows and columns are available for the legend items The default is 1 and means an unlimited number of items where the number of columns 2 parameter counts first E g if you have 6 curves in your plot and you want the legend to have 2 columns and 3 rows set RowCol to 3 and 2 Mind the x position to make sure that all names are fully displayed You can also position a legend in the plot window interactivly by pressing the left mouse button on one of the names in the legend move the mouse and release it at the desired position Editing markerline parameters The position of a markerline has to be given in world coordinates Also be sure that the markerline is inserted after the appropriate axis You can shift a markerline horizontally resp vertically in the plot window by pressing the left mouse button on the markerline move the mouse and release it at the new position Working with plot objects Furthermore you can copy or delete plot objects E g it may be useful for comparison purposes to copy a curve before t
286. no arguments 6 6 BolusGrid In order to simulate electromagnetic fields in regional hyperthermia using the finite element method a tetrahedral grid is required which not only covers the patient area but also the surrounding space which 6 7 BOUNDARY CONDITIONS 101 includes the water bolus of the hyperthermia applicator In order to create such an extended grid three steps have to be performed 1 Create a surface representation of area outside the patient 2 Fill the area outside the patient with tetrahedrons 3 Combine patient grid and grid of outside area this yields an extended grid The BolusGrid module lets you perform the first step It has to be attached to an Antenna module Taking into account the type of the applicator as well as its specific adjustment the module generates a surface which contains the water bolus and a surrounding sphere and which exactly fits to the patient model that the applicator is attached to Sometimes it happens that in the resulting surface the bolus end caps intersect triangles of the patient model boundary You can check this using the Surface Editor In case you found intersections you may try to reduce the value of port Offset Smaller offsets typically produce less intersections You may also try to reposition the applicator sligthly In general intersections occur less often if in creating the patient model the option preserve slice structure of the Simplification Editor has been selected Ca
287. ns Options Y Remove duplicated Remove duplicated causes all duplicated points and triangles to be removed from the output Boundary amp Boundary Y Mark exterior faces W Check exterior faces Mark exterior faces sets boundaryConditionId 1 for all exterior faces BoundaryCondi tionIds may be useful if a numerical simulation shall be performed on the resulting grid Check exterior faces checks whether all exterior triangles lie on a sphere around the center of the bounding box of the grid Action amp Action Dolt The Dolt button triggers computation 170 CHAPTER 6 ALPHABETIC INDEX OF MODULES 6 80 TetraGen The TetraGen module creates a volumetric tetrahedral grid Its input is a description of the 3D geometry by triangulated surfaces The advancing front method is applied to fill each region defined by the surface data with tetrahedra Tetrahedron generation is performed as a batch job There are some reserved region names for the exterior region that should not be filled with tetrahedra oth erwise the grid would extend to infinity no name at all Outside and all names starting with Exterior If you choose a different name for the exterior region tetrahedron generation will fail Currently the GMC module creates correct names Exterior and Exterior2 but the module IvToSurface does not You must edit the region names before applying TetraGen to a surface created by the latter module Co
288. ntabor Edit mode dd 2 Marker type For a Marker posibior E Point Set Port Sei 2 Lines show DrawStyle F sphere poirit Point Set Port Se 2 Chick arprehese to add a maker Du Figure 3 19 The image shows how the viewer toggles and Point Set ports should be set If you want to change the position of an existing landmark set Edit mode Move and select the respective landmark blue or yellow by clicking on it with the left mouse button Then just click at the desired position You can also delete existing landmarks by setting Edit mode Remove and clicking on the respective landmark Both corresponding landmarks blue and yellow will be removed no matter which one was selected You should now be able to create several landmarks You may want to change the view of the objects to set landmarks on the back In case you have problems to define landmarks you may use an existing set of landmarks by loading the file LandmarkSet from the directory data tutorials Once landmarks have been created the next step is to transform the two objects into each other 3 5 3 Registration via a Rigid Transformation To register one object to the other connect a LandmarkWarp module to the LandmarkSet object by clicking with the right mouse button on the LandmarkSet icon in the object pool and selecting Compute Landmark Wa
289. nted many tools can be applied in both 2D and 3D Since the editor does not store contours surrounding regions but region labels a unique and well defined classifi cation is guaranteed 2 2 4 Surface Reconstruction Once the interesting features in a 3D image volume have been segmented Amira is able to create a cor responding polygonal surface model The surface may have non manifold topology if there are locations where three or more regions join Even in this case the polygonal surface model is guaranteed to be topolog ically correct 1 e free of self intersections Fractional weights which are automatically generated during segmentation allow the system to produce smooth boundary interfaces This way realistic high quality models can be obtained even if the underlying image data are of low resolution or contain severe noise artifacts Making use of innovative acceleration techniques surface reconstruction can be performed very quickly Moreover the algorithm is robust and fail safe 2 2 5 Surface Simplification Surface simplification is another prominent feature of Amira It can be used to reduce the number of triangles in an arbitrary surface model according to a user defined value Thus models of finite element grids suitable for being processed on low end machines can be generated The underlying simplification algorithm is one of the most elaborate ones available It is able to preserve topological correctness 1 e self intersect
290. nteractive mode you can pick the handle with the left mouse button and rotate the plane as you please Connections Data required The field of type TetraScalarField3 Colormap optional An optional colormap used for pseudocoloring the values of the scalar field on the cutting plane Ports Orientation E Drientation Axial Coronal S agital This port provides three buttons to reset the slice orientation Axial slices are perpendicular to the 122 CHAPTER 6 ALPHABETIC INDEX OF MODULES z axis frontal slices are perpendicular to the y axis and sagittal slices are perpendicular to the x axis See also PortButtonList Options E Options M adjust view Po rotate P immediate If the adjust view toggle 1s set the camera of the main viewer 1s reset each time a new slice orientation is selected With the rotate toggle you can switch the rotate handle for the cutting plane on and off If the immediate toggle is set the slice is updated every time you drag it with the mouse in the 3D viewer Otherwise only the bounding box of the cutting plane is moved and the update takes place when you release the mouse button Translate a Translate SS Aso This slider allows you to select different slices The slices may also be picked and dragged directly in the 3D viewer Colormap 3 Colomap 0 TT Ap See also PortColormap Interpolation amp Interpolation Gouraud Texture In pseudo color mode you can switch betw
291. o do cd e Go aac Gees de er eer a ee A Gs Ga 143 DOS CS ee e peta A ay hha E E A EA ee Ee 144 Plaats gt Suc eck y ad be eh a we ee te te i ee oe e af ot 145 PIOE TOON sar aa AAA RGR Se SES AA ED OAS GR ES 147 A o sue 4 a oe ee Re Bae SS hee a ER BR ee Se 152 FOMENTA osa do Seer gees dy oe ae el Bese eee eae ae ee Gee 152 RelinedE Pield Simulation merkia eK A ee E ee Ek ee Ee 153 Resampler amp foc 2 4 a de es e Bel a ee ele e ee 154 SOMOD E Er AAA a EEE SEO et SOAS Se SS 155 SECUACES 2 le Rts te a PA eee a ts Be A 156 NCI Par Fo eh het DO de et Sete Gk Gs ee el Oe a a ee a ee oe eA 157 SHOW COMIOU Is aae maa cues Sates ae ae se ir ie Ao ier hte Boe anes 158 SMOG UI ACe ls ta bed eS a or a Ye ee a te Gt eee See fe es 158 SPU a2 IAEA ee OS OR AE A 159 SPUNE PODES Sed tk as Bee Se EA Ae es Gee aa 160 Standard Mew so ce A ch ees os add Boe ie e otk dee ee eS oe 160 DAU TCAs a ori eee as Bt eee Gorse ae Cee ae a ae Be es 161 Statle Heat NOniNEa od o 4 2 44 toe bee ee ee olde Soh la we Be 162 Sedan Ud oes 4 Bea BE EASA OMAR ORES OEE BED SEAS SR SS 163 Superpose Electric Fields ia as eae aaa ae 164 Superpose Temperature Distributions 0000002 eee ee eens 165 UAC EIC casted te as Sten eee ee oa ae IA be ae Be ed 166 DUP ACE NV rele sad da ee ol ba es Se E Be 168 Teta COMPING ano 3 8 Sed AE DRED Cok OE OO REDS ORES 169 Tea ica oa eet ete pho Be A Re te tae GE Bes eee ee ee 170 PEOI dos at a Seay eed ds El ew Oe ere ee
292. o that the slice structure of the original voxel grid is preserved Action Button Simplify starts surface simplification The simplification process will take several minutes You may interrupt it by hitting the stop button of the progress bar 9 11 SURFACE EDITOR 235 Surface 34830 points 72531 faces 49 patches 0 contours 0 edges a Check Intersections Orientation Aspect Fatio Dihed Angle Tetra Quality E Display First Next Previous E Acton Unda Figure 9 8 User interface of surface editor Button Fix Coplanars removes all coplanar triangles from a surface This step is performed automat ically after surface simplification Button Flip Edges automatically flips some edges of a surface if this improves the triangle quality The Quality is defined as the ratio of the circumscribed circle and the inscribed circle of a triangle The smaller this ratio the higher the quality Again coplanar triangles are removed automatically after this operation Commands Simplifier setRadiusRatio lt value gt This command defines a quality threshold for the edge flipping algorithm Edges are flipped only if the radius ratio of a triangle exceeds the given value By default a radius ratio of 20 is used Simplifier smooth lt nSteps gt lt lambda gt This commands shifts the vertices of the surface so that it gets smoother The value for lambda should be in the range of 0 1 This option is experimental and should not be u
293. oad command file Loads and executes the command file The same command is used to load ordinary data objects into Amira 68 CHAPTER 4 PROGRAM DESCRIPTION Gut Quit the application Object allPorts Lists all ports of Object Object clipGeom PlaneModule Causes all geometry display of the object to be clipped by the plane defined by PlaneModule For example a plane module is any module derived from Arbitrary Cut The geometry of an object might be clipped by up to six clipping planes Also see unclipGeom below Object deselect Deselects an object 1 e the object s widgets vanish from the Working Area Object destroy The object is removed as well as certain dependent objects Object fire Calls the internal update and compute methods of the object Object get IconPosition Returns the position of the object s icon in the Object Pool display area Object getTypeld Returns the type of the object Object help Displays all commands specific to that object Object hidelcon Hides the icon of a specific object Object select Selects an object 1 e the object s widgets appear on the Working Area Object setIconPosition xPos yPos Sets the position of the object s icon in the Object Pool display area to xPos yPos Object setLabel newlabel Changes the name of the object to newlabel If already some other object with the same name exists newlabel will be automatically modified Object setViewerMask mask This co
294. odes Ports X Shift The x position of the center of the applicator in cm Y Shift The y position of the center of the applicator in cm Z Shift The z position of the center of the applicator in cm Incline Inclination angle of the applicator around the x axis This is measured in degrees When using large inclination angles make sure that the applicator doesn t intersect with the patient model Applicator This port lets you switch between the BSD Sigma 60 applicator and the BSD Sigma Eye applicator Show This port provides two toggle buttons which allow you to individually turn on and off display of antennas and water bolus Notice that these buttons have no effect if the main viewer toggle of the module is off sphere icon right from module name must be orange Reset Resets the applicator shifts so that the treatment unit is centered around the middle of the patient model 6 3 Arbitrary Cut This module defines a plane which can be positioned and oriented arbitrarily inside the bounding box of a data object connected to port Data Mostly you will work with derived modules displaying some kind of geometry inside the plane defined by this base class Examples of derived modules are ObliqueSlice or PlanarLIC However this base class also serves as a background plane on which so called overlay modules display their geometry Examples of overlay modules are the isoline module or the vector module display their geomet
295. oe Es Se BEERS we eee eee Ss SGA a 233 OO Parameter Edito serde AAA A oe ee a amp ot GS A ore Be ee 233 9 10 Simpliticalon Baton alas a aS Be e Aa at 233 SUL URAC EOL bla a Ba Je Eb a he RA A Ad Se es er 235 9 12 Transform Editor 237 10 CONTENTS Part I HyperPlan Documentation Chapter 1 Hyperthermia Planning HyperPlan is a software system for performing 3D simulations and treatment planning in regional hyper thermia It allows the user to understand the complex effects of electromagnetic wave propagation and heat transport inside a patient s body Optimized power amplitudes and phase settings can be calculated for the BSD radiowave applicators Sigma 40 Sigma 60 and Sigma 2000 the so called eye applicator The planning system as well as the underlying numerical algorithms have been developed at the Konrad Zuse Zentrum fiir Informationstechnik Berlin ZIB in cooperation with the Rudolf Virchow Klinikum Berlin The work has been supported by Dr Sennewald Medizintechnik GmbH Munich HyperPlan is built on top of the modular object oriented visualization system Amira This system already contains powerful algorithms for image processing geometric modelling and 3D graphics display Hy perPlan provides a number of hyperthermia specific modules allowing the user to create 3D tetrahedral patient models suitable for treatment planning In addition all numerical simulation modules required for hyperthermia simulation are
296. of principal curvature Note that the algorithm does not produce meaningful results near locations where the input surface is not topologically flat 1 e where it has non manifold structure 124 CHAPTER 6 ALPHABETIC INDEX OF MODULES Connections Data required The surface for which curvature information should be computed Ports Method Method on triangles on vertices Radio box allowing the user to select between two different computational algorithms Choice on triangles produces a surface field with curvature values or curvature vectors being defined on the surface s triangles Alternatively by selecting on vertices a surface field with data being defined on the vertices can be generated Parameters a Parameters nlayers Es n yerage 4 The first input denoted nLayers determines which triangles are considered to be neighbors of a given triangle and which points are considered to be neighbors of a given point If the value of this input is 1 then only triangles sharing a common edge with a given triangle are considered to be neighbors of this triangle and only points directly connected to a given point are considered to be neighbors of this point For larger values of nLayers successively larger neighborhoods are taken into account The second input denoted nAverage determines how many times the initial curvature values com puted for a triangle or for a point are being averaged with the curvature values of dir
297. of the LabelField makeColormap Creates a new colormap object in Amira s object pool containing the default colors of all materials of the LabelField relabel Computes new labels so that the materials are numbered in consecutive order starting from 0 deleteAltData Deletes the weight information if it is present 7 6 Landmark Set This data type represents specific points or markers in 3D space It can be used to flag markers in medical MRI images or to specify pairs or n tuples of corresponding points in multiple data sets An empty set of landmarks can be created by typing create HxLandmarkSet into the Amira console window cf Section 4 1 7 Individual landmarks can be interactively added reposi tioned or removed from a landmark set by means of the landmark editor Commands setNumSets lt n gt Set number of point sets contained in this data set Upon creation a landmark set contains one set of points If the landmarks are going to be used to specify corresponding points 1t must contain two sets This can be achieved by typing Landmarks setNumSets 2 where Landmarks is the name of your landmarks icon Swapsets setl set2 Exchanges the coordinates of the specified sets If no arguments are given the first and the second set are swapped provided both sets exist appendLandmark lt x gt lt y gt lt z gt Appends a new marker to the data object The new marker will have the same coordinates in all sets 190 CHAPTER
298. olor gt Lets you define the base color of the volume rendered clouds On default an orange color will be used 0 8 0 6 0 1 The color may be specified by either an RGB triple in range 0 1 or by a common X11 color name e g green 6 70 Spline Probe See Section Data Probing for details 6 71 Standard View The StandardView module displays a 3D image data set or more precisely a 3D scalar field with either uniform or stacked coordinates in three different 2D windows at once The windows contain coronal sagittal and axial projections of the data respectively These projections correspond to standard xy yz and xy orientations Note that for the axial xy view the origin is in the upper left corner This is the standard orientation used in radiology In each 2D view the position of the two other slices is indicated by a blue cross hair You may click at any point in a 2D view in order to reposition the two other slices Connections Data required The scalar field to be visualized Planel optional If this port is connected to an OrthoSlice module which is connected to the same input an additional brownish line is displayed in the 2D viewers showing the position of the OrthoSlice module Plane2 optional See above Ports Range a Range min O max 255 Control the mapping of input data to grey values Values below min are mapped to black values abovemax are mapped to white Values between min and max are ma
299. on 4 1 3 View Menu The View menu provides control over several Viewer options affecting the display independent of the Viewer input 58 CHAPTER 4 PROGRAM DESCRIPTION Layout The Layout button lets you select between one two or four 3D viewers All viewers will be placed inside a common window using a default layout If you want to create an additional viewer in a separate window choose Extra Viewer You may create even more viewers using the Tcl command viewer lt n gt show Starting from n 4 viewers will be placed in separate windows Background The Background button lets you select between the three background styles Uniform Gradient Checker board The effect becomes immediately visible independent of the scene being displayed Two different background colors are used by the gradient and the checkerboard background The option Swap colors lets you interchange these colors The option Reset colors resets the default background colors which are a dark blue and a very light blue In order to change the background color via the command interface use the viewer commands viewer lt n gt setBackgroundColor and viewer lt n gt setBackgroundColor2 The command inter face also allows you to place an arbitrary raster image into the viewer background see Section 4 1 6 viewer commands Transparency The Transparency button controls the way of calculating pixel values with respect to object transparencies during the rendering pro
300. on amp Action Duplicate nodes Button duplicate nodes causes a new output grid with duplicated nodes to be computed 6 28 E Field Simulation The E Field Simulation module performs an E field calculation using the finite element method Before starting the E field calculation you must create an extended tetrahedral grid by combining a patient grid and a grid representing the exterior space This can be done using module Combine The grid representation of the exterior space itself 1s generated using modules Antenna and BolusGrid When you have created an extended grid load it into HyperPlan Then you can select the E Field Simulation module from the grid s popup menu E field calculation will take ca 10 20 minutes CPU time per channel of the applicator It is performed as a batch job The status of the job queue can be controled in the Job Dialog Connections Data An extended tetrahedral grid Usually such a grid has the suffix ExtendedGrid Ports Directory EFieldGrid EField Vals The E Field Simulation module creates two output files an E field grid and a file containing a set of E field distributions The E field grid is very similar to the tetrahedral patient model suffix grid However it additionally contains a list of the edges occuring in the grid This ports allows you to specify the names of the output files HyperPlan makes a suggestion for you but you can change it as you please It is recommended to use the suff
301. on complex data fields Port Resolution lets you specify the desired resolution of the output field To start resampling press the Dolt button Resampling labeled data fields Labeled data fields can only be down sampled Instead of Filter and Resolution a port denoted Average appears This port allows you to enter the number of cells to average in every dimension Note that no enlargement is possible As above the Dolt button initiates the resampling Coordinates of the resampled data set Resampling can be performed on any 3 dimensional field with either uniform stacked rectilinear or curvi linear coordinates The resampling operation does not change the coordinate type If you want to convert a data set with stacked rectilinear or curvilinear coordinates into one with uniform coordinates you should use the Arithmetic module instead of Resample The coordinates of the resampled data set are obtained by a resampling operation on the coordinates of the input data set Note that in general the bounding box of the resampled data set will be different from the one of the input data set In particular for uniform coordinates the bounding box will extend from the center of the first voxel to the center of the last one 6 64 SCRIPTOBJECT 155 Resampling in progress While resampling the progress bar at the bottom of the work area indicates the percentage of resampling that is done You may cancel the resampling calculation any time b
302. optimization 1 First you have to load a tetrahedral patient model as well as a set of temperature distributions into Hy perPlan Both are created by module Static Heat The patient model files are called ThermGridFD or ThermGridFE while the files containing the temperature distributions usually have a suffix Ther mValsFD or ThermValsFE The characters FD or FE represent the numerical method finite differ ences or finite element which has been used for electric field calculation 2 Check if the patient model contains a region named Target Tumor or Tumour Optimization will not work if such a region does not exist 3 From the popup menu of the ThermVals icon select module Opt Temp this module lets you enter the name of the file containing the optimized parameters amplitudes and phases that are going to be computed Depending on the name of the ThermVal s file it is recommended to use the suffix PlanFD or PlanFE in the filename 4 If a simulation of the Sigma Eye applicator is performed you can select at port Power Generators whether 4 or 12 power generators are available 5 Now you are ready to submit the job Do this by pressing the Submit button If the output file did already exist a warning message is issued If you don t want to overwrite the file press Cancel and change the filename When the job has been submitted the job dialog window appears showing you the status of the job queue If you press the
303. option is only present 1f the input contains two or more point sets amp DrawStyle spheres points J pi DN m lt Landmarks can be displayed as spheres geometry or as points If the input contains a large number of points several hundred or thousands point style can significantly improve display performance wl amp wn o a Size of displayed spheres or points OQ 5 o SS lt 5 Complexity alt The larger this value is the nicer the spheres look but the lower the rendering speed is 6 50 Line Probe See Section Data Probing for details 6 51 LineSetView This module visualizes data objects of type LineSet Individual lines may be displayed in wireframe mode Alternatively simple shapes like triangles or squares may be extruded along the lines In this way true three dimensional tubes are obtained Additional features of LineSetView are pseudo coloring and the display of little spheres at each line vertex 6 51 LINESETVIEW 139 Connections Data required The line set to be displayed Ports Shape a 5hape Lines Determines how the lines will be displayed If Lines is selected a simple wireframe model will be created The other menu entries denote 2D objects which will be extruded along the lines in order to obtain three dimensional tubes ScaleMode 5 5 caleMode Constant If the line set object contains additional data values per vertex th
304. oriented concepts underlying Amira s design you should think of a module or data object as an instance of an Amira class e g there is a class HxOrthoSlice of which OrthoSlice and OrthoSlice2 are instances and of commands as associated to classes Due to Amira s class hierarchy all commands associated to a particular class are also associated to all of its sub classes 1 e a module command is also available for all other modules that are instances of a sub class of that module s class and the same applies to data classes Moreover there is a class HxObject with sub classes HxModule and HxData from which all modules respectively data classes are derived Therefore the commands provided by HxObject listed below as Object commands are available for all modules and all data objects To execute a single console command just type in its name and arguments and press Enter If you select an object and then press the TAB key on the empty command line in the console window then the name of the object will be automatically inserted Often this saves a lot of typing The Console supports a command history mechanism Use up arrow and down arrow to scroll up and down in the history list To execute a file containing many Tcl commands use load filename or load the script file via Amira s file dialog from the file menu For advanced script examples take a look at Amira s demo files Commands help Shows the help window l
305. ormode nomal mised twisted There are three different coloring modes Normal Each side of a triangle is colored according to the color of the region it points to Mixed Both sides of a triangle are colored in the same color which is a mixture of the colors of the two sides in normal mode Twisted In the twisted mode the colors of the two triangle sides in normal mode are inverted 6 79 Tetra Combine This module takes two tetrahedral grids as input puts them together and creates a new combined grid The module can be used to create an extended grid from a patient grid and a grid representing the exterior space including parts of a treatment device or support to which the patient s body is attached Triangles representing the boundary of the patient s body may be present in both input grids Combine provides an option to remove any duplicated triangles and vertices from its output The order in which the input grids are combined does not matter To make sure that both grids being combined fit exactly together you can attach a Grid Volume module to the combined grid When invoking that module all exterior triangles of the grid are highlighted 1 e all triangles which are incident to only one tetrahedron The displayed triangles should all be located at the outer boundary of the combined grid not in its interior Connections Data required The first input grid GridB required The second input grid Ports Optio
306. other modification of the grid is stored as an output file suffix ThermGridFD or ThermGridFE These grids don t contain any duplicated points nor do they contain an edge list 7 15 Tomographic Image Data Tomographic images are the starting point to create an individual model of the patient as required in radio therapy and more advanced methods in cancer therapy Conceptually tomographic images are interpreted as scalar fields in Amira At each point in space a voxel intensity is defined Usually CT images are used as input because fat muscle and bone structures can easily be identified using this modality In CT images pixel intensity corresponds to tissue density The density is measured in Hounsfield units In Amiranormal ized Hounsfield units are used A value of 1000 corresponds to air and a value of 0 corresponds to water Bones usually have a density value of 140 and higher When a set of equi distant slices is loaded into Amira an object of type HxUniformScalarField3 is created For non equidistant slices a HxStackedScalarField3 is used 7 16 Vertex Sets The HxVertexSet class is an abstract base class It is derived by many other Amira data objects containing a list of 3D vertices for example landmark sets surfaces or tetrahedral grids HxVertexSet provides an interface allowing other modules to access the vertices in a transparent way In order to visualize the vertices of a vertex set you may use the Vertex View module
307. ove with the mouse pointer 1 e the future center of the brush without editing the color channel 1 e the mouse but tons not pressed approximately over it Only in this position it is possible to revert the usual behaviour i e you can raise the channel although you are above the color channel and lower it although you are below it The new colors are displayed in the color bar and in the color buttons If you modify the color channel in the focus cell the new values will also appear in the color sliders 1 e as a new position of the small triangle and as a new value shown by the text entry B Using the color buttons This item offers you the most opportunities to modify the colormap You can set the focus set unset a knot or modify a certain region of the colormap by dragging the focus cell Due to the fact that a focus always exists a special operation for unsetting the focus is not necessary because you unset a focus simply be setting a new one L Setting the focus You simply select a focus by clicking once in a non focus cell The new focus cell will be surrounded by a black and white border while the border of the old focus cell disappers The other displays will be refreshed i e the color index displayed below the color buttons will be set to the focus cell s index the color chart will display a black vertical line in a position corresponding to the new focus cell and the color sliders will show the color channels values in
308. ow to manipulate the internal buffer In order to actually see the buffer content activate the buffer only option e Add adds selected vertices to buffer e Remove removes selected vertices from buffer e Clear removes all vertices from buffer Show Hide Box controls box to select vertices e Invert exchanges buffer content Commands setHighlightColor lt red gt lt green gt lt blue gt Set the color that is used to highlight selected spheres setDefaultColor lt red gt lt green gt lt blue gt Set default color setColorHighlighted lt red gt lt green gt lt blue gt Color all highlighted spheres setColor lt first vertex number gt lt last vertex number gt lt red gt lt Oreen lt blues gt Set color for all spheres from first vertex number to last vertex number If last vertex number is omitted the color is set for the sphere with index first vertex number If first vertex number is omitted too the color for all spheres is set Red green and blue range from 0 to 1 highlight lt first vertex number gt lt last vertex number gt Highlight spheres from first vertex number to last vertex number unhighlightAll Unhighlight all spheres addToBuffer lt first vertex number gt lt last vertex number gt Add all spheres ranging from first vertex number to last vertex number to buffer If last vertex number is omitted only the sphere with index first vertex number is added removeFromBuffer l
309. owest to the highest colormap index and the y axis from 0 0 to 1 0 according to the RGB model Thus a point on a color line indicates the amount of color for the corresponding color channel and color index You can manipulate the course of a line by setting a brush onto any of its points and moving it up or down A brush is set by pressing a mouse button the left one for the red line the middle one for the green line and the right one for the blue line Below the color chart a color bar is displayed which is a larger version of the one used for display in the colormap port Its only function is to show you the actual appearance of the modified colormap in a smoother way by linearly interpolating the colors between the indices The largest area of the editor window is occupied by the color buttons which represent the color in every position index of the chosen colormap each position is called a color cell You can set the focus which is the target index of modifications applicable by the color sliders see below and it is also possible to modify the colormap by dragging a color cell The index of the focus color cell is shown below the color buttons In the lower area of the window there are some color sliders one for each color channel by which you can modify color channel values with respect to the focus cell This means that the values of neighboring cells are affected as well as you can see in the color chart The sliders
310. owever note that the image is not shown if its size 1s greater than that of the viewer window Can I display a colormap in the viewer window as legend First make the colormap icon visible in the Working Area This can be done by selecting the Show or Show All item of Edit in the menu bar of the Working Area Then click on the green colormap icon with the right mouse button and select Show Colormap 5 5 FREQUENTLY ASKED QUESTIONS 87 54 55 56 I 58 59 How can I adjust color and transparency of individual parts of a surface A surface object may consist of multiple patches refering to different materials The color of each material can be adjusted using the Tcl command set Color described in Surface Likewise for each material a specific transparency value may be set using the command setTransparency In this way certain parts of a surface may be highlighted Note that you must choose draw style transparent in order to enable transparencies Also note that color mode mixed is most appropriate for transparent surfaces in terms of performance and meaning How can I create an iso surface with fewer polygons than the iso surface module extracts First of all the iso surface module provides a special option called compact cubes which produces about 40 percent fewer triangles than standard methods Moreover very large data sets may be downsampled on the fly during isosurface generation If you need more flexibility you can c
311. pped linearly SliceX Number of slice currently displayed in sagittal yz window 6 72 STATIC HEAT 161 SliceY Number of slice currently displayed in coronal xz window SliceZ Number of slice currently displayed in axial xy window ZoomButtons amp Z oomButtons ol gt Allows you to decrease reset or increase the current image magnification factor You may also Ctrl z to zoom down or Ctrl Shift z to zoom up 6 72 Static Heat The Static Heat module performs a temperature simulation on a tetrahedral patient model Like for the electromagnetic fields a set of independent temperature distributions are computed For simulating an ap plicator with N independent channels the number of temperature distributions is N N 1 From these distributions the actual temperature distribution for any set of antenna amplitudes and phases can be ob tained very quickly by superposition Note Temperature simulation can only be done if the preceding E field calculation was performed on a tetrahedral grid First you have to load a tetrahedral patient model as well as a set of E field channels into HyperPlan If the FDTD method was used for E field calculation the patient models are called EFie1dGridFD while the files containing the E field channels have a suffix EFieldValsFED If the FE method was used the suffixes are EFieldGridFE and EFieldValsFE respectively Connections Data A set of E field distrib
312. ps defines the number of large loops the other parameters define thresholds for tetrahedron quality which are applied in the first loop and the other loops respectively We recommend to apply the Combined Smoothing and the Remove Inner Vertices methods 9 5 Image Segmentation Editor The Image Segmentation Editor formerly called GI for General Image editor is a tool for interactively segmenting 3D image data Image segementation is the process of dividing an image slice or an image volume into different subregions also called segments In the bio medical context these segments can e g be different organs or tissue types In Amira segmentation is done by assigning a label to each voxel The volume of labels is stored in a Label Field The Image Segmentation Editor lets you edit such a Label Field which can e g serve as input for a surface reconstruction In order to activate the editor push the edit button of a selected Label Field see the icon above Then an instance of the editor will be created and a new window titled Image Segmentation Editor pops up cf Figure 9 3 The major parts of this new window are e Material List In the upper left of the ISE window a list of the materials is presented Here you can add remove and rename materials and select which material is currently active e Tool box Below the material list several tools for interactive manipulation of the segmentation can be selected Depending on the curr
313. ption set to Intersections in order to perform the intersection test The number of intersections is shown in HyperPlan s Console window If there are intersections they are displayed in the 3D viewer You can try to remove them by editing the surfaces manually There are three possible editing operations moving surface points flipping edges and collapsing edges In the Console window you find a short description how to use the mouse buttons and the Shift and Ctrl key to perform those operations In any case the viewer must be in interaction mode 1 e the mouse cursor must be an arrow and not a hand Button 1 select triangle group 20 CHAPTER 1 HYPERTHERMIA PLANNING Shift Button 1 deselect single triangle Ctrl Button 1 deselect triangle group Button 2 activate point dragger highlight edge Shift Button 2 flip edge Ctrl Button 2 collapse edge Once you have repaired an intersection press the Next button until the next intersection is displayed Some times a single intersection will be reported multiple times since three or more triangles were involved When you have repaired all intersections press button Intersections to repeat the intersection test There is another test that should be performed before tetrahedron generation namely the orientation test Choose Orientation from the check mode menu and again press the compute button of the Surface Editor If triangles with wrong orientation exist they are displayed in the
314. quired for my platform You need a graphics board with at least 24 bits of color per pixel 16 bits for Linux At least 64 MB of main memory are required 256 MB or more are recommended What is the recommended hardware for my purpose In principle all features are available even on low end graphics boards However if software emu lation is used rendering performance may drop severely Many visualization techniques applied in Amira make use of texture mapping Therefore it is highly recommended to have a graphics board which supports texture mapping in hardware Amira offers direct volume rendering based on 3D textures This feature is either not available or is very slow on many PC graphics cards In order to use it on Unix systems a high end graphics board is recommended e g a SGI Onyx2 a SGI Octane MXE or a HP C3000 Visualize fx 6 or fx 10 with texture option What is the resource consumption of Amira for memory disk CPU graphics Amira needs roughly about 60 MB of disk space Memory CPU and graphics performance of course depend on the kind of data you are going to visualize CPU speed is less critical than graphics performance Most Amira modules are single threaded Therefore multi processor systems are not a big advantage Enough memory should be available in order to completely store the data to be visualized Are there any limits to the size of textures that graphics boards can use Yes The exact value depends on the
315. r on a regular 3D unit grid for which the number of points can be set by the Resolution port Input data are referenced by variables A B and C this implies pointwise evaluation such that the result for a point 98 CHAPTER 6 ALPHABETIC INDEX OF MODULES x y Z depends on input values for the same point only If the resulting object is based on a regular grid grid indices I J or K may also appear in the arithmetic expression this means that for each grid point its associated I J or K index value will be substituted in the arithmetic expression on evaluation This is useful in connection with comparison operators which produce a result of either zero or one computations may be confined to a specific sub grid this way An expression consists of variables and mathematical and logical operators the syntax is basically the same as for C expressions The following variables are defined A The values of input object A B The values of input object B C The values of input object C I For the resulting object based on a regular grid these are the cell numbers of the x dimension numbered 0 1 In case of a tetrahedral grid I denotes the tetrahedra numbers J The cell numbers of the y dimension K The cell numbers of the z dimension X Y Z The X Y and Z coordinates in the resulting object R The radius r vX Y 22 This is a list of available mathematical and logical operators gt The basic mathematical operators
316. ra reads data it can usually determine the file format automatically You simply select the file in the file browser and click OK When Amira writes data the file browser presents an option menu containing all file formats which can be used to export that data Use this menu to select a non default format How can I define the pixel size for my 3D image volume There is a difference between the number of pixels in a 3D image volume e g 512x512x200 and its physical bounding box e g 30cm x 30cm x 20cm Often voxels are even not equally sized in all directions Many 2D image formats do not contain this extra information When reading images you can supply this information in Amira s image input dialog You can also change this information later by selecting the data set green icon and choosing the Image Crop Editor button What are the data mesh UCD cells types supported by Amira The list of supported data types includes e 2D and 3D grayscale images 8 16 and 32 bits e 32 bit RGBA color images e segmentation results based on labeled voxels e unstructured tetrahedral meshes e unstructured hexahedral meshes e scalar and vector fields defined on uniform stacked rectilinear curvilinear tetrahedral or hexa hedral grids e manifold and non manifold surfaces e colormaps including transparency values e Open Inventor scene graphs How can I read my data with some specific file format Amira supports a number of standard f
317. rary 3D fields The LineProbe module can also be attached to 3D input objects other than fields such as surfaces or Open Inventor geometry In this case the LineProbe doesn t sample any data but simply measures distances Ports Plane Drientation Axial Coronal S agital This port which is used in LineProbe and SplineProbe provides three buttons to specify the probe line orientation Axial probe lines are perpendicular to the x y plane frontal probe lines are perpendicular to the x z plane and sagittal probe lines are perpendicular to the y z plane If one of these buttons is pressed the start and end coordinates of the probe line are set to the minima resp maxima of the corresponding axis and to the center of the two axes perpendicular to the probe line Options a Options immediate M orthogonal The immediate toggle determines whether the samples are taken while the controlpoints are being moved or when the motion is finished If the orthogonal toggle is on all points are moved in sync when the coordinates of one point are changed with the dragger This port is not shown for module PointProbe Evaluate a Vectorcomp vector vector 5 vector 3 If the probe is connected to a vector field these radiobuttons are shown If the magnitude button is set the magnitude of the vectors is shown in the plot window With the normal tangent Comp button set you get the normal and tangential components as two curves Setting the al
318. re attributed to higher up classes and inherited to derived classes as sub classes of a class are commonly referred to Conceptually each object occuring in Amira is an instance of a class and each of its predecessors in the hierarchy that the class belongs to The classes and their hierarchies are defined within Amira As the user you normally deal with instances of classes only For instance there is a class called HxObject with sub classes HxData and HxModule HxData comprises the types of data associated with data objects used for modeling the objects of interest e g volumetric tetraedral grids or surfaces HxModule comprises data types that have been assigned to display and other processing modules again in accordance with principles of object oriented design This is why Amira s data objects and processing modules are commonly referred to as 4 2 GENERAL CONCEPTS 73 objects There are also classes in Amira that are not derived from HxObject and constitute other data types and there are several independent class hierarchies E g there is a class called HxPort from which all classes supporting the operation and display of interface control elements are derived see section Working Area and the List of Ports in the index section of the user s guide A single class hierarchy is usually figured as an upside down tree 1 e with the root at the top Thus the data class tree is the o
319. reate a separate surface object by selecting create surface from the more options menu of the iso surface module You may then use the simplification editor in order to remove as many triangles from the surface as you want You can display the resulting simplified surface using the SurfaceView module How do I visualize data with holes in it There are several choices You can apply a slicing module such as OrthoSlice or ObliqeSlice Alter natively you can clip away parts of a 3D geometry using an arbitrary slicing module Slicing modules are indicated by an orange icon Such modules provide a little push button that must be pressed in order to activate clipping An empty clipping module can be created via the Edit Create menu of the main window If you want to visualize surfaces or finite element grids you can also use the selection box feature of the corresponding viewing modules Most of these modules such as Surface View or Grid Volume support a buffer concept which allows you to select which parts of the object should be displayed Even the sosurface module has such a buffer For this module it can be enabled using the Amira command Isosurface showBox How can I read a series of single image files such that I get a 3D stack Select all image files in the file browser at once This can be done by clicking the first file and then shift clicking the last one Individual files can be selected and deselected by ctrl clicking After pressing the
320. rently We want to look at each lobe in its own viewer e Choose 2 Viewers from the View Layout menu You can see the two lobes in both viewers e Visualize the first lobe yellow in the first viewer and the second lobe blue in the second viewer by switching off the viewer toggles in the isosurface modules 3 5 2 Creating a Landmark Set Now let us create a landmark set object e From the main window s Edit menu select Create Landmarks 3 5 REGISTRATION AND WARPING TWO 3D OBJECTS USING LANDMARKS 51 mmj of i ae i Figure 3 18 Two lobes visualized with isosurfaces in 2 viewer layout in order to create an empty set of landmarks The new object will show up in the object pool We are going to match two objects by means of corresponding landmarks i e we actually have to produce two landmark sets Make this number known to the Landmarks object e Select object Landmarks e Type Landmarks setNumSets 2 in the console window Instead of manually typing the name of the object you want to send commands to e g Landmarks you may simply press the tab key on the empty command line e Start the Landmark Editor by clicking on the button with the disk shaped icon When starting the editor a LandmarkView module is automatically created and connected to the Landmarks data object As indicated on the info line two empty landmark sets are availabe now We use the editor to define some markers in both objects For the following
321. reshold Segmentation 0 0 00 002 eee eee ee ee 46 3 4 2 Refining Segmentation Results 2 2 2 0 47 3 4 3 Extracting Surfaces from Segmentation Results 48 3 4 4 Simplifying the Surface 4 4 4 6 od dea SU a eek Ea edad oe a ek 48 3 4 5 Generation of a Tetrahedral Grid oa a aaa 000000 49 3 5 Registration and Warping Two 3D Objects Using Landmarks 49 3 5 1 Displaying Data Sets in Two Viewers e 50 02 Creatine a Landmark Set Dia a yde ad A Oe a Bed 50 3 5 3 Registration via a Rigid Transformation 204 52 3 5 4 Warping Two Image Volumes 0 000000 eee eee 53 4 Program Description 55 Al Intertace ComponeniS ssis 2 amp i E a we aed a ewe ee a Be eS ee Ge 55 dl PUS MEM e oe lt a ses aps stan Ee EA 55 AD Edt Menu da a a a ee ee a a da 56 Bal On A AAA A a a a a Gey os ke Be S 57 Alde Online HEID deidad dat e ded he i Se hs a ed a a ee Ge le 59 AAS Mam Widow 2 a ee oe Bee a Sa ees 61 CONTENTS 4 2 AEO WACWOEW INC OW we 556 eG E AAA Bec Mt AE es As ME OMSOIE Window e av bik oe Be cy ek eek Re de a we Ae aor ea es ed A AE hid no ae eS Oe ee ee YS e AGO Tile Dale x dam BA a A a BM A OO a EAS 4 1 10 Snapshot Dialog 4 6 amp amp Hae amp Re ws BAO A Oe a General CONCEP S s Du amp x Gee A E ae ee Oe AAA oe ee AN VAS SUCESO AA AA DA A 6S ae 4 2 2 Scalar Field and Vector Fields 0
322. rete grid this ususally involves some kind of interpolation Scalar Fields A 3D scalar field is a mapping R R The base class of all 3D scalar fields in Amira is HxScalarField3 Various sub classes represent different ways of defining a scalar field There are a number of visualization methods for them for example pseudo coloring on cutting planes iso surfacing or volume rendering However many visualization modules in Amira rely on a special field representation Therefore they can only operate on sub classes of a general scalar field Whenever a given geometry is to be pseudo colored any kind of scalar field can be used cf Colorwash Grid Volume Isosurface The class HxTetraScalarField3 represents a field which is defined on a tetrahedral grid On each grid vertex a scalar value e g a temperature is defined Values associated to points inside a tetrahedron are obtained from the four vertex values by linear interpolation This class does not provide a copy of the grid itself instead a reference to the grid is provided This is indicated in the Object Pool by a line which connects the grid icon and the field icon As a consequence a field defined on a tetrahedral grid cannot be loaded into the system if the grid itself is not already present The class HxRegScalarField3 represents a field which is defined on a regular cartesian grid Such a grid is organized as a three dimensional array of nodes In the most simple case these nodes
323. rgument is a run length encoded list like the one displayed by getSelectedTetra 6 37 GridView This module allows you to visualize the grid structure of a regular 3D scalar or vector field with stacked rectilinear or curvilinear coordinates The nodes of the underlying grid can be addressed using an index triple i j k The GridView module extracts slices of constant 1 Jj or k index out of the grid and displays them as a wireframe model In principle the module may also be connected to a field with uniform coordinates However 1t will not be listed in the popup menu of such fields Connections Data required The regular field to be investigated Ports Orientation Orientation ij kC ik Specifies whether slices in the 1 ik or jk plane should be displayed For stacked as well as rectilinear coordinates the indices 1 Jj and k refer to the x y and z direction respectively Geometry amp Geometry coordinates data values 6 38 HEIGHTFIELD 129 This port is only visible if the module is connected to a real valued 3D vector field In this case the grid may be built using the data values instead of the node s coordinates This is a useful option if the vector field contains displacement vectors Allows you to select the constant node index e g the k index if orientation is set to 1 6 38 HeightField The HeightField module offers another method for the visualization of scalar data fields defined on regu
324. rientation port again Choose different slices using the Slice Number port or directly in the viewer with the interaction mode described above 38 CHAPTER 3 FIRST STEPS IN AMIRA me A l ad al al Figure 3 6 The OrthoSlice module is able to extract arbitrary orthogonal slices from a regular 3D scalar field or image volume Each display module has a viewer toggle by which you can switch off the display without removing the module This button is attached to the colored bar where the module name is shown as illustrated below e Deactivate and activate the display of the OrthoSlice or BoundingBox module using the viewer toggle B Orientation E Ass Cocoa Sagittal If you want to remove a module permanently select it and choose Remove from the edit menu Choose Remove All from the same menu to remove all modules e Remove the BoundingBox module by selecting its icon and choosing Remove from the Edit menu e Remove all remaining modules by choosing Remove All from the same menu Now the object pool should be empty again You may continue with the next tutorial 1 e the one on scalar field visualization 3 2 Visualization of Scalar Fields This chapter provides a step by step introduction to the visualization of regular scalar fields e g 3D image data Amira is able to visualize more complex data sets such as scalar fields defined on curvilinear or tetrahedral grids Nevertheless in this section we consider the simplest
325. ript demonstrating the use of the PlanarLIC module Connections Data required Vector field to be visualized ColorField optional A scalar field which may be used for pseudo coloring Colormap optional Colormap used for pseudo coloring If no colormap is connected the default color of the colormap port will be used The port is hidden if pseudo color mode is set to none Ports Orientation a Drientation Axial Coronal S agital This port provides three buttons for resetting the slice orientation Axial slices are perpendicular to the z axis coronal slices are perpendicular to the y axis and sagittal slices are perpendicular to the x axis Options a Options adjust view rotate If toggle adjust view 1s active then the camera of the 3D viewer will be reset whenever one of the orientation buttons is clicked If the rotate toggle is active then a virtual trackball is displayed By picking and dragging the trackball you may change the orientation of the plane Remember that the viewer must be in interaction mode in order to do so The ESC key inside the viewer window toggles between navigation mode and interaction mode The trackball of the last active ArbitraryCut can also be turned on and off by pressing the TAB key inside the viewer window Translate a Translate SS Aso This port lets you translate the plane along its normal direction Colorize amp Colorize None An option menu allowi
326. ristics may not always yield a correct value e AMIRA_MULTISAMP LE On high end graphics systems like SGI Onyx2 a multi sample visual is selected by default In this way efficient scene anti aliasing is achieved If you want to disable this feature set the environment variable AMIRA_MULTISAMPLE to 0 e AMIRA_NO_OVERLAYS If this variable is set Amira will not use overlay planes in its 3D graphics windows The same effect can be obtained by means of the no_overlays command line option Turn off overlays if you experience problems with redirecting Amira on a remote display e AMIRA_LOCAL Specifies the location of an additional local Amira package Any objects redefined in the local package will replace the ones defined in the main Amira package Moreover a local Amira package may be used to install additional objects locally e AMIRA_SMALLFONT Unix systems only If this variable is set a small font will be used in all ports being displayed in the Working Area even if the screen resolution is 1280x1024 or bigger By default the small font will be used only in case of smaller resolutions eo AMIRA_XSHM Unix systems only Set this variable to O if you want to suppress the use of the X shared memory extension in Amira s image segmentation editor e TMPDIR This variables specifies in which directory temporary data should be stored If not set such data will be created under tmp Among others this variable is interpreted by Amira s job que
327. rkWarp module Select the latter and choose Method Bookstein and press the Dolt button To visualize this result the isosurface has to be recomputed Having done that you can see both the de formed and the second lobe in the first viewer To merely see the resulting deformation in the first viewer switch off the viewer toggle of the second lobe s Isosurface module Only a little deformation will be seen because the two original objects were rather similar Using more different data sets results in larger deformations We hope you have had some fun with our tutorials got to know the basic features of Amira and learned to use them For details and more information about other features see chapter 3 the Program Description 54 CHAPTER 3 FIRST STEPS IN AMIRA Chapter 4 Program Description This chapter contains a detailed description of Amira interface components and data types No in depth knowledge of Amira is required to understand the following sections but it is a good idea to have a look at one of the tutorials contained in Chapter 3 particularly the very first one described in Section 3 1 Getting Started 4 1 Interface Components In this section the following interface components are described e File Menu Edit Menu View Menu Help Menu e Main Window Viewer Window Console Window e File Dialog Job Dialog Snapshot Dialog 4 1 1 File Menu The file menu lets you load and save data objects as well as Amira networ
328. rmines the draw style of the surface Five major styles may be selected via an option menu Outlined Opaque shaded display with edges superimposed Shaded Opaque shaded display without edges being visible Lines Shaded wireframe display Points Triangle vertices only Transparent Semi transparent display 6 87 VIEWBASE 179 Transparent mode implies physically correct transparencies 1 e triangles appear more opaque if they are viewed under a small angle It also implies approximate depth sorting 1 e triangles are roughly rendered from back to front in order to obtain correct blending results Note that in some cases visual artifacts may occur for long and thin triangles for self intersecting surfaces or for multiple semi transparent surfaces being displayed simultaneously The drawstyle may be fine tuned by means of an additional popup menu which is activated by clicking on the button labeled more options This menu contains the following items Shaded Enables or disables specular highlights Specular color and shininess may be changed via the Tcl command interface Gouraud Indicates that if a color field is connected pseudo coloring is performed via Gouraud shad ing First colors are looked up at the traingles vertices then these colors are interpolated inside the triangles Texture Indicates that if a color field is connected pseudo coloring is performed via texture mapping The color field s values are interpola
329. rp We want to perform an alignment of the first lobe to the second Therefore the LandmarkWarp module must be connected to the image data of the first lobe use the right mouse button in the tiny rectangle of the LandmarkWarp icon The LandmarkWarp module is able to perform several transformations We start with a purely rigid trans formation to match the corresponding landmarks as good as possible by perfoming only rotations and translations of the first object To do that choose 3 5 REGISTRATION AND WARPING TWO 3D OBJECTS USING LANDMARKS 53 AHH 5 E E B Lx La ie E O E Figure 3 20 Result of landmark based elastic warping using the Bookstein method Method Rigid in the LandmarkWarp module and make sure that Direction is set to Direction 1 2 Then press Dolt to start the computation The module creates a new data object named lobus Warped To visualize the result connect the isosurface that was initially connected to the data of the first lobe to the result select it and press the Dolt button In order to compare the result with the second lobe adjust the viewer toggle of its Isosurface module to display it in the first viewer You should see that the result of the transformation fits the second object quite well 3 5 4 Warping Two Image Volumes Using the rigid transformation the object will not be deformed To perform a deformation and obtain a better fit we can use another transformation method of the Landma
330. rrently the FDTD method supports only the Sigma 60 device for simulation However you can also display the geometry of the Sigma 40 and the Sigma 2000 eye applicator You can change the position of the applicator relative to the patient Next select the FDTD solver from the Antenna s popup menu The interface of the FDTD module lets you select between two different resolutions By default a mesh is used with twice the spacing of the CT slices However the resulting E field is interpolated back to the finer resolution The small resolution should only be used if insufficient memory is available on the computer 1 e less than about 128 MB depending on the size of the data set You have to type in a file name under which you want to store the resulting E Fields HyperPlan makes a suggestion for you but you can change it if you want We recommend to include the filetype EField ValsVX in the filename If you press the button Materials an editor window is invoked that allows you to change the electric proper ties of the different tissue types Note The electrical parameters stored in HyperPlan s material database refer to a frequency of 90 MHz 1 5 E FIELD SIMULATIONS 23 E field calculation will take ca 40 60 minutes CPU time per applicator channel It is performed as a batch job Press the Submit button to submit the job If the output file did already exist a warning message is issued If you don t want to overwrite the file press C
331. rst pending job of the queue starts running 6 74 STREAMSURFACE 163 6 74 StreamSurface This module computes stream surfaces of an arbitrary 3D vector field A stream surface consists of multiple interconnected stream lines started along a predefined line source The algorithm automatically inserts new stream lines in divergent regions of the field Likewise in convergent regions stream lines are automatically removed The resulting stream surfaces can be accumulated in a separate Surface object In this way further post processing is facilitated for example computation of a LIC texture using SurfaceLIC Connections Data required The 3D vector field to be visualized Colormap optional Optional colormap On default the current stream surface will be display in wireframe mode and will be colored according to the arc length of the stream lines forming the stream surface Ports Colormap 3 Cooma MU af Port to select a colormap Origin a Point 4f 0 5 y 0s 205 show This port defines the seed point of the stream surface By pressing the toggle show a cross hair dragger can be activated which allows you to change the seed point interactively in 3D Actually in order to compute a stream surface not only a seed point but a seed line is required Starting from the seed point such a line will be defined automatically taking into account the seed selection mode chosen in port Action re O U p amp
332. rvature direction X axis The seed line is chosen in x direction Y axis The seed line is chosen in y direction Z axis The seed line is chosen in z direction Commands setLineWidth lt width gt Sets line width of wireframe model setTolerance lt eps gt Sets relative tolerance used for field line integration The default is 0 001 times the sampling width set in port resolution doLineSet 0 1 If argument is 1 only stream lines will be displayed instead of the stream surface s triangulation setDrawStyle 1 2 Allows you to set the draw style used in surface mode 1 e when doLineSet is off A value of 1 denotes wireframe mode while a value of 2 denotes shaded surface mode In order to display the surface in a more fancy way convert it into a surface object and use Surface View 6 75 Superpose Electric Fields In simulating regional hyperthermia a separate field is calculated in advance for each channel of the hy perthermia applicator see modules FDTD and E Field Calculation Then the electric field for any set of antenna amplitudes and phases can be obtained very quickly by superposition Connections E Field Set A set of electric fields corresponding to the channels of a hyperthermia applicator as created by module FDTD or E Field Calculation The data files usually have a suffix EFieldVals Plan Data optional A file containing antenna parameters amplitudes and phases Such files usually have a suffix Plan
333. ry In fact if you select an overlay module from a data object s popup menu an instance of ArbitaryCut called EmptyPlane will be created automatically You may also create an instance of ArbitaryCut by selecting Clipping Plane from the global Edit Create menu The module does not display useful geometric output by itself but it can be used to clip the output of any other module in Amira In order to perform clipping you first have to connect port Data to the data object being investigated Then you can simply click on the module s clip button located in the orange header block 6 4 ARITHMETIC 97 Connections Data required Connection to the data object from which the bounding box is taken Ports Orientation a Drientation Axial Coronal S agital By clicking one of the three push buttons the plane s orientation is reset to the xy xz or yz plane respectively The plane will be translated into the center of the bounding box Options amp Options M adjust view Po rotate Po immediate This port provides three toggle buttons If toggle adjust view is active then the camera of the 3D viewer will be reset whenever one of the orientation buttons is clicked If the rotate toggle is active then a virtual trackball is displayed By picking and dragging the trackball you may change the orientation of the plane Remember that the viewer must be in interaction mode in order to do so The ESC key inside the viewer window togg
334. ry Fart y Specifies the real quantity to be computed Possible choices are Real Part Imaginary Part Magni tude and Phase The phase is defined in radians ranging from 7 to r 108 CHAPTER 6 ALPHABETIC INDEX OF MODULES 6 16 Compute SAR In simulating regional hyperthermia the electric field created by a hyperthermia applicator can be calcu lated by superposition of the fields corresponding to the single channels see module Superpose Module Compute SAR computes the SAR distribution corresponding to an electric field Strictly speaking the ARD distribution power per volume is calculated Connections Data An electric field of a hyperthermia applicator as created by module Superpose Ports Mode Select between output of the magnitude absolute value of the electric field and output of the corre sponding SAR distribution Action Press button Dolt to start the calculation 6 17 ComputeContours This module compute contours for a 3D label set using 2D cutting planes orthogonal to the selected axis x y or z There is one cutting plane per each slice of the set the plane has the same coordinate as the slice If the labeled set contains subvoxel accuracy informations weights the contours can be computed using this information too this is an option and by default is on It is possible to compute only the contours that separate one certain material this can be done by selecting a material from a menu The def
335. ry contours or connectivity information Because these data can be computed online they are usually not written into a file If the data are not already present but a certain module requests them they are recomputed automatically You may notice a small time delay in this case Recomputation of the connectivity information can be enforced by the Tcl command recompute You may use the GMC module to extract boundary surfaces from a LabelField describing the results of s segmentation You can visualize surfaces by attaching a Surface View module to it There are two editors that can be applied to modify surfaces the Surface Simplification Editor and the Surface Editor Use the former once to reduce the number of triangles contained in the surfaces The latter allows you to perform an intersection test and to modify the surfaces manually Commands recompute Recomputes any additional data such as edges boundary contours or connectivity information from scratch If the surface contained patches consisting of unconnected groups of triangles these patches are automatically subdivided into new patches consisting of connected triangles only fixOrientation patch Checks if all triangles of a given patch are oriented in the same way If this is not the case some triangles will be inverted in order to fix the orientation If no patch number is specified all patches of the surface will be processed in this way invertOrientation Inverts all triangl
336. s POLmal so 2 ra eta a BA Re acer wee ea a a 195 So DMP Image Ord 44046044 4 246 645 4 OBS oe oe Se eke Be 203 SA Encapsulated Postscript s 6 4 0 2a 4 eee Gh ESS oe ORE OR AAA BEES 203 OD ee OUI ACS Ate ig A Sk a Sas ee a i oe SO ee a eae ee Se We eo oe 204 D0 ICOM is ek ae ee E ue A A ee e na 207 Sal IO VERLO E 4 ants se hs NA Se oes SRE US OG Gh ee ns PG a 207 0 JPEG Maso FOA caida o eee ei A eB EE Bee oe es Ea meee 208 S Leica Microscope 3D TIRE 2 us abe he eS OA a Oe Re A mea oe ee ee 208 9 10 Leica Microscope Slice Senes sa era o OR we ew Roe Ke we OE wwe ole ed 208 Sell PNG imate Format cobra oo Oe BS ORE he oo SS ree Be 208 12 RNM Amase Potasio naa Sk e ee Be A RON ee eee eS 2 eS 208 O IRA Dalal ars a AS he ee A a ee eo ar 209 8 14 SGERGB Image Format amp amp 4 4 eek a eR ee Bw OE Ard ta bok A 210 SM ne as Se Be IS ot ese Se Se te a in rta Stade 210 S16 Stacked Slices 2 2 3 a Boe eS ee Se Sek ek ee ee BO a See 210 CONTENTS 9 Sal TIFF 2S Format e A A A ea a 210 9 Alphabetic Index of Editors 213 9P Color DidloS Es ta a tt ES a ee Bee a E 213 92 Eolormap EQUO ez a e de e EA A En a a be a 215 9 9 e Disita Imane BUSES td AE AA A A el Be eS De Seo 220 OA EOE E ah 9 a eo ul a Y a e bas lbs er 222 9 5 Image Segmentation Editor 2 2 a a ee ee ee ee ee 224 TO WiiaseCrop Editor 2 e da A e Be SOS a 230 Dee Land Mate Ed OE e mal ara Be Sey ee He ey GA a a ee dea 232 O 5 ine SCRE AA oo ee
337. s all currently selected objects The object s icons are removed from the Object Pool but the objects themselves are retained You get the same effect by pressing the Alt d keys Hidden objects can be made visible again using the Show or Show All option 4 1 INTERFACE COMPONENTS 57 Remove The Remove button deletes all selected objects and removes the corresponding icons from the Object Pool You can get the same effect by pressing the Alt x keys If you want to reuse a data object later be sure to save it in a file before deleting it Duplicate The Duplicate button creates copies of all selected data objects For each copy a new data icon is put in the Object Pool The name of a duplicated data object differs from the original one by one or more appended digits The duplicate option will be unavailable if you have selected icons that do not represent data objects Show The Show button lets you select a currently hidden object for having its icon displayed in the Object Pool Among the hidden objects there are usually some colormaps which are loaded at start up This option will be unavailable if there are no hidden objects Show All The Show All button makes all currently hidden objects visible displaying their icons in the Object Pool This option will be unavailable if there are no hidden objects Remove All The RemoveAll button deletes all currently visible icons and the associated objects from the Object Pool A pre
338. s command allows you to write the current LIC texture into a file in raw PPM format 6 59 Plot Tool The Plot Tool is a special purpose viewer designed to display 1 dimensional data e g function curves Instead of being a separate Amira module the Plot Tool will be invoked implicitely by certain modules such as the data probing modules or the Label Voxel module Each of these modules generates 1 dimensional data such as a function plot along a line or a histogram While the data generating modules control the initial settings of the plot window the user can freely adjust these settings afterwards Plot basics The layout of the plot is determined by objects and groups of objects These entities are processed by a plot engine In particular there are objects for 148 CHAPTER 6 ALPHABETIC INDEX OF MODULES Fie Edit sin x 3 14 cos y 3 14 sin z 3 14 o LineProbe ooo LineProbed 1 73205 1 5 Length Figure 6 1 Amira s plot window e Curves e Cartesian Axes e Polar Axes e Plot Areas e Legends e Annotations e Markerlines The plot engine processes the objects top to bottom see Figure The sequence of objects determine their behavior Objects of type PlotArea define the area within the plot window where objects are placed This area is given in normalized coordinates with the origin at the lower left corner An axis is placed in such an area and establishes together with the preceding PlotArea a window viewport
339. s provided in Amira image segmentation can be a time consuming process Due to limited main memory and for performance reasons there is only a limited undo space for 2D interaction and most 3D operations cannot be undone Therefore it is highly recommended to frequently save the label field during the process of segmentation To get started it might be a good idea to choose the image segmentation demo from the Users Guide s demo section and start by modifiying an existing label field Manipulating the material list In the material list the current or active material can be selected with the left mouse button A special behaviour is obtained if one of the Shift Control or Alt keys on the keyboard is held down while selecting the material If Shift is held down all voxels which already are assigned to the newly chosen material are added to the current selection in the current slice or in the whole volume depending on the value of the 3D toggle button in the Selection Command area If Control is held down the voxels with this material are deselected Holding Alt does the same as Shift except that it clears the selection before selecting the new voxels All other manipulation options can be accessed via a popup menu which shows up when the right mouse button is pressed on a particular material entry The menu entries are 226 CHAPTER 9 ALPHABETIC INDEX OF EDITORS e Draw Style A sub menu offers different styles of appearance of the m
340. s selected See also Colormap Ports Orientation Orientation Axial Coronal Sagittal 6 58 PLANARLIC 145 This port provides three buttons for resetting the slice orientation Axial slices are perpendicular to the z axis coronal slices are perpendicular to the y axis and sagittal slices are perpendicular to the x axis Options a Options M adjust view bilinear view If the adjust view toggle is set the camera of the main viewer 1s reset each time a new slice orientation is selected The bilinear toggle determines how color is interpolated within a slice By default the toggle is off and constant interpolation is used With constant interpolation inividual grid cells become visible Bilinear interpolation often produces somewhat blurry results Mapping Type amp Mapping Type Histogram y This option menu lets you select between the three different mapping methods namely a linear grey ramp histogram equalization and colormap mode Data Window Data Window min o mas 3 This port is only visible if linear mapping is selected It allows you to restrict the range of visible data values Values below the lower bound are mapped to black while values above the upper bound are mapped to white Contrast Limit a Contrast Limit 7 This port is only visible 1f histogram equalization 1s selected The number determines the contrast of the resulting image The higher the value the more contrast is containe
341. s the latest version of Amira The latest version is Amira 2 2 How can I test Amira Are there demo keys available For evaluation purposes a fully functional version of Amira can be downloaded from www amiravis com after electronic registration This version will have a time limited license key Is Amira Y2K compliant Yes Installation hardware and platform related questions 5 10 What are the supported platforms for Amira Amira 2 2 runs on Microsoft Windows 9x Microsoft Windows NT4 Microsoft Windows 2000 HP UX 10 20 SGI Irix 6 5 x Sun Solaris 2 7 and on Linux RedHat 6 2 Suse 6 3 Details are described in the user s guide in section System Requirements Is Amira available on Windows 98 NT Yes Amira is available on Microsoft Windows 9x Microsoft Windows NT4 and Microsoft Windows 2000 Compatibility between Windows and Unix version Both the Windows version and the Unix version contain exactly the same set of data objects editors and modules Data files can be exchanged between Windows and Unix without limitations There are only minor differences between different version which are due to differences in the underlying hardware e g the availability of 3D textures for volume rendering The user interface of Amira 2 2 is written using the Qt toolkit This ensures that the GUI looks similar and has the same functionality on both Windows and Unix systems Can I display Amira on a remote screen In
342. same filename previously chosen under Save Data As The button will only be active if the data object to be saved is selected and if this data object already has been saved using Save Data As A common application of the Save button is to store intermediate results during manual segmentation in Amira s image segmentation editor Save Data As This button lets you write a data object into a file To do so you must first select the data object click on the corresponding green data icon Then choose Save Data As to activate Amira s file dialog The file dialog presents a list of all formats suitable for saving that data object Choose the one you like and press OK Note that you must specify the complete file name including the suffix Amira will not automatically add a suffix to the file name However it will update the suffix whenever you select a new format from the file format list Also Amira will ask you before it overwrites an existing file Some file formats create multiple files for a single data object For example each slice of a 3D image data set might be saved as a separate raster file In this case the file name may contain a sequence of hashmarks This sequence will be replaced by consecutive numbers formatted with leading zeros If no file format at all has been registered for a certain type of data object the Save as button will be disabled It will also be disabled if more than one data object is selected in the object pool
343. same way as the intersecting triangles before For simple cases wrong orientations are repaired automatically Otherwise you can try to repair them manually Important A prerequisite for the orientation test is that the outer triangles of the surface are assigned to material Exterior If the surface does not contain such a material or if the assignment to Exterior is not correct the test will report falsely oriented triangles The options Aspect Ratio Dihed Angle and Tetra Quality sort all surface triangles according to different quality measures The worst triangle according to the selected quality measure is displayed and the worst quality is printed in the console window Using the buttons of port Display you can cycle through all other triangles and edit the surface if necessary In order to generate high quality tetrahedral grids afterwards the following quality numbers should be achieved Aspect ratio at least 10 better 20 Dihedral angle at least 10 better 5 Tetra quality at least 50 better 25 If no intersections or wrong orientations are reported anymore and if you have removed all bad quality triangles you may leave the editor by clicking on the pencil icon If you have edited the surfaces save them into a file again 1 4 4 Tetrahedron Generation The last step is generation of a volumetric tetrahedral grid from the surfaces Each tissue type is treated separately for this purpose First a closed surface is constructed from al
344. sed for routine work Simplifier setIntersectionTestStrategy lt mode gt This command lets you choose between different intersection test strategies mode is a three digit number for example 100 The digits specifiy the strategy used for testing modified triangles against existing edges for testing modified edges against existing triangles and for testing planar intersec tions The allowed values are 0 3 for the first 0 2 for the second and 0 1 for the last digit Larger values correspond to more extensive tests which of course also require more computing time By default a value of 211 is used Modes 111 or 101 are faster but more likely to produce intersecting triangles 9 11 Surface Editor The surface editor allows you to check an arbitrary surface for intersecting triangles It also provides some tools for interactively editing the surface In this way intersections may be removed manually Also the quality of the surface can be improved The editor works in conjunction with the Surface View module If such a module is not already active an instance of it will be automatically created when the editor is invoked Then in the viewer interaction mode the following editing operations can be performed by clicking mouse buttons and using the Shift or Ctrl keys Button 1 All triangles surrounding the picked triangle become visible Shift Buttonl The picked triangle is deselected and disappears 236 CHAPTER 9 ALPHABETIC INDEX OF E
345. sitivity lt value gt Direct contrast adjustment with the mouse Shift Left Mouse Button in interactive mode can be amplified or damped using this command The default value is 0 5 times percent of the total image data range The value is clipped to 0 1 and 1 setPosition lt x gt lt y gt The position of the window graph can be modified with setPosition Negative values are relative to the right and upper border of the viewer If no window graph appears with showWindowGraph try setPosition 0 O which should set the display to the lower left corner Ssetscaleractor lt Lacvuor gt The size of the window graph can be modified using setScaleFactor This might be useful if the window graph is disturbing the visual output of the viewer 6 21 Curl The Curl module computes the curl of a vector field consisting of floats defined on a uniform grid The output is another uniform vector field OV OV OV OV OV Connections Data required Vector field defined on a uniform grid UniformVectorField3 The vector components must be floats Ports This module has no ports 6 22 DATAPROBE 113 6 22 DataProbe The three data probing modules PointProbe LineProbe SplineProbe are used to inspect scalar or vector data fields They have many features in common so they are described in one section The probes are taken at a point PointProbe or along a line LineProbe SplineProbe which may be arbitrarily placed The controlpoints
346. stations with fx 4 or fx 6 graphics or on Sun Creator 3D and Elite graphics boards For details on hardware acceleration see below Apart from 3D graphics hardware probably the most important system parameter is main memory You should have at least 128 MB preferably 256 MB or more Amira can also be started with only 64 MB but working with large data sets definitely requires more main memory Keep in mind that a single 3D image data set can easily occupy 60 MB of memory 240 slices with 512 x 512 pixels of 1 byte The speed of the processor of course is also an important parameter However it is less critical than the graphics system and the main memory size For the PC versions we recommend at least a 500 MHz PIII processor 5 6 1 On System Stability Amira is a very demanding application that extensively uses high end features Experience shows that such applications tend to reveal instabilities in system hardware hardware drivers and the operating system A common problem is insufficient main memory We recommend you configure enough swap memory in addition to physical memory The total amount of virtual memory should be at least 512MB 1GB would be even better Especially on PC platforms OpenGL drivers today are often not as robust as desired Also system crashes due to bad memory chips or unstable power supply are not rare If you experience problems or instabilities with Amira on your Windows platform we recommend that you follow th
347. sted Faces which belong to the boundary between the selected materials are displayed using a red highlighted wire frame in the viewer You may crop the faces by turning the viewer into interactive mode and move the green handles of the selection box Only the faces inside the bounding box can be added to the buffer also see PortButtonList Color Mode 5 Color Mode normal mixed twisted Here you may choose among several color modes For details see the module Surface View 6 35 Grid Cut The Grid Cut module is a tool for visualizing cross sections of labeled tetrahedral volume grids made up of different materials A 2 dimensional cutting plane has to be defined for this purpose and may be shifted through the 3 dimensional tetrahedral grid in orthogonal direction an Orientation port is provided for setting the orientation of the cutting plane perpendicular to one of the main axes and a Translate port for specifying an orthogonal translation GridCut renders a slice with the material compartments in their associated colors The cutting plane is usually clipped to a rectangle with the 3D viewer turned into interactive mode you can pick one of its edges and shift 1t through the volume grid To define arbitrary cutting planes you have to set the Rotate toggle which makes a rotation handle appear in the center of the cutting plane Having turned the viewer into interactive mode you can pick the handle with the left mouse button and rotate t
348. t command line options Amira accepts 21 How can I check the version of my Amira package 22 Are there any examples or demos 5 5 FREQUENTLY ASKED QUESTIONS 81 23 24 25 26 Dl Is there a specific newsgroups Is there a mailing list Is there a web site Where can I find free modules for Amira Is there a public repository for 3rd party contributions How can I learn Tcl Technology 28 29 30 31 32 33 34 35 What graphics libraries are used by Amira What is Open Inventor What is OpenGL What is Tcl What is Qt Is Amira dataflow oriented How do modules communicate What is the firing order of modules Data input output printing 36 ST 38 39 40 41 42 43 44 45 46 What are the supported data formats input and output How can I use Amira to import export image formats other than the Amiira image format How can I define the pixel size for my 3D image volume What are the data mesh UCD cells types supported by Amira How can I read my data with some specific file format How can I interface to my database How can I reuse my work with Amira Can I compose modules How can I print with Amira How can I take a snapshot of the viewer window What image formats are supported for snapshots How can I create printed reports including Amira images How can I publish Amira images or animations on the Web Visualization 47 48 49 50 51 IZ 53 54
349. t first vertex number gt lt last vertex number gt Remove all spheres ranging from first vertex number to last vertex number from buffer If last vertex number is omitted only the sphere with index first vertex number is removed getNumVertices Print number of vertices getCoords lt vertex number gt Print coordinates of vertex with number vertex number setTextSize lt size gt Set size with which the text 1s displayed Sec TexCOLTiset lt x gt lt y gt lt I gt Set offset which is added to the text position setTextColor lt red gt lt green gt lt blue gt Set text color 178 CHAPTER 6 ALPHABETIC INDEX OF MODULES updateTextures To both plates and spheres textures are applied to make the spheres look smoother If the direction from which the light comes changes those textures need to be recomputed Updating is invoked by this command only 6 87 ViewBase This module is the base class for several other Amira modules displaying a set of triangles like Isosurface Surface View GridVolume and others ViewBase is not useful on its own but provides special features common to all derived modules In particular these features comprise the following e A dedicated port allowing the user to modify the draw style of a triangular surface in an easy and con sistent way All modules derived from ViewBase thus have a similar GUI Among the supported draw styles is a physically correct transparency mode e A generic buffer
350. t icons visible use the Show all icons option For more information about lights please refer to the Reference Section of this manual Fog The Fog button introduces a fog effect into the displayed scene and controls how opacity increases with distance from the camera The fog effect will only be seen on a uniform background More fine tuning is provided by the fogRange Viewer command 4 1 INTERFACE COMPONENTS 59 None No fog effect default Haze Linear increase in opacity with distance Fog Exponential increase in opacity with distance Smoke Exponential squared increase in opacity with distance Axis The Axis button creates an Axis module named GlobalAxis which immediately displays a coordinate frame in the viewer window This button is a toggle so clicking on it again deletes the GlobalAxis module and removes the coordinate frame from the viewer window The axes will be centered at the origin of the world coordinate system You may also create local axes by selecting the appropriate entry from a data object s popup menu Fading effect The Fading effect toggle lets you switch on a fading effect which is applied to all kinds of scene movements Before a new image is rendered only a certain fraction of the background will be cleared In this way older images remain visible until they fade out after a while Note that this mode requires single buffer rendering and therefore flickering may be visible in some cases 4 1 4 O
351. t rescaling does not mean resampling 1 e the number of voxels will not be changed The total data volume can be seen as consisting of slices in every dimension Each slice in a dimension is referenced by an index ranging from zero to the number of slices minus one This editor gives you the opportunity to add new slices on every side in every dimension Last but not least you can simply flip these slices 1 e revert the order in every dimension When clicking on the crop button see the icon above shown in the Working Area of uniform scalar data field the ImageCrop Editor pops up It looks as shown in Figure 9 4 In the Viewer you should see a grey box with green corners marking the bounding box of the scalar data field The green corners are draggers by which you can control the data volume you want to preserve This means that there are two ways to crop such a scalar data field e Dragging and moving the box e Setting indices explicitly in the cropping text fields Adding slices is simply done by setting indices in the cropping text fields beyond the limits of the total data volume The only way to manipulate the bounding box is to set new values in the corresponding text fields For flipping slices click on one of the three flip buttons labeled FlipX FlipY and FlipZ which on activation revert the order of slices in the desired dimension All changes take effect if you press the OK or Apply buttons they are discarded by activa
352. tained in antenna parameter files are ignored The scale factor is calculated according to maximal temperatures defined for each type of healthy tissue The maximal temperatures are defined in HyperPlan s material database They are currently set to 44 C for most tissues and 42 C for some heat sensitive tissues like bladder and intestine By default the toggle is set Note This toggle has a different meaning than AutoScale in module Superpose as applied to electric fields Other Ports Same functionality as in module Superpose as applied to electric fields 6 77 SurfaceLIC This module visualizes a vector field defined on an arbitrary triangular surface using line integral convo lution LIC Alternatively a 3D vector field projected onto such a surface can be visualized The LIC algorithm works by convolving a random noise function along field lines tangential to the surface using a piecewise linear hat filter In this way for each triangle a small piece of texture is computed and mapped back onto the surface The final surface texture clearly reveals the directional structure of the surface vector field A similar 2D algorithm is implemented by the PlanarLIC module Click here to execute a script demostrating the SurfaceLIC module Computation of the surface LIC texture may take about half a minute Connections Data required Surface for which a LIC texture is to be computed VectorField required Surface vector field or 3D
353. ted for every vertex a triangle No averaging is performed if two neighboring triangles form an angle bigger than the crease angle set via the Tcl command setCreaseAngle The default is 30 degrees Buffer Buffer Add Remove Clear Show Hide Draw This port can be used to modify the list of currently visible triangles All triangles being visible are stored in an internal buffer You may add or remove triangles from this buffer via an Open Inventor tab box dragger Triangles selected by this dragger will be highlighted 1 e displayed in red wireframe If the dragger is not visible click on one of the buttons to activate it Add Adds highlighted triangles to the buffer Remove Removes highlighted triangles from the buffer Clear Removes all triangles from the buffer Show hide Shows or hides the tab box dragger without modifiying the internal buffer 180 CHAPTER 6 ALPHABETIC INDEX OF MODULES Commands createSurface name Converts set of visible triangles into a surface setAlphaMode opaque constant fancy Triangles may be drawn either opaque or transparent Two transparent modes are possible with a constant alpha value constant or an alpha value varying according to triangle normal fancy setNormalBinding perTriangle perVertex Normals can be bound either per triangle or per vertex In the first mode the triangles appear flat setPointSize size Sets the size of points setLineWidth width Sets the width of
354. ted in Hyper Plan First of all a stack of computer tomographic images of a patient is loaded into the system In these images regions of different tissue type as well as the tumor have to be identified This task is called image segmentation For each region specific values of the electric and thermal parameters are assumed The next step is to solve Maxwell s equations and to compute an electromagnetic field distribution In HyperPlan all channels of the radiowave applicator are simulated separately This makes it possible to obtain the result ing field for any set of amplitudes and phase shifts by simple linear superposition HyperPlan provides an FDTD method which directly works on a segmented image volume or so called label field This method can be used to investigate the resulting SAR distribution without generating a geometric patient model However the use of a voxel grid imposes some artificial rasterization effects To obtain more accurate results the interfaces between different tissue compartments have to be represented more precisely In Hy perPlan this is achieved by using a three dimensional tetrahedral patient model Based on such a tetrahedral model an E field simulation can be performed using a modified FDTD method or using a high precision finite element method When the E fields have been computed a resulting temperature distribution can be simulated For this a fast multi level finite element method is used Similar to the E fields
355. ted linearly before color lookup is performed In this mode no specular colors can be used Opaque All triangles will be rendered opaque Const alpha Opacity values of a triangle will be taken as is Usually if no pseudo coloring is done all parts of the surface will have equal opacity Fancy alpha Enables physically correct transparencies The triangle s opacity values will be modi fied according to their orientation with respect to the viewing direction Causes the silhouette of the surface to be fully opaque thus enhancing perception for very transparent surfaces Depth sorting Enables approximate depth sorting The triangle s centers are presorted along the major coordinates axes Create surface Creates a Surface object containing the set of currently visible triangles The following items are only present for a subset of derived modules e g Isosurface or Surface View Both faces Indicates that triangles are rendered both from back and front Front face Enables back face culling Increases rendering speed but may lead to artifacts for non closed surfaces Back face Enables front face culling Increases rendering speed but may lead to artifacts for non closed surfaces Triangle normals Enables per triangle normals Shading will be discontinuous at the triangles edges Vertex normals Enables per vertex normals An average normal is computed for all triangle vertices Direct normals An averaged normal is compu
356. teger compression factors for x y and z direction Choose a compression factor yielding a resolution of about 128 in the x and y direction e g a factor of 2 to reduce dimensions from 256 to 128 If the slice distance is 0 5 cm or larger choose a factor of 1 no compression for the z direction Hint You can determine the slice distance by clicking on the green icon representing the LabelField The voxel size is displayed in HyperPlan s work area The voxel size in z direction is the slice distance Press the Do t button to perform the actual resampling operation Now apply the Generalized Marching Cubes algorithm Select the GMC module from the popup menu of the resampled LabelField Be sure that the toggle add border is set This ensures that the surfaces being created will be closed If the LabelField contains probability information see Section 1 3 3 the toggle sub voxel accuracy should be set as well If the sub voxel accuracy can t be set then you probably have 1 4 GRID GENERATION 19 forgotten to call the smooth filter at the end of manual image segmentation Press the Triangulate button of the GMC module to start surface extraction Surface extraction using the GMC module will take about 30 seconds Therefore it is not really necessary to save the results to a file In case you want to do this anyway you should use the filetype gmc surf 1 4 2 Simplifying Surfaces The surfaces generated by the GMC module typically consist o
357. termined the files will be loaded in raw mode When you click Ok in the file dialog an additional dialog box will appear In this dialog you can enter the dimensions of your image volume and of the bounding box The bounding box should be entered in centimeters If no more information is available like CT table position you may simply set the lower left front corner of the box to 0 0 0 while the upper right back corner is determined by the physical size of the scanned image volume Usually CT data are stored in two byte format using 12 bits of gray level information Therefore the primitive data type should be set to short Many CT scanners produce images with a resolution of 512 x 512 pixels per slice In HyperPlan such images should be resampled to 256 x 256 pixels per slice The smaller resolution is well suited for treatment planning It results in smaller data files and requires less memory To resample your images select the Resample module from the popup menu of the green data icon repre senting the CT data The Resample module appears as a red icon When you click on it the user interface of the Resample module appears in HyperPlan s work area In the line labeled Resolution you can enter the desired resolution Type in 256 for both x and y resolution Click on the Dolt button to start resampling After a few seconds a second green data icon representing the resampled volume should appear in the net work area You can investigate the effe
358. the focus cell As mentioned above you simply unset a focus by setting a new one Setting a knot Because every focus cell must have a knot you set a knot simply by setting the focus 1 e by clicking once in a non focus cell without a knot The knot appears as a small black box with a white surrounding 220 CHAPTER 9 ALPHABETIC INDEX OF EDITORS in the middle of the new focus cell The color chart displays it with the focus as a black vertical line If you change the focus the knot still remains in the color cell but without the focus it is displayed in the color chart as a white vertical line Unsetting a knot You unset a knot by clicking another time into a focus cell This does two things First the knot is removed from the color buttons and the color chart Second the focus is set to the first color cell i e to the upper left corner of the color button panel and to the left edge in the color chart The displays are refreshed 1 e no small black box in the color cell and no vertical line at the corresponding position in the color chart will be shown Dragging the focus cell When you click the first time in a non focus cell you can hold the mouse button be careful a click in a focus cell unsets a knot and drag the focus cell over the color buttons The corresponding color values will be temporarily copied to its new position and the color channels between the next knots to the left and to the right from the actual position will
359. the port labeled Slice Number allows you to change the slice number via a slider e Select different slices using the Slice Number port By default OrthoSlice displays slices with axial orientation 1 e perpendicular to the z direction However the module can also extract slices from the image volume perpendicular to x and y direction These two alternate orientations are referred to as sagittal and coronal these are standard phrases used in radiology 3 1 4 Interaction with the Viewer The 3D viewer lets you look at the model from different positions Moving the mouse inside the viewer window with the left mouse button pressed lets you rotate the object With the middle mouse button you can translate the object For zooming press both the left and the middle mouse button at the same time and move the mouse up or down Notice that the mouse cursor has the shape of a little hand inside the viewer window This indicates that the viewer 1s in viewing mode By pressing the ESC key you can switch the viewer into interaction mode In this mode interaction with the geometry displayed in the viewer 1s possible by mouse operations For example when using OrthoSlice you can change the slice number by clicking on the slice and dragging it Select different buttons of the Orientation port of the OrthoSlice module Rotate the object in a more general position Disable the adjust view toggle in the Options port Change the orientation using the O
360. the results of thresholding are refined interactively Both steps are described in separate sections 1 3 1 Importing CT Data Before you can perform any kind of planning for a new patient you first have to load a stack of the patient s CT images into HyperPlan Use the file dialog for loading the data 1 e select Load from the File menu of HyperPlan s main window At the hospital when the CT scans are taken make sure that all images have the same pixel size Although not strictly required it is also advantageous to choose equal slice distances throughout the whole image stack If you are going to use one of the FDTD based simulation methods equal slice distances are obliga tory In case of the Sigma 60 or Sigma 2000 eye applicator the area covered by the image stack should have an extension of at least 50 better 60 cm in the direction of the patient s axis The tumor should be centered somewhere in the middle of the image volume We recommend to use a slice distance of 1 cm or smaller The ACR NEMA file format and its successor the DICOM format are widely used to store medical images of various types In HyperPlan the import of stacks of axis aligned CT or MR images stored in these formats is supported The read routine checks whether the spacing between subsequent slices is equal or not In the first case an image volume with uniform coordinates is created otherwise stacked coordinates are used To check which coordinate type is used s
361. this entry you select the RGB color model Hue Saturation Value When you activate this entry the display is changed according to the HSV color model Show Alpha Each color model has got a so called alpha channel which determines the transparency of the colormap When you handle a colormap with small alpha values you might be irritated by the transparency shown in the color bar and you perhaps will not be able to make out the correct color By the toggle Show Alpha you control whether the alpha channel is shown or not At startup it is not shown Immediate Mode If this mode is active all changes made to the current colormap are immediately passed to the colormap object that has been selected for editing with all impacts on dependent objects c Brush Menu This has only relevance to the color chart Here you can set the brush type which is one of the types shown in the Brush Menu B Color Chart The color chart shows the graphs of the colormap s colorchannel components Four or three color channel 218 CHAPTER 9 ALPHABETIC INDEX OF EDITORS graphs are displayed depending on whether Show Alpha is set or not Three color channels are always displayed according to the currently set color model The red graph shows the course of the first color channel R H the green the course of the second G S and the blue the third s course B V If Show Alpha is enabled the alpha channel is shown in black color The knots
362. tic module by any of the ordinary display modules Specific features 60 Does Amira support Stereo viewing 88 CHAPTER 5 TECHNICAL INFORMATION Yes You will need special shutter glasses e g Stereographics Crystal Eyes Stereo viewing is successfully being used on SGI and HP UX systems The Windows version is also be stereo enabled You can use red blue stereo as well as shutter stereo if your hardware supports stereo for OpenGL applications 61 Does Amira support VR devices such as 3D mouse head mounted displays or CAVE systems The public version of Amira does not yet support these features However custom solutions have already been implemented e g to support tracking devices Contact indeed zib de if you have any requirements in this field 62 Can I use anti aliasing Yes On SGI Onyx2 Infinite Reality systems Amira will automatically use a multi sample visual On other systems you may use the command viewer 0 antiAlias 3 to enable 3 pass jittered rendering To reset type viewer 0 antiAlias 1 5 6 System Requirements Amira 2 2 runs on Microsoft Windows 9x Microsoft Windows NT HP UX 10 20 SGI Irix 6 5 x Sun Solaris 2 7 and on Linux RedHat 6 x Suse 6 3 Amira relies on fast hardware accelerated OpenGL 3D graphics We strongly recommend hardware texture mapping since many visualization tools in Amira rely on it Hardware texture mapping is available for example on SGI 02 Octane and Onyx systems on HP work
363. tient whose treatment is simulated e filetype describes the data type Usually when data sets are created HyperPlan already suggests a suitable value for this part of the name For example if you perform a threshold segmentation on a data set called Exam ct data the resulting label field storing the segmentation results will be called Exam LabelField In particular the following type names should be used details are given in subsequent chapters ct data for the patient s CT data LabelField for segmentation results surf for triangular surface models grrad for tetrahedral patient models EFieldVals forthe result of an E Field calculation ThermVals for the result of a temperature calculation Plan for the result of an optimization of treatment parameters e version number allows you to distinguish between different simulations for the same patient You might for example perform several E field calculations with different patient positions within the hyperthermia applicator or several temperature calculations assuming different thermal tissue properties HyperPlan takes the version number into account by propagating it along proposed filenames for result data of successive planning steps 1 3 Segmentation In this section we describe how to import CT images in HyperPlan and how to segment them 1 e how to separate different tissue types Segmentation is performed in two steps First an automatic thresholding operation is applied Then
364. ting plane e g OrthoSlice or ArbitraryCut Inside this plane a 3D vector field can be visualized using a regular array of vector arrows Connections Data required The 3D vector field to be visualized Module required The module which defines the cutting plane where the arrows are placed Colormap optional An optional colormap used for pseudo coloring Ports Colormap Port to select a colormap Resolution amp Resolution 50 y 50 Provides two text inputs defining the resolution of the regular array of vector arrows in the plane s local x and y direction The larger these values are the more arrows are displayed Scale Scaling factor used to control the length of the vector arrows Options Options projection constant arrowz W points This port provides the following toggle buttons Projection If this option is set then 3D vectors are projected into the current plane Otherwise the arrows will indicate the true direction of the vector field Constant If this option is set then all arrows will be of equal length Otherwise the length of the arrows is chosen to be proportional to vector magnitude 6 86 VERTEX VIEW 175 Arrows If this option is set then true arrows will be displayed Otherwise only simple line segments will be drawn Points If this option is set then a little dot will be drawn at the bottom of an arrow This is useful to highlight a sampling point at locations where the v
365. ting the Cancel button As usual the editor is closed by pressing OK or Cancel Apply will leave it open Cancel restores the previous state NOTE All calculations in this dialog were designed with the assumption that at least two slices exist in all direc tions A warning dialog appears if you want to run this editor on a smaller number in any direction The consequences are not predictable 9 6 IMAGECROP EDITOR 231 125 x41x21 kmin kmax Threshold 200 Auto crop Bounding box 0 230572 max 1 14939 Image crop min JO imag 124 min 0 imag 40 ymin 0 369029 ymax 0 377229 amin o zma 0 783471 Flip and s ap flip flip y flip z Map ey Sap AZ Slap pz OF Cancel Figure 9 4 User interface of Amira s ImageCrop Editor Cropping an image by dragging and moving the box A little experience with manipulating draggers and moving objects is assumed Using the draggers you can reduce or enlarge the data volume you want to preserve enlarging is of course possible only up to the size of the bounding box The size of the dragging box can be manipulated intuitively in every direction of the three axes 1 e along the x the y or the z axis The values in the text fields of the editor change according to your manipulations A certain minimum thickness is preserved while reducing a dimension of the box for further reductions the text fields have to be used Using th
366. tion Load the extended tetrahedral grid filetype Extend edGrid into HyperPlan Select the module called E Field Simulation from the grid s popup menu In this module you must enter two filenames one for the output grid and one for the file containg the E field values which are going to be computed The output grid is very similar to the original tetrahedral patient grid However it additionally contains a list of the edges of all tetrahedra HyperPlan suggests two filenames Check if these are ok It is recommended to include the filetypes EFieldGridFE and EFieldValsFE in the filenames If you press the Materials button a dialog window is popped up that allows you to change the electric properties of the different tissue types Note The electrical parameters stored in HyperPlan s material database refer to a frequency of 90 MHz The material database itself can be modified permanently by editing the file HyperPlan share materials databsse hm E field calculation will take ca 10 20 minutes CPU time per applicator channel It is performed as a batch job Press the Submit button to submit the job If one of the output files does already exist a warning message is issued If you don t want to overwrite the file press Cancel and change the filename When the job has been submitted the job dialog window appears showing you the status of the job queue If you press the Start button the first pending job of the queue starts running When th
367. triangle number to each triangle Action a Action Dot Press the Dolt button to start calculation of triangle qualities 6 84 VectorProbe The VectorProbe module allows you to interactively investigate a 3D vector field by moving around a dynamic vector field probe The probe displays certain quantities associated to the first order derivative of the field in an intuitive way This kind of probe has been originally proposed by W C de Leeuw and J J van Wijk in A Probe for Local Flow Field Visualization Proceedings of Visualization 93 pp 39 45 It looks as follows Connections Data required The 3D vector field to be visualized Ports Dragger a Dragger Y show Shows or hides the dragger and the vector field probe attached to it The dragger provides a cylinder handle and a square plate handle The cylinder handle allows you to translate the icon along the center axis The orientation of the cylinder can be changed using the Ct r1 key while the mouse is located somewhere over the dragger Buffer amp Buffer _Add Clear 174 CHAPTER 6 ALPHABETIC INDEX OF MODULES Adds the current vector field probe to an internal buffer In this way multiple probes can be displayed at once Scale a Scale I A Scales the overall size of the vector field probe Length Adjusts the length of the probe s arrow part 6 85 Vectors This is a so called overlay module which can be attached to any module defining a cut
368. ts of other types such as Surfaces Tetrahedral Grids Line Sets or Molecules The vertices can be displayed in three different modes spheres plates and points The vertices may be colored according to a scalar field and a color map Alternatively colors may also be defined via the command interface of the Vertex View module Furthermore an internal buffer exists that allows you to view only those vertices that are of interest to you Connections Data required The data object from which the vertex set is read ColorField optional 3D scalar field which is used along with a color map to color the vertices according to the value of the scalar field at the position of a vertex Colormap optional Used to color the vertices in connection with the ColorField 176 CHAPTER 6 ALPHABETIC INDEX OF MODULES Ports Colormap Port to select a colormap Draw Style Draw Style Spheres Plates Points Vertices may be drawn in three different styles e Spheres Points are drawn as triangulated spheres with equal radius e Plates Points are drawn as quadrats with mapped on image of a sphere e Points Points are drawn as points The size of the points does not differ according to the distance of the vertex from the viewer they all have the same size SphereRadius D 5phereR adius A 0 0023930 Specifies unique radius for all spheres This port is only visible if Spheres or Plates is chosen as draw style Point Size
369. tside this intensity range are considered to be part of the background Size amp Size Min 10 Max j 0000000 Minimal and maximal size in voxels of regions to be considered Regions smaller or larger than this range are considered part of the background Output a Output Region Field W Spreadsheet If Region field is checked a scalar field of type byte will be created in which those voxels which were considered to belong to a region are set to non zero while background voxels are set to zero Voxels belonging to non connected regions will be assigned different colors The detected regions can be visualized in 3D by using e g an Isosurface module with threshold 0 5 on this output Alternatively the result can be casted to a Labelfield using the CastField module and then the GMC can be applied If Spreadsheet is checked a spreadsheet object will be created which contains a list with size and position of all detected regions Action Action Dolt Triggers the computation 110 CHAPTER 6 ALPHABETIC INDEX OF MODULES 6 19 ContourView This module displays contours of a surface Contours are typically computed automatically and they are defined to be the boundaries of patches If a surface contains no contours this module will not display anything You can automatically compute contours by using the recompute command of the Surface This module is mostly useful for developers Connections Data required The un
370. ture 7 9 SAR Distributions The specific absorption rate SAR is given by a 2 E 2 where o is the electric conductivity and E is a complex E field vector In Amira it is represented either as an object of type HxTetraScalarField3 or as an object of type HxUniformScalarField3 depending on the simulation method used In both cases SI units are used so the SAR is given in Watt m 7 10 SpreadSheet This data type represents a spreadsheet A spreadsheet will be created e g by the module TissueStatistics 7 11 Surface In Amira data objects of type Surface are used to represent non manifold triangulated surfaces Such surfaces are required as an intermediate step in generating a tetrahedral patient model from the results of segmentation of a 3D image stack Surfaces mainly consist of a list of triangles as well as a list of 3D coordinates Each triangle is defined by three indices pointing into the list of coordinates Moreover triangles are grouped into so called patches 7 11 SURFACE 191 Conceptually a patch describes the boundary between two adjacent regions tissue types These two regions called inner region and outer region are represented by indices into the surface s material list Although required for grid generation the patch structure of a surface does not necessarily define a valid space partitioning However any surface must have at least one patch Surfaces may also contain additional data such as edges bounda
371. ual You may add some more tissue types to the ones created by LabelVoxel For this press the right mouse button over the list of tissue types to activate a popup menu In this menu select the entry New Material You can edit the name of the newly created material by selecting the entry Rename Material from its popup menu If you later want to perform an optimization of treatment parameters you should at least mark the tumor region and name it Target Important Optimization will not work without a region called Target or Tumor There are a number of predefined tissue types for which HyperPlan s database contains electrical and ther mal properties Fat Muscle Bone Target Intestine Abdomen Bladder Kidney Liver Spleen Stomach Pancreas Heart Lung Arteries Veins You should preferably use these names In order to check the contents of the database choose Database from the Edit menu of the main window In the dialog which 18 CHAPTER 1 HYPERTHERMIA PLANNING is popped up then open the folder called Materials Each material may contain a blank separated list of alternative names in a parameter called name In order to extend or modify the database permanently edit the file HyperPlan share materials database hm with an arbitray text editor One remark should be made about the names Intestine and Abdomen If you perform a detailed seg mentation of the abdominal region separating fatty and real intestinal regions you sho
372. ucture e Scalar and Vector Fields e Coordinates and Grids e Surface Data e Vertex Set e Transformations e Parameters 4 2 1 Class Structure In this section we discuss the object oriented design of Amira in a little more detail You already know that data objects e g grey level image data or vector field sets appear as separate icons in the Object Pool You also know that there are certain display modules which can be used to visualize the data objects While some modules can be connected to many different data objects e g the Bounding Box module others cannot e g the Ortho Slice module The latter can only be connected to voxel data or to scalar distributions on voxel grids The reason is that internally both are represented as a scalar field with uniform cartesian coordinates Consequently the same visualization methods can be applied to both On the other hand for example a volumetric tetrahedral grid model of the object of interest usually looks completely different But since it is also a 3D data object the same Bounding Box module can be connected to it In summary there are Amira data objects that might be conceived of different type but with respect to mathematical structure applicability of viewing and other processing modules as well as programming interface design have many common properties Obeying principles of object oriented design the data types of Amira are organized in class hierarchies where common properties a
373. ue 5 4 User defined start up script Amira may be customized in certain ways by providing a user defined start up script The default start up script called Amira init is located in the subdirectory share resources of the Amira installation directory This script is read each time the program is started Among other things the start up script is responsible for registering file formats modules and editors and for loading the default colormaps If a file called Amira init is found in the current working directory this file is read instead of the default start up script If no such file is found on Unix systems it is checked if there exists a start up script called Amira in the user s home directory Below an example of a user defined start up script is shown Execute the default start up script source SAMIRA ROOT share resources Amira init 0 Set up a uniform black background 80 CHAPTER 5 TECHNICAL INFORMATION viewer 0 setBackgroundMode OU viewer 0 setBackgroundColor black Choose non default font size for the help browser help setFontSize 12 Restore camera setting by hitting F2 key proc onKeyF2 1 viewer setCameraOrientation 1 0 0 3 14159 viewer setCameraPosition 0 0 2 50585 viewer setCameraFocalDistance 2 50585 In this example first the system s default start up script is executed This ensures that all Amira objects are registered properly Then some special settings are made Finally a hot key procedure
374. uide from the Help menu of Amira s main window 3 1 1 Loading Data Usually the first thing you will do after starting Amira is to load a data set Let s see how this can be done e Choose Load from the File menu After selecting this menu item the file dialog appears see Figure 3 2 By default the dialog displays the contents of the the first directory defined in the environment variable AMIRA_DATADTR If no such variable exists the contents of Amira s demo data directory are displayed You can quickly switch to other directories e g to the current working directory using the directory list located in the upper part of the dialog window Amira is able to determine many file formats automatically either by analyzing the file header or the file name suffix The format of a particular file will be printed in the file dialog right beside the file name Now we would like to load a scalar field from one of the demo data directories contained in the Amira distribution e Change to the directory data tutorials select the file Lobus am and press OK 3 1 GETTING STARTED 35 d j Ja Wooo 7 Figure 3 2 Data sets can be loaded into Amira using the file browser In most cases the file format can be determined automatically This is done by either analyzing the file header or the file name suffix Figure 3 3 Data objects are represented by little green icons in the object pool Once an icon has been selected in
375. uld use the name Intestine If you perform a less detailed segmentation and mark the whole abdominal region as one tissue type you should name it Abdomen The electrical and thermal parameters assigned to Abdomen are mean values of those for fat and muscle tissue We strongly recommend to apply the smooth filter as a final step before leaving the segmentation editor preferably the 3D variant In order to activate the smooth filter choose Smooth Labels from the Label Filter menu of the editor In the dialog choose 3D volume and press Apply The smoothing filter may sligthly change the labeling Besides that it calculates a probability for each voxel to belong to the assigned tissue type The probability is 1 in the interior of a region and decreases at the region s boundaries Subsequent planning steps applying the generalized marching cubes procedure can take the probabilities into account in order to create better results Manual image segmentation may take a considerable amount of time especially for an unexperienced user Therefore it is a good idea to save the segmentation results frequently For this choose the Save Data As item from the File menu For convenience we recommend the filetype LabelField Once you have stored the segmentation results for the first time you can use Save Data or simply Ctrl S to save the data again under the same filename If you have applied the smoothing filter the LabelField file will not only
376. ults Second 1t provides a command line interface 1 e a shell where Amira commands can be entered Amira s console commands are based on Tel Tool Command Language This means you can write com mand scripts using Tcl with Amira specific extensions For a complete description of Tcl and its control structures we refer to the text book Tel and the Tk Toolkit by John K Ousterhout the creator of Tcl Like many other books about Tcl this also covers the Tk GUI toolkit Note that Tk is not used in Amira Concerning Amira extensions there are some fixed command names like load or viewer and temporary ones which are associated to modules and data objects The general format of the temporary commands is object command word target value In particular when creating an OrthoSlice module a command with the same name is introduced e g OrthoSlice or OrthoSlice2 or OrthoSlice3 depending on how many instances of OrthoSlice modules already exist and removing the module from the Object Pool also removes the command As long as the module exists all 1ts associated command words are available By these commands you may set the more specialized functional options that the module provides The command interface of a particular module is described in the User s Reference Guide A help function that displays all functions provided by a module is also available You activate it by entering the module command with the he lp option Because of the object
377. um 3 In uniform mode this port contains three text fields allowing the user to define the lower and upper bound of the isoline interval as well as the number of isolines being computed in this interval Values Values AO 75 100 5 Me N S lt e A O Q O ab 5 jas gt o Z 5 c g O g O h o jas 5 a separated threshold values can be defined in this text field For each threshold a corresponding isoline is displayed Parameters amp Parameters line width 2 The input of this port determines the width of the isolines in pixels Options Options update min max If update min max 1s set then the isoline thresholds are automatically reset to some default values whenever the data range of the incoming scalar field changes Colormap 3 Colomap 2 TT af Port to select a colormap 6 44 Isosurface Regular This module computes an isosurface within a three dimensional scalar field with regular cartesian coordi nates slices The module contains optimized code for uniform coordinates 1 e grids consisting of equidistant 134 CHAPTER 6 ALPHABETIC INDEX OF MODULES Very high resolution datasets can be downsampled to reduce the number of polygons being produced In addition an internal polygon reduction method is provided that merges certain triangles of the original triangulation This way the number of triangles can be reduced up to 50 A second independent scalar field may be
378. umbers of the three OrthoSlice modules in the respective ports or directly in the viewer as described in section Getting Started In addition to the OrthoSlice module which allows you to extract slices orthogonal to the coordinate axes Amira also provides a module for slicing in arbitrary orientations This more general module is called ObliqueSlice You might want to try it by selecting it from the lobus data popup menu 3 2 2 Simple Data Analysis The values of the data window port of the OrthoSlice module determine which scalar values are mapped to black or white respectively If you choose a range of e g 30 100 any value smaller or equal to 30 will become black and all pixels with an associated value of more then 100 will become white Try modifying the range This port provides a simple way of determining a threshold which later can be used for segmentation e g in biology or medicine to separate background pixels from anatomical structures This can be most easily done by making the minimum and maximum values coincide e Remove two of the OrthoSlice modules e Select the remaining OrthoSlice module e Make sure that the mapping type 1s set to linear 40 CHAPTER 3 FIRST STEPS IN AMIRA ed aE Al e Figure 3 8 By adjusting the data window of the OrthoSlice module a suitable value for threshold segmentation can be found Intensity values smaller than the min value will be mapped to black intensity values bigger than the max
379. ution If you want to use the Surface Editor to remove the intersections you have to be very careful You must not change any triangles of the patient s surface at this time because they are prescribed by the patient model Connections Data This port connects the BolusGrid module with an Antenna module Ports Smooth This port controls two different smoothing strategies If toggle boundary 1s set the curve where the water bolus is attached to the patient is smoothed somewhat If toggle End caps is set the triangles of the bolus end caps are smoothed 1 e vertices are shifted such that the triangles become more equilateral Usually both toggles should be on Option If toggle Flip Edges is set the triangular grids of the bolus end caps are improved by edge flipping Offset This defines where the water bolus touches the patient s skin The curve where this happens is shifted inwards by the given distance The offset is measured in centimeter Action The compute button of the action port initiates computation of the bolus surface 6 7 Boundary Conditions The Boundary Conditions module visualizes boundary conditions defined in a tetrahedral grid for a finite elements simulation Visible faces are stored in an internal buffer similar to the GridVolume module Likewise the selection domain can be restricted interactively by adjusting a selection box Ctrl clicking on a face makes it invisible In Amira there are predefined bound
380. ution is too low The resolution value also has an effect on the granularity of the resulting LIC image The size of the LIC texture being computed is chosen to be the next power of two larger or equal than the sampling resolution For example if the resolution is set to 128 the size of the LIC texure will be 128x128 If the resolution is set to 129 then a LIC texture of size 256x256 will be computed resulting in much finer structures Phase S Phase Ad This port will only be visible if a complex valued vector field is connected to the module It provides a phase slider controling which part of the complex 3D vectors is visualized by the arrows A value of O degree corresponds to the real part while a value of 90 degrees corresponds to the imaginary part Action Action I Dot Starts computation of the LIC texture If no LIC texture has been computed yet a default checkerboard pattern is displayed This pattern is also displayed as soon as filter length or resolution are changed Press the Do t button again in order to update the texture Commands setNumSubPixels 1 21 13 Allows you to change an internal parameter of the LIC algorithm Since LIC images contain very high spatial frequency components they are susceptible for aliasing Aliasing can be almost eliminated by choosing the number of sub pixels to be 2 or even 3 However this is achieved at the expense of in increased computing time writeTexture lt filename gt Thi
381. utions as created by modules FDTD FDTD method or E Field Simulation FE method The data files usually have a suffix EFieldValsFD or EFieldValsFE Ports Directory ThermGrid ThermVals The Static Heat module creates two output files a temperature grid ThermGrid and a file con taining a set of temperature distributions ThermVal s The temperature grid is very similar to the initial electromagnetic coarse grid However 1t does not contain any duplicated vertices nor does 1t contain information about the grid edges By this ports you can specify the names of the output files HyperPlan makes a suggestion for you but you can change it as you please It is recommended to use the suffixes ThermGridFD and ThermValsFD or ThermGridFE and ThermValsFE depending on the suffix of the EFieldVal ss input data Action If you press the Parameters button an editor window appears where some global parameters for temperature simulation are presented Changes can be made by simply selecting an item and typing a new value The ok button in the editor window saves the changes If you press the Materials button you can change the thermal properties of the different tissue types After you have setup the simulation you can commit it by pressing the Submit button The job dialog window should appear showing you the status of the job queue If you press the Start button the first pending job of the queue starts running 162 CHAPTER 6 ALPHABETIC INDEX OF
382. utton adjustments made by moving the value sliders are shown almost immediately You may change the histogram layout scales plots of lines and curves colors using the Object Editor which pops up when you select Edit Objects in the Edit menu of the histogram window For more details please refer to the Plot Tool description Segmentation starts when you click on the Dolt action button Before doing so several options may be set These options are described in detail below The segmentation results are stored as a LabelField data object You may use the Image Editor to further process this object Connections Data required Image data to be segmented Ports Regions a Regions Exterion Fat Muscle Bone This port lets you specify the names of the different regions to be segmented Between two and five regions may be specified The indivdual region names must be separated by blanks Exterior Fat Lets you set the threshold separating the first and second region Fat Muscle Lets you set the threshold separating the second and third region Muscle Bone a Muscle Bone AR roo Lets you set the threshold separating the third and fourth region Options a Options subwoxel accuracy remove couch M bubbles Toggle subvoxel accuracy causes certain weights to be computed indicating the degree of confidence of the assignment of a voxel to a particular region This information 1s used by the surface reconstruc tion a
383. values is covered Finally colormap can be used to activate pseudo coloring Port mapping is hidden if the module is connected to a color field Data Window a Data Window min 200 max 200 This port is only visible 1f linear mapping is selected It allows you to restrict the range of visible data values Values below the lower bound are mapped to black while values above the upper bound are mapped to white ContrastLimit a ContrastLimit This port is only visible if histogram equalization is selected The number determines the contrast of the resulting image The higher the value the more contrast is contained in the resulting image A 8 gz S Colomap 38 j This port is only visible if colormap is selected Choose a colormap to map data to colors Sampling amp Sampling fine interp data interp texture This port provides several toggles controlling the way how oblique slices are reconstructed The first toggle labeled fine lets you switch between low and high sampling resolution On default 150x150 or 300x300 sample points are taken in these modes respectively These numbers can be changed via Tcl commands The next toggle denoted interpolate data will only be active if the scalar field to be visualized is defined on a uniform grid In this case if the toggle is off nearest neighbor interpolation is used If it is on or if the data is not defined on a uniform grid then the field s nat
384. vector field to be visualized ScalarField optional An optional scalar field which can be used for pseudo coloring Colormap optional Colormap used for pseudo coloring If no colormap is connected the default color of the colormap port will be used Ports Colormap 3 Cooma B Ap Port to select a colormap 6 77 SURFACELIC 167 ColorMode a ColorHode Constant Three different color modes are provided If Constant is selected then a uniform overall base color is used for the LIC texture This will be the default color of the colormap port or the left most color of the colormap connected to this port if any If Magitude is selected then the LIC texture will be colored according to the magnitude of the vector field Finally if Color field is selected and a scalar field is connected to the module then the LIC texture will be colored according to the values of this scalar field Texture Interpolation a Interpol constant bilinear A radio box determining how the triangle textures are being filtered by the underlying OpenGL driver Possible choices are constant or bilinear interpolation Usually you will not see a big difference unless you zoom up the image very much Contrast a Contrast center 175 factor 00 This port provides two parameters controlling the amount of contrast of the final LIC texture Input field center specifies the average grey value of the texture Higher values result in brighter ima
385. ware shall be classified as Commercial Computer Software and the Govern ment shall have only Restricted Rights as defined in Clause 252 227 7013 c 1 of DFARS Notwithstanding the foregoing the authors grant the U S Government and oth ers acting in its behalf permission to use and distribute the software in accordance with the terms specified in this license e The libtiff library developed by Sam Leffler subject to the following license terms Copyright c 1988 1997 Sam Leffler Copyright c 1991 1997 Silicon Graphics Inc Permission to use copy modify distribute and sell this software and its docu mentation for any purpose is hereby granted without fee provided that i the above copyright notices and this permission notice appear in all copies of the software and related documentation and ii the names of Sam Leffler and Silicon Graphics may not be used in any advertising or publicity relating to the software without the specific prior written permission of Sam Leffler and Silicon Graphics THE SOFTWARE IS PROVIDED AS IS AND WITHOUT WARRANTY OF ANY KIND EXPRESS IMPLIED OR OTHERWISE INCLUDING WITHOUT LIMITATION ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE IN NO EVENT SHALL SAM LEFFLER OR SILICON GRAPHICS BE LIABLE FOR ANY SPECIAL INCIDEN TAL INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND OR ANY DAMAGES WHATSOEVER RESULT ING FROM LOSS OF USE DATA OR PROFITS WHETHER OR NOT ADVISED OF THE PO
386. ween both peaks In some CT images a couch may be visible in the same Hounsfield range as human tissue Switch on the remove couch toggle to prevent that the couch is assigned to either fat muscle or bone If this toggle is set the biggest connected component in the 3D volume is searched for This is assumed to represent the patient All other voxels are set to air After thresholding the voxels labeled as air are separated into two classes the exterior of the patient and air filled cavities within the patient s body called bubbles Such cavities occur within the intestine and the stomach the lung is also classified this way Note that the separation between exterior and bubbles doesn t take place if the bubbles option of the Label Voxel module is unset For hyperthermia planning always ensure 1 3 SEGMENTATION 17 that this option is set Push the Dolt button to actually perform the labeling A new data object of type HxUniformLabelField3 will be created It is a regular cubic grid with the same dimensions as the underlying CT data set For each voxel it contains a label indicating the tissue type You may visualize the result of the labeling operation by attaching an OrthoSlice module to it 1 3 3 Manual Segmentation Of course simple thresholding in general cannot produce satisfactory results In most cases additional interactive segmentation is necessary You may wish to merge segments split segments remove islands etc HyperPl
387. wer window to be captured The format of the output file is determined automatically from the file name suffix What image formats are supported for snapshots Snapshots can be stored in TIFF JPEG SGI RGB PNM BMP PNG or EPS format The file type is determined automatically from the file name suffix How can I create printed reports including Amira images You may use any desktop publishing or word processing system of your choice Probably all of them allow you to import either TIFF or JPEG or EPS files How can I publish Amira images or animations on the Web Make snapshots and save them as JPEG images or create animation sequences as described below Visualization 47 48 49 50 51 a2 23 Can I display axes Yes Use the menu entry Axis in the view menu This will display global axes located at the origin of the world coordinate system You may also attach local axes to any data object by selecting Display LocalAxis from the object s popup menu Can I do image processing with Amira Basic image processing functionality is provided although Amira is not a dedicated image processing program For example the Image Filters editor supports smoothing sharpening as well as certain morphological operations Does the surface reconstruction support non manifold topologies Yes In contrast to many other products non manifold topologies are handled in a consistent way by Amira Is it possible to start
388. wever the option can only be selected if the surface was created from image data with uniform slice distance Press button Simplify to perform the simplification This operation will take about 5 minutes depending on the number of triangles that have to be deleted The progress bar at the lower border of the main window will give you an idea how long you will have to wait Button Flip Edges allows you to improve the quality of the resulting surface triangulation HyperPlan searches pairs of triangles with a common edge and large obtuse angles and tries to remove them by flipping edges In the Console window you get an information about the number of bad triangles and how many of them were removed If you want to visualize the simplified surfaces select module SurfaceView from the popup menu of the surface data icon For a detailed description of this module refer to the documentation under Section Surface View in the Amira reference manual Save the simplified surface data into a file with filetype surf 1 4 3 Checking Surface Quality Before starting tetrahedron generation it is a good idea to check if the surfaces contain intersecting trian gles We have integrated strategies to avoid intersections into the simplification algorithm so this should not occur too often Click on the green icon representing the surface Then invoke the Surface Editor by clicking on the button displaying the pencil icon Press the compute button with the check o
389. won dee Ree eB ER A pe Be Be 11 13 13 14 15 15 16 17 18 18 19 19 20 21 21 22 23 23 25 26 26 27 4 CONTENTS 224 Suae Reconstruction 5235 wh ce E AAA Sik ee a Ee 31 229 Surlace SIMPlUCION s ds ih deve a da da da E 31 2 2 6 Generation of Tetrahedral Grids ee eee 31 3 First steps in Amira 33 Sul Geum Stalled 2 2 ad a A a o oR ee a A a ee a a 33 Sled hoading Data ooo seg ho aa a Ba a aa ate 34 S22 TOK Pato a et EA ea ee A Bae Be oS ae eo 35 ols Visualizing Data 3 5622 dida GES SSS SE PS EO ESS 36 3 1 4 Interaction with the Viewer a8 dar a a oe ek ae ae 37 32 VMisualizati n OF Scalar Fields e s a hae Bea A CR eee BS Be Be es 38 sal OMNOVONa SCS al Gos o eS Ge ea ak Ee a a Gt Bae x 39 3 2 2 SOMPE Data Analysis 4 h 4 4 ob a St hee RSS TAS Oe R 39 323 ReSsamplin the Data 5 poa o ra ee hak A OY Pe See Be eS 40 3 2 4 Displaying anIsosurface oaoa 0 ee ee 40 2 Groppins Me Data rosas amp Yd ene Mahe ee dm A eae 41 32 0 Volume Rendenmne 4 o gt i448 GEES oe Ss oe SG SS 41 3 3 Visualization of Vector Fields csa aei aa io Xe E oe eR a ae wk ee we BO 43 3 3 1 Loading the Wing and the Flow Field 43 3 552 Line Integral Convoluuion loma Soe Wa a at Bae ne x 44 333 illuminated Stream Lines 26230 a e a a A AA a 45 3 4 Grid Generation from 3D Image Data 2 0 000000 46 3 4 1 Th
390. world coordinates to normalized coordinates transformation Notice that the objects have to be kept in the following sequence 1 PlotArea 2 Axis 3 Curves and Markerlines Every object is identified by a unique name You need to know these names if you want to change certain object attributes via the command interface of the Plot Tool Editing parameters In order to change the parameters of a plot object select the Edit Objects item from the Edit pulldown menu of the Plot Tool A window appears with the list of names of all objects currently in use By selecting one of these objects the parameters of that object are displayed and can be changed The is active toggle near the lower left corner of the window can be used to switch the processing of the selected object on or off In the following sections all not self describing parameters are documented 6 59 PLOT TOOL 149 Edit Mew Anchor PlotArea Annotation Legend Axis Grid axis Grid Markerline Markerline Pt Group LinePre Plottaroup LLineProbe Curve M Croup Object Plotroup L LineProbe2 Curve is active Figure 6 2 List to select a plot object x v axs Range 0 4 a4 _ Auto Nice Mums Ticks f1 j Format lg Intersection Min s Mid Max 0 0 Type Lin Log F is Visible Attributes Linewidth 2 Label value Figure 6 3 Editable axis parameters Editing axis parameters To choose the x or y component of
391. x of File Formats 8 1 ACR NEMA DICOM The ACR NEMA file format and its successor the DICOM format are widely used to store medical images of various types In Amira the import of stacks of axis aligned CT or MRI images stored in these formats is supported The read routine checks whether the spacing between subsequent slices is equal or not In the first case an image volume with uniform coordinates is created otherwise so called stacked coordinates are used Both image data with uniform or stacked coordinates can be segmented using the image segemen tation editor and can be converted into polygonal models using the GMC module If you want to create a uniform data set from a stacked one you may use the arithmetic module When reading ACR NEMA or DICOM files all files of the data volume must be selected simulanteously in the file browser This is done by clicking the first file and then shift clicking the last one Amira assumes that a file is a ACR NEMA or DICOM file if the file name suffix is ima or ani or if the file name matches a DICOM unique instance ID e g 1 3 12 2 1107 5 1 2 20395 19980429221554713 4 In dividual files are automatically uncompressed if they were compressed using gzip and if the file name ends with the suffix gz 3 2 Amira Mesh Format AmiraMesh is Amira s native general purpose file format It is used to store many different data objects like fields defined on regular or tetrahedral grids segmentation results co
392. xel per pixel into values representing the four tissue compartments exterior fat muscles and bones These labels are directly used as input for the FDTD module The size of the Yee cells has to be adapted to the distance between the CT slices typically 1 cm The size is automatically set to either the slice distance option fine lattice or twice the value of it option coarse lattice A size of about 1 cm is recommended Note Whether you have to enter 1 or 2 to achieve 1 cm cells depends on the slice distance e FDTD on tetrahedral grids modified FDTD Solver This algorithm requires a tetrahedral patient model as input The tetrahedral grid is used to create a region based regular geometry model The solver takes into account the field discontinuities at tissue boundaries You can choose the size of the cubes as you like A size of about 1 cm is recommended There are some restrictions that you have to keep in mind when working with the FDTD modules The maximal possible number of cubes Yee cells is 82 in x and y directions and 106 in z direction For mod elling the Sigma 60 applicator the number of cubes should be chosen such that 5 10 cells of background medium lie between the applicator patient bounding box and the boundary of the FDTD lattice e g the number of cubes should be set to about 80 for a cube size of 1 cm and about 48 for a size of 2 cm The program will stop if the chosen number of cubes is too small to cover the p
393. xt to be displayed 6 2 Antenna The Antenna module represents a treatment unit for regional hyperthermia Currently two different device types are supported the BSD Sigma 60 applicator and the BSD Sigma Eye applicator However note that the Sigma Eye applicator cannot be used together with the FDTD module You may attach the antenna module either to a LabelField or to a TetraGrid In the former case you can use the FDTD module to compute a SAR distribution using a straight forward finite difference method In the latter case you may also use the FDTD module and invoke a modified finite difference method Alternatively you may proceed with the BolusGrid module which allows you to perform highly accurate treatment planning using a finite element method c f E Field Simulation In any case in order to obtain realistic results the applicator should not exceed the upper and lower bound of the patient model In addition the tumor should be located somewhere in the middle of the applicator 95 96 CHAPTER 6 ALPHABETIC INDEX OF MODULES Connections Data A LabelField or a tetrahedral grid which defines the patient model to be used in a subsequent E field simulation step Notice that a tetrahedral grid must contain duplicated nodes if you want to use the FDTD module later on Therefore you might have to use module Duplicate Nodes On the other hand if you want to proceed with BolusGrid the tetrahedral grid must not contain duplicated n
394. y easily visualize a subset of all tetrahedra using a 3D selection box or by drawing contours in the 3D viewer 3 5 Registration and Warping Two 3D Objects Using Landmarks This is an advanced tutorial You should be able to load files interact with the 3D viewer and be familiar with the 2 viewer layout and the viewer toggles 50 CHAPTER 3 FIRST STEPS IN AMIRA ten Pe A ad of a jaa Figure 3 17 Volumetric representation of optical lobe as tetrahedral grid We will transform two 3D objects into each other by first setting landmarks on their surfaces and then defining a mapping between the landmark sets As a result we shall see a rigid transformation and a warping which deforms one of the objects to match it with the other The steps are 1 Displaying Data Sets in Two Viewers 2 Creating a Landmark Set 3 Alignment via a Rigid Transformation 4 Warping Two Image Volumes 3 5 1 Displaying Data Sets in Two Viewers The data we will be working with in this tutorial are of the same kind you have already seen before Two optical lobes of a drosophila s brain e Load the two lobes by executing the script share examples landmark hx This script will load two data sets called lobus am and lobus2 am In addition two isosurface modules connected to each of the data sets will be created In the viewer the two lobes are visualized by isosurfaces the first in yellow and the second in blue As we can see the lobes are orientated diffe
395. y RGBA quadrupels where every quadrupel specifes a color by its R ed G reen and B lue value in the RGB color model each value ranging from 0 0 to 1 0 The fourth value the so called A lpha value is a measure for the opacity also ranging from 0 0 to 1 0 where 0 0 means that the color cannot be seen and 1 0 that the color does not shine through Internally these values are stored as floats Each colormap has a size 1 e the number of RGBA quadrupels in this colormap Usually the size defaults to 256 but every other positive non zero value is possible Every RGBA quadrupel in a colormap can be accessed by an index starting with 0 and ending with size 1 To make a long story short take a look at this picture 1 00 0 30 1 00 0 30 0 97 0 29 0 73 0 18 0 45 0 06 0 30 0 00 RGBA quadrup R G B 188 CHAPTER 7 ALPHABETIC INDEX OF DATA TYPES Beside the raw RGBA values the colormap also stores two coordinates defining a range used for color interpolation Color lookup requests for a parameter smaller than the minimum coordinates evaluate to the first colormap entry Requests for a parameter greater than the maximum coordinate value evaluate to the last entry Connections Master The objects using the colormap Ports Colormap 3 Colomap 0 ZT Ap The Colormap Port 7 4 E Field Sets During E field simulation not only a single field is computed but a separate field for each channel of the hyperthermia applicator
396. y pressing the stop button on the right of the progress bar Connections Data required The underlying data field to be resampled Ports Input Resolution E Input Resolution 128 128 x 87 Displays the resolution of the input data set Filter a Name Triangle This lets you select one of the resampling filters mentioned above This will only be visible if the input data set does not contain labels Resolution 5 Resolution 45 y 48 2 48 Specifies the resolution of the output data set This port will only be visible 1f the input data set does not contain labels Average amp Average y 2 2 1 Specifies how many labels should be averaged during down sampling This port will only be visible 1f the input data set contains labels Action Action Dolt Starts resampling 6 64 ScriptObject The Amira system is fully scriptable by its built in TCL interface The ScriptObject module allows the user or custom solution provider to make its scripts accessible from Amira s graphical user interface Here is the most simple example of how this can be done Write a simple Amira script using your favorite text editor and put the special header for script objects in its first line Amira Script Object V0 1 echo Hello world a script is called Load this file into Amira A blue icon will appear Each time you click on the Call button the script will be executed and a message in Amiras consol
397. you to save or print the contents of a viewer window Changing Directories You can change the current directory by double clicking a subdirectory in the file list or by entering a new directory in the dialog s path list By default the path list contains the current directory the directory containg the demo data sets provided with Amira as well as all directories defined by the environment variable AMTRA_DATADIR In AMIRA_DATADIR multiple directory names have to be separated by colons on Unix systems or by semicolons on Windows systems In addition on Windows system the names of the twelve most recently visited directories are stored in the path list Selecting Files To select a single file just click on it or type in its name in the file name text field In some cases you might want to select more than one file at once e g when loading a 3D image data set as a series of single 2D images You can do this by selecting the first file first and then shift selecting the last file Then all intermediate files will be selected as well Moreover you may ctrl click a file in order to toggle its selection state individually Using the Filename Filter The filename filter is visible when the dialog is in import mode Load File It is useful to restrict the list of filenames to a subset matched by the filter expression The filter expression may contain the wildcard characters matches any character and matches an arbitrary charact

Hyperthermia Treatment Planning with HyperPlan

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