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1. Save image volume as This command saves the active volume in iMagic format giving the opportunity for selecting a new filename for it Open surface This command loads the surface in iMagic format to process When activated a dialog for selecting the desired surface appears Once loaded the surface appears in the Surface View work sheet and becomes the active surface After the surface is loaded the Surface item in the horizontal menu 1s enabled the Volume item is only enabled when loading image volumes Save surface With this command the active surface is saved in iMagic format see Appendix 8 Save surface as This command saves the active surface in iMagic format giving the opportunity for selecting a new filename for it Import image volume This command allows loading image volumes single volumes in other image formats When activated another submenu allows to select 1f the operation will be carried out through one or multiple files Immediately after a standard Windows dialog is presented for selecting the file s to import and from which format iMagic imports ANALYZE DICOM MNC and Brain Voyager VMR files formats plus a raw format If the raw format is selected a dialog is presented for setting the volume properties as shown in the figure iMagic PRO User Manual 32 Set information about image volume Number of columns 256 Offset in file fo Humber of rows 256 Gers RN a Humber of slices 256 AMETS R
2. ooooonnnnnnnncncnnnnnocnnnnnnnnnnnnnnnos 28 Loadimne the ima ec Vollmer NAAN MN EE dI MODE EE aNG 28 calme the IMACS YVONNE cta 28 Int rpolatine the imd e VOL UTDE NANA in aii 28 oesmentine the Mate VOLUME ANTON 28 ON 28 Fitting electrodes to image Volume iioi eei eue pee BANA o eae Pee Do Rey eia 20 Calculating Prid and nete DOES aded Aa E UP aga de oo med 20 Processing image volumes for 3D topography sse 20 T oadime the ania SS Vol mais adia tuted n a rants lede bitten tad 29 Interpolatins the image volume uc e Mt de ist o aR chai Aa 20 Fitting electrodes to image volume sse 20 Segmenting the skin in the image volume eeeeessssseeeeeeennneneeeenennns 20 CAN Ss ACC AA bes ome NAAN AA aa oM EN 30 Fitio electrodes TO SKIN Uan 30 Constructine cortical Urano dence 30 Description ol commands anna pac diripere aaa 31 Open image volume P e 3l Dave A SO AA Hed I 3l aye maso v0 POTE Ste a aa ete tenre mec ate tee en ones ard a aay een etre 31 OPTICA AA Mato ion aU 31 AN iia 3l DAVE SULLAG S ET RN E TO TU 3l Import i mare VOLUME a DA kA 31 Convert VOLUME iaa 33 Export image VON una 33 APO se omena NAAN DOU EE M M IM CMM EIU M DE 33 Porc 33 NS amne a DT AN am morer a AN 33 a MEAN ssa ia o ta dd De a A O a iene 34 Save SCOM ALON AA 34 SAO MALO AS RR RS RR RR RR RR RN RR 34 Dave See CME ALON S MH AMM AA 34 CPO GRC IRR T E 34 O NG DIKE
3. figure In the left part of the dialog the current image volume dimensions are presented To the right appear the new dimension values for editing iMagic PRO User Manual 42 Interpolate image volume Set igotropic 1 92 Columns x 192 251 Sii 251 ices Pr Dk 251 Rows 431 Cancel The Set isotropic button allows calculating automatically the new dimensions for achieving an isotropic image volume with a voxel size of 1 mm Resize volume This command allows resizing the active image volume When activated another submenu for selecting the desired operation Add or Remove appears In both cases another submenu is presented for selecting the dimension Columns Rows Slices to resize Immediately after a dialog is presented for specifying where field At to carry out the operation and how many field Quantity items columns rows or slices will be involved If the operation to carry out is Add then the Value field 1s enabled for specifying the value to set at the items Fix segmentations This command allows to carry out several operations for fixing altering segmentations When activated another submenu for selecting the desired operation is presented The operations implemented are described in the following OR This command makes a new segmentation by carrying out a logical OR between the current segmentation and another one given by the user When activated a standard Windows dialog is presented to
4. screen During this process it 1s possible to abort the movie generation by pressing the ESC key The Surface color control allows to set the rendering color of the surface By using the mouse the surface can be rotated zoomed in out and panned The surface can be rotated by pressing the left button and dragging in the desired direction For zooming in out the mouse wheel can be used Another way 1s by pressing simultaneously left and right buttons and moving at the same time the mouse in the vertical direction on screen The surface can be panned by pressing the right button and dragging in the desired direction iMagic PRO User Manual 24 Working with iMagic Once it has been initialized iMagic is ready to start the working session At the beginning of the working session no work sheets are present the work sheets will appear as soon as at least one image volume is loaded In the following several common procedures for working with iMagic are described in detail Loading image volumes The image volumes are loaded by means of the Open image volume if the image volumes are in iMagic format and the Import image volume for other formats commands Once loaded the image volume in the 2D View sheet the axial plane should appear in the superior left corner the coronal plane in the superior right corner and the sagittal plane in the inferior left corner as shown in the following figure This 1s the correct position and orientation
5. see Show Id Markers command Save markers Saves the active markers iMagic PRO User Manual 35 Save markers as This command saves the active markers giving the opportunity for selecting a new filename for them Open grid amp index This command loads a grid file see Appendix 4 and an index file 1f read see Appendix 6 for displaying over the image volume see commands Create grid and Create index When activated a standard Windows dialog for selecting the grid file to load 1s presented immediately after another dialog is presented for selecting an index file associated to that grid The grid becomes the active grid Once loaded the grid can be visualized over the image volume by means of the Show grid command see Show grid command If the index file reading is canceled then the whole grid will be displayed otherwise only the grid points belonging to the index will be visualized Save index as This command saves an index file see Appendix 6 associated to a surface It 1s enabled only when a surface 1s loaded and one or more vertices are marked see Set point matker The index file will contain the indexes corresponding to the vertices NOT marked When activated a standard Windows dialog for selecting the filename index file to save 1s presented Open Atlas This command loads an atlas file see Appendix 9 for displaying over the image volume When activated a standard Windows dialog for selecting the grid file t
6. Columns Rows Slices Slices Correct position and orientation for the image volume Rows If any of the slices fails to appear in the expected position and orientation the image volume must be transformed Before make any transformation to the image volume it is necessary FIRST to fix the image properties if needed The iMagic PRO User Manual 25 Properties command allows to inspect and fix any wrong value see Properties command Properties Filename Dimensions Vomel size Columns 1 8l Column Roms a T How Slices 1 al Slice Data type Byte Plane Axial The value for the Plane field in the dialog MUST match the orientation observed in the superior left corner of the 2D View sheet In that position the axial plane is expected but 1f not then the real plane observed in that position should be set in the Plane field of the Properties dialog The voxel size for each dimension can be fixed here too 1f needed Once the 1mage volume properties match the observed situation in the 2D View sheet the transformations if needed can be carried out All the transformations must be targeted to the slice displayed in the superior left corner of the 2D View sheet When the slice plotted in that position reaches the correct position and orientation axial plane nose up the other slices will have automatically the correct orientation and position too The first transformation to carry out 1f needed shoul
7. can be used for deleting the marker iMagic PRO User Manual 57 When used in the Surface View sheet pressing the left mouse button over or in a vertex vicinity will mark that vertex The range of that vicinity will be given by the Detection radius field in the Options command It is recommended to use the Hidden shading mode see Surface View sheet for a more precise location of the vertices coordinates for marking Set cloud markers This command sets a function for the left button mouse When it is active by pressing the left mouse button over one of the slices in the 2D View sheet or in the 3D View sheet a marker of cloud type 1s set Immediately after a dialog 1s presented for identifying the marker As long as the command remains active all the subsequent marked points will be considered belonging to the cloud identified by the first point The command is mutually exclusive with the Set orthogonal planes Set point marker Set curve markers Set fiducial markers and Measure distance commands When used the mouse cursor takes a pencil shape The right button mouse can be used for deleting any of the cloud points Set curve markers This command sets a function for the left button mouse When it 1s active by pressing the left mouse button over one of the slices in the 2D View sheet or in the 3D View sheet a marker of curve type is set Immediately after a dialog 1s presented for identifying the marker As long as the command remain
8. format 1111101 7 eene nnne 65 Appendix 3 1Magic markers format eene eene eene nnns 65 Appendix 4 Magic grid format oooooooonnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnonnnnnnnnccnnnnnnnnnnnnnnnnnnnanannss 66 Appendix 0 1MapiC index TOMMAL tert NA doe Bac ue GAAN esos i eus 66 Appendix 7 Plug ins specification in 1Magic ccccccccnnnnnnnnnnnnoonncnnnnnnnnnnnnnnononononononananonos 67 NIETO ue dot note obo dott tas RM Aen cL eer ee EP LEE Sed 67 DE Bg 67 ad AA ie 68 A ppendix S TMASICSUMHACETOEMAL AA ANGAS 69 A pbendix 9 1Masic atlas Omnia 69 Appendix 10 1Magie electrodes Format ia 70 Appendix 11 iMagic electrodes over surface Or Mat oooooooonnnnncncnnnnnnnnnnnnnnnnnnnnnnnnnnnnnno 70 Appendix 42 Magic normals loan aa 70 Appendix 13 iMagic INP Lormal 2 treten ied een Donee aree bas be oho deett ai 70 iMagic PRO User Manual 7 Introduction iMagic is a Windows MDI Multiple Document Interface software application for processing brain images Magic is able to process images in its own format see Appendix 1 as well as other image formats see Open image volume command The following figure shows the different elements of the application on screen 4 iMagic PR C MMGINORSINORS VOX Seles File Edit volume winda Ep zl OX MEDII a A ELS General zs jd dEn A e NA T H Ta pa id Cy eth Zoom 1
9. loaded are indicated 1n the status bar When pressing the left button of the mouse over any of the slices present in the sheet the active command Set orthogonal planes Set point marker Set cloud markers Set curve markers Set fiducial markers or Measure distance will be executed iMagic PRO User Manual 10 The segmentation toolbar is disabled in this sheet Manual Segmentation In this work sheet the manual segmentation is carried out through the commands Set thresholds for segmenting Edit segmentation Clip segmentation and Fill region In the sheet two images are displayed the current slice and its segmentation from left to right Only one of the orthogonal planes 1s available for segmentation and can be selected by using the Select plane for segmenting command at the segmentation toolbar The segmentation is plotted over the current slice to the left and as a binary image to the right When an image volume is loaded its associated segmentation is empty until segmentation is loaded or created When pressing the left button of the mouse over any of the slices present in the sheet the active command Edit segmentation Clip segmentation or Fill region will be executed iMagic PRO User Manual 11 In this sheet the commands Set orthogonal planes Set point marker Set cloud markers Set curve markers Set fiducial markers and Measure distance from the general toolbar are disabled The grid or atlas can be viewed over the sli
10. segmenting Save segmentation Load segmentation for plotting Set thresholds for segmenting Edit segmentation Clip segmentation Fill region Get statistics Restore slice segmentation from disk Delete slice segmentation Fill holes in slice Select segmentation iMagic PRO User Manual 9 dg Show hide segmentation Y Merge segmentation color Colo ER Change segmentation color Size 5 Change brush size for editing segmentation Shape Change shape for editing segmentation A detailed explanation of these commands will be given in the following chapters Work sheets iMagic has 4 work sheets 2D View Manual Segmentation 3D View and Surface View 2D View This work sheet visualizes the image volume in 3 orthogonal planes axial coronal and sagittal It is also possible to set different markers inside the image volume Once loaded the 1mage volume the axial plane should appear in the superior left corner the coronal plane in the superior right corner and the sagittal plane in the inferior left corner as shown in the figure If any of the slices fails to appear in the expected position and orientation the image volume must be transformed see Loading image volumes In each one of the visualized slices the orientation is indicated in the superior border where R indicates right L left A anterior and P posterior When the mouse is moved over the slices the value and voxel coordinates as well as atlas information 1f
11. select the segmentation file to or The result becomes the new active segmentation AND This command makes a new segmentation by carrying out a logical AND between the current segmentation and another one given by the user When activated a standard Windows dialog is presented to select the segmentation file to and The result becomes the new active segmentation Set This command allows setting a given binary value to selected voxels inside the segmentation When activated a dialog very similar to the dialog presented for the Set values command is presented for specifying the coordinates and value to set The checkbox Segmented when checked means that the value to set will mark the voxel as part of the segmentation and 0 in the other case With this iMagic PRO User Manual 43 command it is possible to set the value for a single voxel or subset of voxels inside the segmentation by setting intervals where the value will be set The result becomes the new active segmentation Delete This command clears the current segmentation all slices Dilate This command carries out a dilation by applying the morphological operator dilation to the voxels inside the segmentation With this operator every voxel belonging to the segmentation 1s dilated specifically if a voxel has at least one of their 26 neighbors belonging to the segmentation the voxel is retained in the segmentation When activated a dialog 1s presented for
12. the DEF file and at the end the plug in control parameters if specified in the DEF file A check box Show window is present also for setting the plug in window visibility during its execution works only for console applications The Load DEF and Save DEF buttons allow loading and saving respectively the definitions in DEF files With Run the plug in execution starts and with Cancel can be canceled The plug ins run in the background as independent threads thus the working session with iMagic is not interrupted Once finished the plug in execution the output image volumes generated by the plug in are loaded automatically by iMagic iMagic PRO User Manual 69 Appendix 8 iMagic surface format The iMagic surface format defines how the surfaces created with iMagic are stored The surfaces are stored in only one binary file with extension SRX The file has the following structure BYTES DATA TYPE DESCRIPTION 4 Integer 32 bits Number of vertices NV 4 Integer 32 bits Number of triangles NT NV 4 3 Float 32 bits X Y Z coordinates for all vertices NT 4 3 Integer 32 bits Sequence of three indices to constituting vertices of each triangle OPTIONAL FROM HERE 2 Integer 16 bits Number of triangles connected to vertex 0 NTC NTC 4 Integer 32 bits Indices to triangles connected to vertex 0 2 Integer 16 bits Number of triangles connected to vertex NV 1 NTC NTC 4 Integer 32 bits Indices to triangles connected to vertex NV 1 The
13. which will be considered segmented image for the active slice With the Set all slices button the range thresholds are applied not only to the active slice but also to the all slices in the active image volume Edit segmentation This command sets a function for the left button mouse When it 1s active by pressing the left mouse button over the slice in the Manual Segmentation sheet the voxel s pointed by the mouse cursor is selected for segmentation If the button pressed 1s the right one the voxel s are deselected The area covered by the command with a single click is determined by the Change brush size command and the shape of this area 1s determined by the command Change shape The command is mutually exclusive with the Set orthogonal planes Clip segmentation and Fill region commands When used the mouse cursor takes a pencil shape Clip segmentation This command sets a function for the left button mouse When it 1s active by pressing the left mouse button over the slice in the Manual Segmentation sheet it is possible to build a region of interest inside the active slice Every voxel marked is Joined to the previous one by line segments in red color The region 1s closed by pressing the right mouse button which will join the first marked voxel with the last one Once delimited the region the user should set a seed point inside one of the two regions the active slice has in that moment The region containing the iMagic PRO Use
14. 27 This last step produces a brain segmentation which contains the full brain tissue including white and gray matter This segmentation should be saved for allowing the gray matter segmentation and for its possible use in 3D brain renderings For obtaining the gray matter the Set thresholds for segmenting command is applied again over the entire image but in this case the thresholds are selected for identifying only the gray matter as shown in the following figure In order to clip the brain tissue the segmentation saved previously is joined with this one by means of the command Fix segmentations OR The result is shown in the following figure This segmentation can be saved then for representing the gray matter in the image volume iMagic PRO User Manual 28 Processing image volumes for electrical tomography The process for obtaining from image volumes all the elements needed for calculating and visualizing electrical tomography 1s divided in several steps that should be carried out in the following order Loading the image volume Scaling the image volume Interpolating the image volume Segmenting the image volume Fitting sphere Fitting electrodes to image volume Calculating grid and neighbors plns Sr a Loading the image volume See Loading image volumes Scaling the image volume In order to save space the image volume must be scaled to a byte 8 bits data type The command Scale image in the Volume menu should b
15. 59 163 119 79 151 119 86 151 119 96 151 119 106 161 119 106 178 119 124 171 119 129 158 119 126 141 119 101 128 119 94 96 119 Appendix 4 iMagic grid format The iMagic grid is stored in an ASCII file with XYZ extension The file will have as many lines as points in the grid Every line will have the point X Y and Z coordinate values separated by spaces Appendix 5 iMagic neighbors format The iMagic neighbors are stored in ASCII files with NEI extension The file will have as many lines as points in the grid Every line will have six values separated by spaces that are the neighbors for the point given by the ordinal line It means that the 1 line will have the neighbors for the 1 point of the grid and so on The six values have the following meaning value 1 indicates the neighbor for the point in the X decreasing direction value 2 indicates the neighbor for the point in the X increasing direction value 3 indicates the neighbor for the point in the Y decreasing direction value 4 indicates the neighbor for the point in the Y increasing direction value 5 indicates the neighbor for the point in the Z decreasing direction value 6 indicates the neighbor for the point in the Z increasing direction If there 1s not any neighbor in the given direction it will be indicated by a zero Appendix 6 iMagic index format The iMagic index is stored in an ASCII file with IND extension The file will
16. A An 57 Set curve markers C MM 57 Set fiducial markers m 57 Measure distance AA 58 Show markers c cccccsecssssecscssecsecsessessessesscsuesuesussvssessessessessessessesuesuesusaussestsseereesesseeses 58 Show grid 88 ettet ttt 58 Show Id markers H sse tette teret 59 Show fitted sphere as 59 Show atlas over image EE 50 Yoke windows D iet tette 50 Set zoom factor Change slices a EA AS 50 Change plane for segmenting Es cl 5 50 Save segmentation A 50 Load segmentation for plotting BE essere 50 Set orthogonal planes T E EE E E n 60 Set thresholds for segmenting D nnn 60 Edit segmentation O mira dia err e ne 60 Clip segmentation c 60 Fill region DR MM 61 Get statistics Bicis 61 Restore slice segmentation ULA NANANA ANAN 61 Delete slice segmentation ccccsuessecsucsucsussasssucsacsutssecsucsursaessecsucsatsaessussatsateateneesees 61 Fill holes in slice se ai Me 61 Select segmentation E fc ccccccssssssssctassssssuusasssssssuvassssssssesssssesenenessee 62 Show hide segmentation 62 Merge segmentation color Y O 62 Change color for segmenting End m 62 Change brush size p Is x 62 Change shape Shape o 62 PRIN CS ann dI NNNM RES ANAN NAA AAO 63 Appendix 1 Magic volume format esses nnne nennen nennen 63 Appendix 2 Magic segmentation
17. Close the iMagic application Copy Copies the contents of the active work sheet to the Windows clipboard If Surface View 1s the active work sheet the surface will be copied using the active DPI settings see Options command Copy to This command allows copying the content of the active work sheet to a Windows bitmap file When activated a dialog for selecting the name and format type BMP or JPG of the file appears If Surface View is the active work sheet the surface will be copied using the active DPI settings see Options command Options The DPI field can be edited for setting the dots per inch to achieve with the Copy commands see Copy and Copy to commands The Detection radius field can be edited to set the detection radius used for marking points in surfaces see Set point marker The Use 16 bit sign field checkbox allows to load by using Impor image volume or Open image volume when checked 16 bits integer images taking into account the sign The Load complement index in surfaces checkbox when checked marks as loaded the complementary indexes when the Open grid amp index command is used in surfaces The Talairach coordinates checkbox when checked enabled only for Talairach aligned studies allows to work in Talairach coordinates at the slice s selector commands in the toolbar iMagic PRO User Manual 27 Flip horizontal This command carries out a horizontal flip flip columns in the image volume The resul
18. N me mm Image plane Asia Slice size Thickness Data type Byte a D ata format Little endian Cancel The field Offset in file set the amount of bytes to skip at the beginning of the file The multiple files option 1s available only for DICOM format With this option it is possible also to load a DICOMDIR file DICOM directory for selecting from it the desired serie to import In this case a dialog showing all the series included in the DICOM directory 1s shown for selecting Select serie from PERFUSION Study description Serie description Special BrainPerfCT Adult Topogram 0 6 T s Special BrainPerfCT Adult Head5eg 4 8 H31s Special BrainPerfCT Adult DynMulti 12 0 H30s Cancel Special BrainPerfCT Adult Perfusion CT Color If the DICOM file s has a MOSAIC structure the slices are stored in a matricial way inside one logical slice and iMagic is unable to determine the MOSAIC definition a dialog is presented for getting from the user that definition number of columns and number of rows MOSAIC definition Slices per column rows 5 Slices per row columns 5 Lancel Output volume dimensions 64 x Bd 25 iMagic PRO User Manual 33 Convert multivolume This command allows the conversion of multivolume images In contrast to the Import image volume command which imports only single volume images and loads immediately the image volume this command convert the image volume to the iMa
19. a toggle When turned on plots in the 2D View and 3D View sheets over the slices or rendering the identification of the visible markers including electrodes in the 3D View sheet Show fitted sphere This command acts as a toggle When turned on plots in the 2D View sheet over the slices the fitted sphere according to the current sphere parameters see command Fit sphere Show atlas over image This command acts as a toggle When turned on plots in the 2D View sheet over the slices the atlas loaded see command Open atlas Yoke windows This command acts as a toggle and 1s enabled 1f there is more than one image volume or surfaces loaded When turned on every slice movement in the active volume will be carried out also in the other loaded volumes as well as any change in rotation position or size in the case of surfaces Set zoom factor l This command sets the zoom factor for displaying the image volume in the work sheets Change slices These commands change slices in every orthogonal plane With the X command the sagittal plane is changed the Y command the axial plane and the Z command the coronal plane In the Manual Segmentation sheet will appear enabled only the command attached to the selected plane for segmenting Change plane for segmenting aia y This command changes the plane for segmenting in the Manual Segmentation sheet Save segmentation ml This command saves the
20. active segmentation Load segmentation for plotting This command loads a segmentation file in iMagic format see Appendix 2 for plotting purposes It means that this segmentation can be used only as a reference iMagic PRO User Manual 60 over the image volume it cannot be edited or altered in any way When the command is activated a standard Window dialog for selecting the segmentation file to load is presented Once selected the file the segmentation is plotted in the Manual Segmentation sheet and another item besides the Active item corresponding to the current segmentation 1s added to the Select segmentation combo list The segmentation to load must match in dimensions with the active volume Set orthogonal planes ft This command sets a function for the left button mouse When it 1s active by pressing the left mouse button over the slice in the Manual Segmentation sheet the 3D coordinates pointed by the mouse are reflected in the other slices If the image volume is loaded twice the previous described operation can be appreciated more easily if the Yoke windows command is turned on The command is mutually exclusive with the Edit segmentation Clip segmentation and Fill region commands When used the mouse cursor takes a cross shape Set thresholds for segmenting Y Sets the thresholds for segmenting When activated a dialog is presented for setting then Min and Max parameters These parameters define the intensity range
21. ady presented montage in the current electrodes file Create surface This command creates a surface see Appendix 8 from the current segmentation When activated another submenu for selecting two different creation methods appears There are 2 possibilities create by deformation and create by tiling When the option for creating surfaces by deformation 1s selected another submenu is presented for selecting the surface resolution to create Very Low Res Low Res Medium Res and Hi Res These options create surfaces with 1280 5120 20480 and 81920 triangles respectively The deformation method create the surface by deformating a predefined sphere to the current segmentation The sphere 1s centered in the centroid segmentation and its radius adjusted to segmentation size The best results are achieved when the segmentation volume has a shape similar to a sphere The surface creation process is very fast and after completion a new child window 1s created with the recently created surface see Surface View sheet When the option for creating surfaces by tiling is selected a tiling method is applied to the segmentation to construct the surface Every voxel in the segmentation which has at least one of its six faces facing the background is processed Every face 1s tiled then with two triangles With this method even the most complex surfaces in detail can be created The process can be very time consuming depending on the size and com
22. an be very time consuming The figure below shows a surface of a outer white matter with 2 different number of triangles From left to right original surface 590 140 triangles and simplified surface 80 000 triangles iMagic PRO User Manual 54 Join This command allows to join several surface files into only one surface When activated a standard Windows dialog for selecting the surface files to join 1s presented The new resultant surface 1s loaded in another child window Expand This command allows to expand the current surface This procedure is very useful for constructing cortical surfaces see Constructing cortical surfaces With this procedure a white cortex surface can be expanded to match the gray cortex surface in the image volume When activated the following dialog 1s presented Set expanding parameters Segmentation mask ES Background threshold po Surface gap 0 75 With the Image volume edit box the image volume in iMagic format from where the current surface was created 1s set The Segmentation mask edit box 1s used for setting a segmentation indicating the expansion limits When going from white to gray this segmentation should indicate the outer border of the cortex can be a rough segmentation of the brain The box Background threshold indicates the upper limit between O and this number for considering a voxel in the image volume already set part of the background The Surface gap box indica
23. ange color for segmenting El With this command the color for plotting the segmentation selected can be changed Size 5 y Change brush size Bod With this command the brush size for segmenting with the Edit segmentation command can be changed Change shape 5 si With this command the shape for segmenting with the Edit segmentation command can be changed iMagic PRO User Manual 63 Appendixes Appendix 1 iMagic volume format The format is characterized by having 2 files one for storing the image volume itself and another one for storing the minimum information header for describing it with VOX and HDR extensions respectively The VOX file is a binary file the 2D slices are sequentially stored in an uncompressed way The HDR file 1s an ASCII file where every field text line in the file has the following information FIELD DESCRIPTION 1 Number of columns X for each 2D slice 2 Number of 2D slices Y 3 Number of rows Z for each 2D slice 4 Amount of bytes stored for voxel 5 Size in mm for each pixel 6 Slice thickness in mm for each 2D slice 7 Orthogonal stored plane axial 0 sagittal 1 and coronal 2 5 Skin threshold detection 9 Cortex threshold detection 10 Left Pre Auricular LPA point coordinates X Y Z 11 Right Pre Auricular RPA point coordinates X Y Z 12 Nasion coordinates X Y Z 13 Vertex coordinates X Y Z 14 Talairach system origin coordinates X Y Z 15 A
24. are reported The first line has the number of vertices and after that as many lines as vertices After the ordinal number the number of triangles connected to that vertex and immediately after the indexes of every triangle connected to that vertex Open segmentation This command loads a segmentation file in Magic format see Appendix 2 When activated a standard Window dialog for selecting the segmentation file to load is presented Once selected the file the segmentation 1s loaded in the manual Segmentation sheet and becomes the active segmentation The segmentation to load must match in dimensions with the active volume Save segmentation This command saves the active segmentation Save segmentation as This command saves the active segmentation giving the opportunity for selecting a new filename for it Save segmentation as image This command saves the active segmentation as an iMagic volume giving the opportunity for selecting a filename for it Open markers This command loads a markers file see Appendix 3 When activated a standard Windows dialog for selecting the markers file to load 1s presented Once loaded it is possible to visualize the markers from now on the active markers in the 2D View sheet The markers can be visualized depending on the status of the Show markers command see Show markers command The identification of the markers can be visualized depending on the status of the Show Id markers command
25. ce to the left if they are loaded When the mouse is moved over the slices the value and voxel coordinates as well as atlas information 1f loaded are indicated in the status bar 3D View In this work sheet the 1mage volume can be visualized in 3D To the left of the work sheet a dialog for setting different parameters for 3D viewing 1s shown When a new study 1s loaded the sheet appears empty in order to produce a 3D rendering the Render button in the dialog must be pressed The rendered image can be zoomed by using the Set zoom factor command When the mouse is moved over the rendered image the voxel coordinates as well as atlas information 1f loaded are 1ndicated 1n the status bar iMagic PRO User Manual 4 iMagic PRO E ANALYZE DICOMFILES YO O VOX E MNALYZEWDICOMFILESWOWOB 5 EX E File Edit volume Window Help c A 6411 wv MK Plane Calor Size 2D View Manual Segmentation 3D View Box Lut Light Movie Rotation General Visibility Thresholds amp Colors Skin EO Segmentation 120 E I Use segmentation o Smooth Electrodes Color EG w Precise rendering buga v 149 Z 103 The sheets composing the 3D parameters dialog are described next Rotation In this sheet the rotation angles for the 3D rendering are set Rotation iMagic PRO User Manual 13 There are two ways for setting the angles by directly editing the desired value in the boxes existent fo
26. d be the plane rebuilding see Rebuild plane command After that and depending of the resulting position and orientation obtained the Flip horizontal Flip vertical Flip slices and Transpose slices commands could be used The final goal to reach is to place the image volume in the correct position and orientation as shown in the figure Segmenting image volumes iMagic allows the segmentation of the image volumes in the Manual Segmentation sheet The segmentation itself can be carried out by means of the Set thresholds for segmenting command which binarizes the image volume depending of the parameters used or interactively by means of the Edit segmentation Clip segmentation and Fill region commands A typical segmentation of grey matter begins by applying convenient thresholds by means of the command Set thresholds for segmenting for delimiting brain tissue from background and cerebro spinal fluid as shown in the following figure iMagic PRO User Manual 26 With the command Clip segmentation it is possible to isolate brain tissue from the outer tissues In the following figure to the left the region of interest 1n red color obtained by the Clip segmentation command is shown To the right the segmentation obtained by placing the cursor inside the region The same process is carried out using the Clip segmentation command for removing the cerebellum and brain stem as shown in the following figure iMagic PRO User Manual
27. e used for that see Scale image command After scaled the resulting image volume must be saved in iMagic format using the command Save image volume as Interpolating the image volume The electrical tomography processing requires that the image volume must be isotropic it means the same size in every dimension preferably to 1 mm The command Interpolate image volume in the Volume menu should be used if needed for that see Interpolate image volume command After interpolated the resulting image volume must be saved in iMagic format using the command Save image volume for overwriting the previous image volume and keeping the same filename Segmenting the image volume The electrical tomography calculation and visualization requires two different segmentations one describing brain tissue without scalp skull and cerebellum and another one describing gray matter inside the brain The procedure for obtaining such segmentations is already explained in Segmenting image volumes The segmentations should be saved with the command Save segmentation as Fitting sphere See Fit sphere command After obtaining the desired fit use the Save INF button in the dialog s Fit sphere command for saving the sphere parameters for its use in the calculation of the electrical tomography iMagic PRO User Manual 20 Fitting electrodes to image volume See Create electrodes command After obtaining the desired fit use the Save button in the dialog s Cr
28. e when the current study is an image volume By pressing the All slices button the same statistic values are displayer for all slices When the current study is a surface the dialog shows the surface area The Save button allows to save the values to an ASCII file Restore slice segmentation This command restores the previous segmentation on disk corresponding to the active slice Delete slice segmentation This command deletes the segmentation corresponding to the active slice Fill holes in slice This command fills holes inside the active slice segmentation All the voxels not belonging to the slice segmentation but completely surrounded in a 8 neighborhood by segmented voxels are set as part of the segmentation The result becomes the new active segmentation iMagic PRO User Manual 62 Select segmentation Active v This command selects the segmentation to be used with the commands Show hide segmentation Merge segmentation color and Change color for segmenting Show hide segmentation This command acts as a toggle When turned on plots the segmentation selected in the Manual Segmentation sheet over the active slice Merge segmentation color Y This command acts as a toggle When turned on plots the segmentation selected merged with the image intensity in the Manual Segmentation sheet over the active slice In this way the anatomic details present in the active slice could be better visualized Ch
29. eate electrodes command for saving the electrodes to a file for its use in the calculation of the electrical tomography Calculating grid and neighbors See Create grid command Before using the command the segmentation created for gray matter must be loaded with the Open segmentation command This segmentation will be used for creating the grid and neighbors by means of the checkbox Use segmentation in the dialog s Create grid command The checkbox Calculate neighbors must be checked too for creating the neighbors Processing image volumes for 3D topography The process for obtaining from image volumes all the elements needed for visualizing 3D topography is divided in several steps that should be carried out in the following order Loading the image volume Interpolating the image volume Fitting electrodes to image volume Segmenting the skin in the image volume Creating skin surface Fitting electrodes to skin surface e DR a Loading the image volume See Loading image volumes Interpolating the image volume The 3D topgraphy 1s better visualized 1f the image volume from where the surface will be created 1s 1sotropic 1t means the same size in every dimension The command Interpolate image volume in the Volume menu should be used if needed for that see Interpolate image volume command Fitting electrodes to image volume See Create electrodes command After obtaining the desired fit use the Save button in the dialog s Crea
30. egmentation format The format is characterized by having 2 files also one to store the segmentation volume itself and another one for storing the minimum information for describing it with VOX and HDR extensions respectively The SEG file is a binary file the 2D slices are sequentially stored in an uncompressed way The HDR file is an ASCII file where every field text line in the file has the following information FIELD DESCRIPTION Number of columns X for each 2D slice 2 Number of 2D slices segmented 3 Number of rows Z for each 2D slice After that in the file will appear as many lines as indicated in the 2 field where every line indicates the slice segmented an ordinal starting with zero relative to the first slice in the image volume associated with the segmentation file Appendix 3 iMagic markers format The iMagic markers are stored in ASCII files with MRK extension Every marker in the file will have the following information per line Marker type Point Cloud or Curve Marker Identifier Identifier given by user Number of points in the marker lt XYZ gt lt X Y Z gt point coordinates for every point in the marker The markers will appear in the file in the same order they were inserted Ex Point p l 95 110 104 Cloud n 9 63 110 194 80 110 199 75 110 182 53 110 177 60 110 172 iMagic PRO User Manual 66 80 110 172 88 110 202 90 110 187 70 110 164 Curve C 11
31. er them with the left button mouse With these two cursors it is possible to know the amount of voxels for a given value in the horizontal axis The boxes Cursor 1 and Cursor 2 show first the image value corresponding to the current cursor position and separated by the amount of voxels for that value When the checkbox Log is checked the histogram is shown with a logarithmic transformation applied When the checkbox Preview is checked the slices in the 2D View and Manual Segmentation sheets are scaled according to the current cursor s values The Expand button recalculates and plots the histogram over the range defined by the current cursor s values The Default button calculates and plots the histogram over the entire image range The Scale button scales see Scale image command the image volume the output data type will be Byte according to the current cursor s values and closes the dialog Swap bytes This command swaps the byte order little endian big endian for every voxel of the active image volume The command is enabled if the active image volume has more than 1 byte per voxel Set values This command allows setting a given value to selected voxels When activated a dialog is presented for specifying the coordinates and value to set as shown in the figure With this command it 1s possible to set a value for a single voxel or subset of voxels inside the image volume by setting intervals where the value will be set iMagic PRO U
32. ers checkbox is checked the animation depending on the Movie type will start from the active values of the 3D parameters already set Rotation Light BoxCut etc The Movie type combo select the movie type These are the types available iMagic PRO User Manual 18 Spins Cortex visibility User defined This type of animation generates rotations of the image volume around one of the 3 possible axes When selected the edit box Step is presented As many frames as needed will be generated to complete a full rotation of 360 around the selected axis using the step selected This movie type generates views of the image volume with increasing or decreasing visibility of the image volume see Visibility sheet When selected the edit boxes Step From and To are presented As many frames as needed will be generated taking into account the parameters set This type of animation generates animations defined by the user When selected a dialog is presented for loading the file that contains the animation definition These files have extension MUS Once loaded the filename 1s shown in the User file box Format of the MUS files The MUS files are ASCII files and will have as many lines as frames in the animation Each line has the following format AX AY AZ YV AppC XPC YPC ZPC XSC YSC ZSC XL YL ZL IR where AX AY AZ YV AppC XPC YPC ZPC XSC YSC ZSC XL YL ZL Rotation angle on the axis X Rotation angle
33. eview The segmented structures will be visible at vertical values above the selected level Y coordinate The figure above right shows a 3D rendering with a brain segmentation loaded and a visibility limit set BoxCut This sheet sets the parameters for cutting out a cubic box from the image volume Box Cut W Apply BoxCut Position Size Ex ce e m ar 4 JE per Jm E m gt Ars iMagic PRO User Manual 16 Activating the Apply BoxCut checkbox makes possible to see into the interior of the image volume The controls on the sheet set the position and size of the cube to extract The preview showing a model human head shows approximately the position and size of the boxcut in the image volume The figure above right shows a 3D rendering with a boxcut applied Light This sheet sets the illumination parameters for the 3D rendering There are three parameters for controlling the rendering illumination position of the light light intensity and amount of reflection Light Na zn Position Ce p H Ped Labi z Jl no E uE E 2 cm Intensity 10 50 Default Reflection 1 The position of the light indicated through the coordinates X Y Z can be set by directly editing the values for each coordinate or by pressing the 6 buttons that increase or decrease the coordinate for each axis in steps of 1 The default initial iMagic PRO User Manual 17 position of the light is 0 0 1 meaning that the li
34. ght points to the front of the head The intensity 1s a real value between 0 0 and 1 0 The rendering process combines this coefficient with other factors to achieve the depth effect An intensity coefficient of 0 0 ignores the incident light whereas an intensity coefficient of 1 0 ignores all other factors The default initial value is of 0 5 The reflection coefficient 1s an integer value between 1 and 10 that controls the amount of reflection of light from the 3D surface Higher values cause highlights and give a metallic appearance to the surface The Default button allows restoring the implicit values for each parameter In the preview of the sheet the result of applying the active values for each parameter 1s shown with a model human head The default illumination parameters lead to reasonable renderings In general the light parameters should be changed only if some unusual illumination effect 1s searched The figures above show several 3D renderings with different light parameters set Movie This sheet sets the parameters for carrying out a 3D animation The resulting animation is stored in standard AVI Windows format Movie Use current parameters Movie type Spins once around axis Y Step 5 Render When the Generate movie checkbox is checked a 3D animation will be generated instead of a single view when pressing the Render button Otherwise the remaining controls will be disabled When the Use current paramet
35. gic format and saves the converted volumes on disk When activated another submenu allows to select the format for converting from ANALYZE or DICOM If the format selected is ANALYZE a standard Windows dialog is presented for selecting the ANALYZE multivolume file If the format selected 1s DICOM a dialog for selecting the directory where the DICOM files are 1s presented This directory must contain only the DICOM files to convert In both cases after the conversion is done a window reporting the filenames generated in iMagic format is presented to the user If the DICOM file s has a MOSAIC structure the slices are stored in a matricial way inside one logical slice and Magic is unable to determine the MOSAIC definition a dialog 1s presented for getting from the user that definition number of columns and number of rows Export image volume This command allows exporting to ANALYZE format When activated another submenu allows to select if the operation will be carried out for the current volume or multiple volumes When selecting the current volume option a dialog for selecting the ANALYZE filename for the current volume appears In the other case a dialog for selecting multiple image volumes in iMagic format is presented The volumes exported will have the same filename but with a letter A appended at the beginning of the filename At the end a window reporting the filenames generated in ANALYZE format is presented to the user Im
36. have a value per line This value indicates the ordinal starting with 1 of the point indexed in the grid file XYZ iMagic PRO User Manual 67 Appendix 7 Plug ins specification in iMagic To install a plug in for Magic at least 3 files must be copied to the Plug Ins directory already created by the installer in the path where the iMagic software was installed The 3 files are plug in filename INI initialization file any filename gt DEF definition file plug in filename gt EXE plug in executable program More files for internal use can be stored and used for the plug in but these 3 files must be present for controlling the plug in execution The INI file allows to include the plug in iMagic the DEF file define the parameters that could be used for the plug in these parameters are presented to the user by means of dialog before executing the plug in The EXE file the plug in receive in the command line when executed by iMagic the DEF file once edited by the user INI file This 1s an INI Windows standard file Below the section 1Magic the following keys must appear Command DEFName Message Command string indicating the plug in name in the Magic menu DEFName indicates the DEF filename without extension Message string to be shown by Magic while executing the plug in Ex INI file iMagic Command Scaling DEFName Scaldef Message Scaling image DEF file This file is an INI Windo
37. hbors is set a neighbors file will be created also This neighbor s file see Appendix 5 is used also in the calculation of the electrical tomography When the Ok button is pressed a standard Windows dialog for selecting the filenames to create grid and neighbors file if selected is presented For displaying the grid already created over the image volume the Open grid amp index command should be used Create index This command creates an index file see Appendix 6 for the active grid according to the active segmentation The index will contain the references to the erid points inside the grid that belong to the active segmentation When activated a standard Windows dialog for selecting the index filename to create is presented This command is enabled only if there is an active grid a loaded grid Create electrodes This command creates an electrodes file see Appendix 10 When activated another submenu for selecting from where to create electrodes appears There are 3 possibilities create from standard montages create from Polhemus data and create from SFP files When the option for creating electrodes from standard montages is selected a check 1s made for the presence of the fiducial markers Nasion LPA RPA Vertex iMagic PRO User Manual 50 and Inion see Appendix 1 If any of these markers 1s missing it s not possible to create the electrodes file and the user must to set the missing fiducial marker see Set fiducial ma
38. i COORD PU NONA E EET 34 DANG NAIC TA O OPA Un a e o on 35 doo AA CA AA 35 SALA REPE 35 Open ADS NERO T UU TM 35 Iii AA AA 35 RSS KO AA 33 OS Gioco istituti A AA 36 dii M 36 PPX E saa eauteseaseueesaeescatesavesdoacquseseaseueessaetescadesavesdoe auseseasaueesoaeescatesavesdaacauscseasauecte 36 ea 36 COD m Y X nase 36 A RR O RUDE CR RR NERD RD 36 EH NON On Llanta seers 37 ERRO VORA AA 37 NANA AA 38 TransDOSO S HUBS AKOA NADAAN APA AA 38 KA AG 39 CAIC A A Aa Aka 39 A e o Un E 39 NO In A 40 DEL TII PTATEM 40 PRE AA 41 Iter POlate AMA Ce V OUIMNG a o elec 4 ESTEVO MMS oro 42 BANNA NITE 42 Do AAA A e e 5 E A 49 s IND T 49 C rc ape en AA 49 Ee E 5 10 6 ida 52 Ae UM AA A adeniotemnesbiees 52 A y m uum 53 SAL RP ue 53 SII t 53 ro 54 EXP M 54 PN AG AA UN rd da Oda UM AA AA 22 ena NAA 55 CE INO e MISI E 56 Open no inca EsG aaa 56 Set contrast El 56 Show cursors in orthogonal planes den O 56 Set orthogonal planes RN 56 Set point marker A ada 56 Set cloud markers 2 NEE N
39. iMagic PRO Version 2 0 asie Ly Ko p gt MENS LI bz ey User Manual WYNEURONIC s A 2007 DISCLAIMER The iMagic software is designed for use in medical research it has not the status of a medical product 1 e it 1s not allowed to use it directly or indirectly for medical prevention diagnostic and or treatment of humans It is solely for academic use in the field of scientific research NEURONIC S A does not grant warranty or assume liability for the results of using the software The content of this document is the intellectual property of NEURONIC 5 A and is subject to change without specific notification NEURONIC S A does not grant warranty or assume liability for the correctness of individual statements herein Nor does NEURONIC S A enter into any obligation with regard to this document Any trademarks mentioned in this document are the protected property of their rightful owners Index Mtro PIDE 7 Elements or the general todabia aiii Aaahh 8 Elements of the segmentation toolbar unica KAG BANANA BUKANA 8 WO SNC asas Cea DD LL 9 DIN cl 9 Mantal Se Sme ntablOB aaa 10 SPI TD rr 11 Sire m AT A M 19 Working WAL EN IA IO anistia a E Pigaan 24 Ba a mace VO UMES xt site css io AOS Anette a nana UE 24 beement ns Imate VOLUMES csi oa arca 25 Processing image volumes for electrical tomography
40. mand where the cursor is placed in the Commands in movie list The 1 Y buttons move up and down in the list the active command respectively The zl button shows the dialog for editing the active command parameters When the Ok button is pressed the user animation definition is saved in the MUX file Once the movie type and its parameters are already defined the Ok button can be pressed for editing the movie filename The Cancel button aborts the movie creation After selecting the movie filename the following dialog is presented Video Compression Compressor Cinepak Codec by Radius Cancel Compression Quality 100 ad Configure About Key Frame Every frames Data Rate EB sec iMagic PRO User Manual 23 In this dialog a compressor codec for generating the movie 1s selected The Compressor combo box lists all the codecs installed in the system Depending on the codec selected additional parameters can be set Depending on the codec characteristics and requirements the movie 1s generated with more or less quality iMagic is not responsible for the performance of the codecs listed Sometimes 1s not possible by unknown reasons to create the movie when using some codecs The Full Frames Uncompressed codec always works and give optimal results from the quality point of view but the movies generated got a lot of space on disk Once the compressor is selected the movie generation begins frame by frame on
41. me for the second receiver The markers will come at the end of the file in the following order Nasion Nose LPA and RPA Once the file has been loaded iMagic will calculate automatically the best fit for the Polhemus measurements over the skin image volume Immediately after an standard Windows dialog 1s presented for selecting the filename for saving the ELE file When the option for creating electrodes from SFP files 1s selected a check 1s made for the presence of the fiducial markers Nasion LPA and RPA see Appendix 1 iMagic PRO User Manual 92 If any of these markers is missing it won t be possible to create the electrodes file and the user will have to set the missing fiducial marker see Set fiducial markers command After the check is made a standard Windows dialog is presented for loading the SFP file iMagic expects the markers in the first 3 lines of the file in this order Nasion LPA and RPA Once the file has been loaded iMagic will calculate automatically the best fit for the SFP file over the skin image volume Immediately after an standard Windows dialog is presented for selecting the filename for saving the ELE file Edit electrodes With this command it 1s possible to edit electrodes created by the previous command When activated the same dialog used for creating electrodes see Create electrodes is presented The only one difference 1s that the Electrode montages group is disabled It is possible only to fix the alre
42. ntation checkbox is checked then the ray casting continues until reaching a voxel who belongs to the segmentation loaded and meets the Segmentation threshold condition if the slice where that voxel belongs is visible see Visibility sheet If the slice is not visible then the segmentation is ignored and the ray casting process only uses the Skin criteria for getting the voxel When the checkbox Show Electrodes is checked the electrodes are rendered also as part of the final 3D rendering It s enabled when an electrode file 1s loaded see Open electrodes command The Electrodes Color control allow to set a color for the rendered electrodes The figure above right shows a 3D rendering including the electrodes When the Smooth checkbox is checked a smoothed volume image is used for the rendering The Precise rendering checkbox allow to get a better but slower rendering iMagic PRO User Manual 15 Visibility This sheet allow to set the visibility level for the 3D rendering Visibility Skin visible un 143 The Skin visible until checkbox allows to set the slices which will be rendered by using only the Skin threshold in the ray casting process With this parameter it 1s possible to reduce the rendering time by inhibiting the rendering in the part of the head that does not correspond to the segmented structures With the left mouse button it 1s possible to set the visibility level by pressing over the rendered image shown in the pr
43. o load is presented The atlas structure can be visualized in the 2D View and Manual Segmentation work sheets depending on the status of the Show Atlas command see command Show Atlas and the atlas information about the structures 1s always presented at the status bar Open electrodes This command loads an electrodes file see Appendix 10 for displaying over the 3D image volume renderings See in 3D View work sheet General sheet When activated a standard Windows dialog for selecting the electrodes file to load 1s presented Save electrodes as This command saves the active electrodes giving the opportunity for selecting a new filename for them The command is enabled when an electrodes file has been loaded or created see Create electrodes and Set fiducial markers commands iMagic PRO User Manual 36 Properties When the active study has an image volume this command shows a dialog with the characteristics of the image volume The fields related to the voxel size Column Row and Slice and the stored image volume plane can be edited in order to fix any incongruence of the image volume see Loading image volumes The other fields are shown only for informative purpose When the active study has a surface this command shows a dialog with the characteristics of the surface The fields are shown only for informative purpose and are self descriptive Close Close the child window associated to the active volume or surface Exit
44. on the axis Y Rotation angle on the axis Z Coordinate Y for visibility 1 if Box Cut is carried out O 1f not X coordinate for positioning the Box Cut Y coordinate for positioning the Box Cut Z coordinate for positioning the Box Cut Size in X axis of the Box Cut Size in Y axis of the Box Cut Size in Z axis of the Box Cut X coordinate for positioning the light Y coordinate for positioning the light Z coordinate for positioning the light iMagic PRO User Manual 19 Intensity coefficient of the light R Reflection coefficient of the light Once the Render button is pressed a dialog window requests a filename for the animation that will be generated in A VI format During the animation the number of frames rendered can be monitored in the progress window shown In this window if the Cancel button is pressed the user can save the frames generated until that moment The animation can be played with any multimedia player supporting the A VI format Surface View This work sheet is visible only when a surface has been loaded see Open surface command or created see Create surface command 32 iMagic PRO EVAMALYZEMDICOMF ILESYY OW Y OGO 753 5RX Surface Window Help Shading mode Smooth m 4 Q Qs Surface calor OH ll Y 191 44 z 125 60 To the left of the work sheet a dialog for setting different parameters for surface viewing is shown The control in the top position allows to set rotation angles in 5 inc
45. or out depending on the option selected of the surface loaded When selected the field Frames is presented The Frames edit box sets the number of frames to generate in the movie The zooming carried out in every frame is fixed by the system and 1s similar to the zooming effect carried out by the Zoom in out commands This movie type generates animations defined by the user This animation type 1s made of a combination of the other movie types The definition of this movie type is stored in MUX files which can be created edited through the Edit command shown in the dialog when this movie type is selected When the Edit button is pressed the user is prompted to open an already existent MUX file for editing If a non existent filename is given a new MUX file will be created Immediately after the following dialog 1s presented iMagic PRO User Manual 22 Edit E tanalyze DICOMfiles Vyo de MUX Available commands Commands in move Spins around s opins around 4 180 2 Spins around Y gt x Es al 2 Cancel Spins around z The left side shows a list box with the available commands Using the gt button commands can be added to the Commands in movie list The commands are added to the end of the list Every time a command is added a dialog 1s presented for setting parameters related to the command The parameters for Spins and Zoom commands were already explained before The x button deletes the active command com
46. out over the white matter first see Segmenting image volumes This segmentation should be carefully carried out and revised for guarantiyng the expected results for ex ventricles filled etc The options Fill holes and Region growing from Fix segmentations should be used in order to validate the white matter segmentation After the segmentation step execute the command Create surface using the option by tiling in order to achieve better results This option should generate a huge amount of triangles that s why is highly recommended to simplify the surface obtained by using the Simplify command Inmediately after the command Expand see Expand command must be executed for getting the final gray cortical surface iMagic PRO User Manual 3 Description of commands Open image volume This command loads the image volume in iMagic format to process When activated a dialog for selecting the desired volume appears Once loaded the volume appears in the 2D View and Manual Segmentation work sheets and becomes the active volume iMagic will try to place the volume in the correct position and orientation in the 2D View sheet according to the information specified in its header see Loading image volumes After the image volume is loaded the Volume item in the horizontal menu is enabled the Surface item is only enabled when loading surfaces Save image volume With this command the active volume is saved in iMagic format see Appendix 1
47. plexity of the segmentation The progress of the creation process can be monitored with progress windows during the two phases of the process creation and optimization When the option is invoked the user 1s prompted to remove peaks in the surface Peaks are defined as sequences of voxels connected to one another by opposite faces After completion of the creation a new child window is created with the recently created surface see Surface View sheet The surfaces created with this method have a brick appearance thus they should be smoothed with the Smooth command iMagic PRO User Manual 53 Plug ins Shows a menu with the plug ins installed for iMagic see Appendix 7 The command is disabled 1f there is not any plug ins installed Smooth This command carries out a smoothing of the active surface When activated a standard Windows dialog for selecting the smooth factor to use is presented The smoothed surface is loaded in another child window The figure below shows a surface of a skin head with different smooth factors From left to right original surface smoothed 2 times and smoothed 10 times Simplify This command carries out a simplification reduction of the number of triangles of the active surface When activated a standard Windows dialog for selecting the new number of triangles to use is presented The simplified surface is loaded in another child window Depending on the amount of triangles to reduce this operation c
48. port segmentation This command imports segmentations in Brain Voyager format When activated a standard Window dialog for selecting the file to import 1s presented Import surface This command allows loading surfaces in other surface formats When activated a standard Windows dialog is presented for selecting the file to import and from which format iMagic imports STL VTK and Brain Voyager SRF files formats Once loaded the surface appears in the Surface View work sheet and becomes the active surface Export surface This command allows exporting to other surface formats When activated a standard Windows dialog is presented for selecting the filename to export and to which format iMagic exports to STL ASCII and binary and ASCII files When exporting to ASCII the output file will have the following structure The first line will have the number of vertices in the surface After that as many lines as iMagic PRO User Manual 34 vertices in the surface will come Every line will have an order number indicating the vertex index as well as the x y z coordinates After the vertices section the triangles section appears with a similar structure First the number of triangles and after as many lines as triangles In this case instead of coordinates the 3 vertices indexes for every triangle will come after the ordinal number for every line Finally the connection section appears In this section the triangles connected to every vertex
49. r Manual 61 seed point will be considered segmented and the other one will be clipped from the segmentation The command is mutually exclusive with the Set orthogonal planes Edit segmentation and Fill region commands When used the mouse cursor takes a pencil shape Fill region This command sets a function for the left button mouse When it 1s active by pressing the left mouse button over the slice in the Manual Segmentation sheet it is possible to build a region of interest inside the active slice Every voxel marked is Joined to the previous one by line segments in red color The region 1s closed by pressing the right mouse button which will join the first marked voxel with the last one Once delimited the region the user should set a seed point inside one of the two regions the active slice has in that moment The region containing the seed point will become segmented The command is mutually exclusive with the Set orthogonal planes Edit segmentation and Clip segmentation commands When used the mouse cursor takes a pencil shape If instead of the left button mouse the right button is pressed over the slice in the Manual Segmentation sheet an automatic filling region only over the active slice 1s carried out without need for a previous region drawing Get statistics This command shows a dialog with some statistics number of voxels area volume mean and standard deviation about the active segmentation in the active slic
50. r each angle or by means of the 6 buttons which can increase or decrease the rotation angle in steps of 5 A preview in the sheet shows the results of applying the active values of the angles for each axis using a model human head When the rotation angles are 0 the head looks directly at the observer The following figures show different 3D renderings the captions show the angle s value for every axis in order to obtain that particular position X 0 Y 0 Z 0 X 90 Y 180 Z 0 X 0 Y 180 Z 0 X 30 Y 30 Z 0 iMagic PRO User Manual 14 General In this sheet different parameters for the 3D rendering are set The 3D rendering 1s obtained by using a volume rendering approach ray casting through the use of thresholds for detecting the desired tissue or structure inside the volume image General Threshalds amp Colors Skin 60 H El Segmentation 120 C W Uze segmentation w Show Electrodes W Smooth Electrodes Calor We Precise rendering The group Thresholds amp Colors allow to set the detection thresholds and rendering colors in the anatomical image for the skin and segmented tissue These values can be changed using the controls available The Skin threshold is used for detecting the most external structure inside the volume image During the ray casting process from the observer to the volume image the first voxel meeting the Skin threshold condition is retained in the final rendered image If the Use Segme
51. rements around the 3 axes When the mouse is moved over the surface the current coordinates of the surface where the mouse is placed are indicated in the status bar iMagic PRO User Manual 20 The combo box Shading mode allows to select the shading mode Examples of the available modes are shown in the following figure From top to bottom and left to right the modes Smooth Flat Hidden and Wireframe are shown The A button resets the data loaded in the active window to the default position data looking to the user and size The a a buttons zooms in and out respectively the surface With the button a movie can be generated The resulting animation is stored in standard Windows format AVI When activated the following dialog is presented iMagic PRO User Manual Create movie FPS 15 p 21 EZ Movie type Spins around Y axis Cancel Frames 180 p zl Deg t 2 The FPS edit box sets the Frames per second ratio to be used in the movie The Movie type combo box allows the selection of different movie types Spins around axis Zoom in out User defined This movie type generates rotations of the surface loaded around one of the 3 possible axes When selected the fields Frames and Deg f degrees per frame are presented The Frames edit box sets the number of frames to generate in the movie The Deg f edit box sets the degrees to rotate 1n every frame This movie type generates zooms in
52. rkers command After the check is made the following dialog is presented Create electrodes Electrode montages 13 ch 10 20 32 ch BESA 64 ch Quik Cap 4 ch BrainCap 128 ch ElectroCap 128 ch Biosemi 128 ch GSH 4 ch BrainCap Bb ch Brainbap 128 ch Quik Cap x A x A x A x m x Over sphere The group Electrode montages has several predefined standard montages for selecting the closest to the user s needs The checkbox On Scalp when checked fits the electrodes directly over the subject s scalp When the checkbox Over sphere is checked the electrodes are created over the best fit sphere see Fit sphere command given by the INF file The INF file is specified with edit box INF file Once the electrode montage and INF file 1s set 1f creating over sphere the Automatic Fit button can be pressed to fit automatically the selected montage over the image volume or sphere After the fit the dialog 1s expanded and enables and shows other elements iMagic PRO User Manual 51 Create electrodes View Electrode montages lfset xp TED 18 ch 10 20 ent P d 32 ch BESA Offset 20 al m p C Right 64 ch Quik Cap Offset zo 74 ch BrainCap C Front 128 ch ElectraCap Angle H 6 2680 C Back 128 ch Biosemi Angle Y 0 0000 l 128 ch GSN a A iw Show ld 0 0000 24 ch BrainCap Ang s 5B ch BrainCap iw Un Scalp 128 ch Quik Cap ry z m z m a Ng m Over sphere No
53. s active all the subsequent marked points will be considered belonging to the curve identified by the first point Every marked point will be joined with the anterior one by line segments in red color The curve will be considered finished when a new slice or plane be selected or another command 1s executed The command 1s mutually exclusive with the Set orthogonal planes Set point marker Set cloud marker Set fiducial markers and Measure distance commands When used the mouse cursor takes a pencil shape The right button mouse can be used for deleting any of the curve points Set fiducial markers This command sets a function for the left button mouse When it 1s active by pressing the left mouse button over one of the slices in the 2D View sheet a dialog for selecting the fiducial marker to be set 1s presented When activated from the 3D View sheet another possible element 1s added to the list of fiducial markers in this case Electrodes iMagic PRO User Manual 58 Set fiducial markers Fiducial markers Ok ps C Left Pre amp uricular Cancel t Right Pre amp uricular C Vertex t nion f Anterior Commisure Hose Base When adding electrodes another dialog is presented to the user for setting the electrode identifier Changing an electrode position is done just by adding again the same electrode identifier in this case the old position is removed It is possible also to remove completely a fiducial marker incl
54. s lo 30 Y E 2 Plane C Size Shape Segmentation toolbar Work sheets NIT Status bar milal lol 1106 In the application title the active image volume filename will be shown as well as the segmentation filename loaded if any In the general toolbar are located buttons for the most frequently used commands The segmentation toolbar shows has commands used in the manual segmentation The status bar shows the coordinates in the Magic space coordinates corresponding to the current cursor application the image value for that point the image space coordinates in Talairach space 1f the loaded study 1s aligned in that space as well as the atlas anatomical information if loaded By pressing the right button mouse over the status bar in the image coordinates areas a window with the coordinate system used Magic or Talairach 1s shown iMagic PRO User Manual Elements of the general toolbar Zoom 1a xf oS Open volume Set contrast in volume Show cursors in orthogonal planes Set orthogonal planes Set point marker Set cloud marker Set curve marker Set fiducial markers Measure distance Show markers Show grid Show markers identifiers Show fitted sphere Show Atlas over image Yoke windows Set zoom factor Select slice in orthogonal planes Elements of the segmentation toolbar Plane Axial z Lap gm d sea eg x 5 Active Select plane for
55. ser Manual 4 54 fram 100 to 120 Y from po to 5 Cancel Z from 3 to 45 Value o Fit sphere This command set the sphere parameters for fitting that sphere to the brain cortex When activated a dialog 1s presented for specifying the sphere center coordinates and radius The dialog allows to save and load also those parameters in from an INF file see Appendix 13 for its use in the calculation of the 3 spheres volume conductor model for the electrical tomography see Processing image volumes for electrical tomography When the dialog appears automatically the Show fitted sphere option see Show fitted sphere is turned on and thus it is possible to fit the sphere interactively by moving the parameters values The sphere should fit as tight as possible the border of the cerebral cortex This requirement can be checked by moving from slice to slice in the 2D View sheet keeping the Show fitted sphere option turned on In this way the sphere fitting can be visualized in the orthogonal planes Any needed fix can be carried out by activating again this command and adjusting any parameter Fit Sphere Lx Center Load INF js EUR Y Center save INF 128 I Center EN 128 Hadius E 78 Close Interpolate image volume This command carries out an image volume interpolation When activated a dialog is presented for setting the new image volume dimensions as shown in the
56. specifying how many times the operator will be applied The result becomes the new active segmentation The figure below shows the effect of applying the operator Erode This command carries out an erosion by applying the morphological operator erosion to the voxels inside the segmentation With this operator every voxel belonging to the segmentation 1s eroded specifically if a voxel has all of their iMagic PRO User Manual 44 26 neighbors belonging to the segmentation the voxel is retained in the segmentation if not the voxel 1s deleted from the segmentation When activated a dialog is presented for specifying how many times the operator will be applied The result becomes the new active segmentation The figure below shows the effect of applying the operator Opening This command carries applies the morphological operator opening which consists in the sequential application of an erosion and dilation operators to the voxels inside the segmentation The net effect of this operator is removing the areas not completely connected in the segmentation The result becomes the new active segmentation iMagic PRO User Manual 45 The figure above shows the effect of applying the operator Closing This command carries applies the morphological operator closing which consists in the sequential application of a dilation and erosion operators to the voxels inside the segmentation The net effec
57. t of this operator is filling the gaps between areas in the segmentation iMagic PRO User Manual 46 The result becomes the new active segmentation The figure above shows the effect of applying the operator Smooth This command smooth the voxels inside the segmentation The result becomes the new active segmentation The figure below shows the effect of applying the operation iMagic PRO User Manual 47 Fill holes This command fills holes inside the segmentation All the voxels not belonging to the segmentation but completely surrounded in a 26 neighborhood by segmented voxels are set as part of the segmentation The result becomes the new active segmentation The figure below shows the effect of applying the operation Region Growing This command allows to remove voxels from the segmentation regions not connected in a 4 neighborhood with the voxel given as seed When activated a warning is given to the user for setting with the mouse left button the coordinates of the seed voxel This seed should be placed in the segmented region All the voxels connected to that seed will remain as part of the segmentation the rest are iMagic PRO User Manual 48 removed Take into account that this process 1s carried out in 3D The result becomes the new active segmentation The figure below shows the effect of applying the operation In this example the operation was carried out only in the slice presented for illustration p
58. te electrodes command for saving the electrodes to a file for its use in the step Fitting electrodes to skin surface Segmenting the skin in the image volume In the Manual Segmentation sheet the Set thresholds for segmenting command should be used The Min value in dialog should be incremented until the background in image appears completely empty black The Set all slices button in the dialog must be used to set the intensity range for all slices iMagic PRO User Manual 30 Creating skin surface Inmediately after the segmentation the Create surface command option By deformation must be used It s up to the user the resolution selection for the surface Once the skin surface appears in a new child window the Save surface as command must be used for saving the surface Fitting electrodes to skin surface The Fit electrodes command must be used with the skin surface for generating the vertex oriented electrodes file SRE Constructing cortical surfaces There are two approaches for obtaining cortical surfaces The first one starts by segmenting the cortex as accurately as possible see Segmenting image volumes and after that execute the command Create surface preferably using the option by tiling in order to achieve better results The option by deformation can give much faster results but if a medium or high resolution 1s selected some triangles can appear distorted In the second approach the starting segmentation is carried
59. tes the minimum distance allowed between two regions of the surface iMagic PRO User Manual 55 After pressing the Ok button the expanding process begins This process can be very time consuming depending on the resolution and complexity of the surface The progress of the process can be monitored with a progress window After completion a new child window is created with the expanded surface see Surface View sheet The figure below shows from left to right a white cortical surface and the expanded surface matching the gray cortex Fit electrodes This command allows to fit an electrode montage already fit over an image volume over a surface the active surface extracted from that image volume the command Create electrodes fit electrodes over image volumes When activated a standard Windows dialog is presented for loading the ELE file already fit over the image volume from where the surface was extracted Inmediately after a standard Windows dialog is presented for selecting the filename for saving the electrodes as well as the fitting type There are two different ways for fitting the electrodes over the surface vertices oriented and triangles oriented It means that the electrode coordinates will have the closest vertex coordinates and the closest triangle centroid coordinates respectively With the Save as type combo box in the dialog the user selects the type desired When fitting vertices oriented the resulting filename will ha
60. the real plane appearing in the position corresponding to the axial slice in the 2D View sheet for achieving the desired goal Scale image This command scales the active image volume When activated a dialog 1s presented for setting the scaling parameters The input parameters Minimum and Maximum are presented to the left of the dialog as well as the data type and two additional fields reporting the Minimum and Maximum values in the whole volume To the right of the dialog three fields for entering the Minimum Maximum and data type for the output image are shown The Minimum and Maximum input values are initialized with values equivalents to the current contrast settings see Set contrast command Scale mage X Output Mininnur o Input Miniman 24 809 In volume 0 000 bd aim 283 241 In volume 527 201 Data type Single Data type Bute x ia HMasimum 255 Histogram This command shows tha histogram of the full current image voulme When activated the following dialog is presented iMagic PRO User Manual 40 Histogram Expand Default Log Preview 1 555 Scale Cursor 1 20711314 Cursor 2 2464075 Close The histogram shows the distribution of the image voxel values over the entire image range At the borders of the horizontal axis the min and max values in the image are plotted Over the histogram two cursors are plotted also The cursors can be moved by dragging ov
61. tice that an electrode identified with REF is always fit approximately below LPA This electrode can be deleted or changed its position with the Set fiducial markers command The preview to the right shows over a 3D rendering of the image volume the electrodes fit With the group View a particular 3D view can be selected The checkbox Show Id allows to set visibility for the electrodes identifiers The box Vertical offset should be used for moving in the vertical direction the electrodes fit The boxes Angle X Angle Y and Angle Z are used for changing the rotation angles calculated automatically for the fit The change on these settings is carried out after pressing the Fix button and immediately after the result is visualized in the preview The Save button saves the electrodes fit in a ELE file When the option for creating electrodes from Polhemus data is selected a check is made for the presence of the fiducial markers Nasion LPA RPA and Nose see Appendix 1 If any of these markers is missing it won t be possible to create the electrodes file and the user will have to set the missing fiducial marker see Set fiducial markers command After the check is made a standard Windows dialog is presented for loading the file with the Polhemus measurements This file 1s an ASCII file The file will have 2 lines per electrode and marker measured The first line will have the x y z coordinates measured by the first receiver and the second line the sa
62. ting image volume exchanges the left and right sides and can be visualized clearly at the 2D View sheet in the axial and coronal planes The following figure shows the image volume before and after the operation Flip vertical This command carries out a vertical flip flip rows in the image volume The resulting image volume exchanges the upper and down sides and can be visualized clearly at the 2D View sheet in the axial and sagittal planes The following figure shows the image volume before and after the operation iMagic PRO User Manual 38 Flip slices This command flips the slices order in the image volume The resulting image volume exchanges the upper and down slices and can be visualized clearly at the 2D View sheet in the coronal and sagittal planes The following figure shows the image volume before and after the operation Transpose slices This command transposes the slices in the image volume The columns in every slice become rows and vice versa The following figure shows the image volume before and after the operation iMagic PRO User Manual 39 Rebuild plane This command rebuilds an orthogonal plane to the active image volume current plane When activated another submenu allows selecting the desired plane The new plane to be built will be placed in the position corresponding to the axial slice in the 2D View sheet The plane specified as storing plane Plane field in the Properties command must match
63. tlas filename associated to the image volume 16 MIP filename associated to the image volume 17 Inion coordinates X Y Z 18 Nose base coordinates X Y Z The 4 field indicates also the image volume data type 1 indicates the Byte data type Word 16 bits integer without sign 1s indicated by 2 Integer 32 bits integer with sign is indicated by 4 and Single floating point simple precision 1s indicated by the alphanumeric chain 4F In the 5 field if the pixel 1s not square then it 1s possible to specify the two values separated by one space first the horizontal value and after the vertical value in mm The 8 and 9 fields correspond to the thresholds used for detecting the skin and cortex in 3D visualization The fields from 10 to 13 and 17 18 are landmarks whose X Y Z coordinates are set interactively and will be used for coregistering with other coordinate systems The following figure shows these points iMagic PRO User Manual 64 Vertex LPA l Nasion Nose base The image system coordinates used by iMagic is shown in the following figure It is a left handed system the thumb finger indicates the X axis the index finger Y axis and the middle finger the Z axis very suitable for 3D visualization X Y X The 14 field allows reporting Talairach coordinates 1f the image volume is placed in that system The fields from 10 to 18 are optional iMagic PRO User Manual 65 Appendix 2 iMagic s
64. uding electrodes by pressing the right mouse button over the marker position approximately instead of the left mouse button as usual The fiducial markers set with this command can be shown with the commands Show markers and Show Id Markers The electrodes added with this command can be shown when rendering in the 3D View sheet see 3D View sheet and the Show Electrodes checkbox is turned on but if the checkbox was already turned on when adding the electrode the rendering is automatically carried out to reflect the electrode position The command is mutually exclusive with the Set orthogonal planes Set point marker Set cloud marker Set curve marker and Measure distance commands Measure distance f This command sets a function for the left button mouse When it is active by pressing the left mouse button over one of the slices in the 2D View sheet a starting point for a distance masurement is set As the mouse is moved the distance between that starting point and the current mouse position is calculated and shown in the status bar Show markers This command acts as a toggle When turned on plots in the 2D View and 3D View sheets over the slices or rendering the visible markers Show grid This command acts as a toggle When turned on plots in the 2D View and Manual Segmentation sheets over the slices the grid points present in the active slices iMagic PRO User Manual 59 Show Id markers This command acts as
65. urposes the seed was placed in the middle of the segmented cerebellum but take into account that the region growing operation is carried out in 3D Thresholding This command allows to remove voxel regions connected in a 4 neighborhood from the segmented regions Every connected region is checked to test 1f the number of voxels in the region 1s less or equal than the threshold given by the user If the condition 1s met then the whole region is removed When activated a dialog is presented for specifying the threshold to be used in the operation Depending on the threshold selected and the dimensions of the segmented image volume this operation can be very time consuming The result becomes the new active segmentation iMagic PRO User Manual 49 Create grid This command creates a grid see Appendix 4 over the entire image volume The grid 1s a 3D mesh composed by selected points inside the image volume This grid is used for calculating the electrical tomography When activated a dialog for setting the grid creation parameters 1s presented as shown in the figure Create grid Step X E step Y 2 Cancel Step 2 Calculate neighbours W Use segmentation The fields Step X Step Y and Step Z define the gap between one grid point and the next one for each dimension When the check box Use segmentation is set only the grid points belonging to the active segmentation will be generated When the check box Calculate neig
66. ve extension SRE see Appendix 11 When fitting triangles oriented the resulting filename will have extension SRT see Appendix 11 When fitting vertices oriented another dialog will be presented for selecting the filename corresponding to the the image volume associated with the surface Get normals This command calculates and saves on file the normals calculated over vertices or triangles in the active surface When activated a standard Windows dialog is presented for selecting the filename for saving the normals as well as the normal type There are two different ways for calculating the normals over the vertices and over the triangles With the Save as type combo box in the dialog the user iMagic PRO User Manual 56 selects the type desired The resulting filename will have extension NOR see Appendix 12 Get index region This command generates a new surface with a particular feature the triangles containing the vertices marked by the command Set point marker are shaded in a different color red The new surface 1s loaded in another child window With this surface it 1s easier to check a correct marking of a determined region OpenGL info This command shows a dialog with technical information about the OpenGL driver in use Set contrast This command allows getting a better contrast for visualizing the image volume A dialog is presented for setting the Min and Max parameters These parameters always appear normali
67. vertex coordinates are in the same coordinates system of image volumes see Appendix 1 All indices are relative to 0 Appendix 9 iMagic atlas format The iMagic atlas format is very similar to the image volume format see Appendix 1 The atlas has also 2 files with extensions VOX and HDR and the same meaning but another file is added a code file which is an ASCII file with extension COD Another difference 1s that datatype for atlas 1s always Byte 1 in the 4 field of header The COD file will have as many lines as different coded values voxel values are present in the image volume itself Every line will have the following structure code value description where code value is the coded value voxel value for a particular structure and description is an alphanumeric string of characters describing the structure itself This alphanumeric string will appear in the status bar when an atlas is loaded and the mouse is passed over that structure in the iMagic work sheets see Open Atlas command iMagic PRO User Manual 70 Appendix 10 iMagic electrodes format The iMagic electrodes are stored in an ASCII file with ELE extension The file will have as many lines as electrodes Every line will have an identifier followed by the X Y and Z electrode coordinates in iMagic coordinates separated by spaces Appendix 11 iMagic electrodes over surface format The iMagic electrodes over surface are stored in an ASCI file
68. with SRE or SRT extension for the vertex oriented or triangle oriented respectively see Fit electrodes command The file will have as many lines as electrodes Every line will have an identifier followed by the index of the vertex or triangle closest to the electrode depending on the type Notice that all indices are relative to O In the case of the vertex oriented file SRE extension there will be another 3 lines with a similar structure plus another value following the index defining the indices for the fiducial markers NAS LPA and RPA Appendix 12 iMagic normals format The iMagic normals are stored in an ASCH file with NOR extension The file will have as many lines as vertices or triangles depending on the type of file selected when the file was created see Get normals command Every line will have an ordinal number followed by the X Y and Z normal component separated by spaces Appendix 13 iMagic INF format The iMagic INF format stores information about the volume conductor model 3 concentric spheres properties It is an ASCII file with 4 lines The first line has the x y z cordinates of the sphere fit tho the cortex see Fit sphere command The second line has the information for the inner sphere cortex radius and conductivity The following lines have information for the other spheres in ascending radius size skull and skin
69. ws standard file also Below the section Magic 3 different key types can appear Image volumes Input Image volumes Output Plug in control parameters iMagic PRO User Manual 68 Every key will be a field in the dialog to be presented to the user before the plug in execution The Image volumes Input keys will have the following syntax Input any full filename gt where indicate an ordinal starting in 1 for specifying the order and amount of image volumes used as input to the plug in By giving as the key value the field will appear empty in the dialog The Image volumes Output keys will have the following syntax Output any full filename gt where indicate an ordinal starting in 1 for specifying the order and amount of image volumes generated as output by the plug in By giving as the key value the field will appear empty in the dialog The Plug in control parameters keys will have the following syntax any name value 5 These keys allow editing for any parameter needed by the plug in for running The key name will be used as field name in the dialog Ex DEF file 1Magic Inputl Outputl Lambda 0 5 Plug ins execution Once the plug in to execute has been selected with the Plug ins command in the Volume menu a dialog is presented to the user In the dialog will appear the image volume input fields 1f specified in the DEF file the image volume output fields 1f specified in
70. zed between O and 255 Show cursors in orthogonal planes This command acts as a toggle When turned on shows in the 2D View and Manual Segmentation sheets over the slices cursors indicating the orthogonal planes Set orthogonal planes 4 This command sets a function for the left button mouse When it 1s active by pressing the left mouse button over one of the slices in the 2D View the other two slices are updated to reflect the orthogonal planes In the 3D View sheet this command can be used to locate in the 2D View and Manual Segmentation sheets the 3D coordinates pointed by the mouse If the image volume is loaded twice the previous described operation can be appreciated more easily if the Yoke windows command is turned on The command is mutually exclusive with the Set point marker Set cloud markers Set curve markers Set fiducial markers and Measure distance commands When used the mouse cursor takes a cross shape Set point marker This command sets a function for the left button mouse When it 1s active by pressing the left mouse button over one of the slices in the 2D View sheet or in the 3D View sheet a marker of point type is set Immediately after a dialog 1s presented for identifying the marker The command is mutually exclusive with the Set orthogonal planes Set cloud markers Set curve markers Set fiducial markers and Measure distance commands When used the mouse cursor takes a pencil shape The right button mouse

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