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TIVMI V2.1 USER MANUAL

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1. 8 2 Make plane e Input 1 Point 1 2 Point 2 3 Point 3 e Output 1 Name of plane e Callable name in scripts Plane_Construct_3Points Creates the plane passing through the 3 points given as input 8 3 Medium plane e Input 1 Plane 1 2 Plane 2 e Output 1 Name of plane e Callable name in scripts Plane Medium 2Planes 41 Figure 14 Medium plane computation the medium plane green on the left and yellow on the right is obtained from the blue and red planes On the right the red plane normal has been inverted Creates the medium i e mean or average plane between the 2 given planes The plugin starts to compute the medium normal and then computes the po sition of the intersection between the two planes So the normal orientation of input planes is important If you get an orthogonal plane to the expected plane try to invert one plane normal and run again the plugin see fig 14 8 4 Orthogonal plane from 2 planes through 1 point e Input 1 Plane 1 2 Plane 2 3 Point e Output 1 Name of plane e Callable name in scripts Plane_Orthogonal_2PlanesThrough1Point Creates a plane that is orthogonal to the two planes given as input Both planes must not be parallel At this step there is an infinite number of solutions The point given as third input will leave only one solution 42 8 5 Orthogonal to a plane including a straight line e Input 1 Plane 2 Straight line e Output
2. e The third column is the color of the material displayed in the slice view Simple click on it to change the color The fourth column is used to lock the material More details about this feature is detailed below 66 21 ae Mo XX R Pj Figure 28 Material list for segmentation with locks The fifth column is a brush lock If set pencil crossed tools will not have effect on this material The sixth column is used to delete the material All voxel with this ma terial label will be set to label 0 zero e The seventh column will select all voxels of the material e The eighth column will hide or show the material in the slice view The material with the label 0 is a special material Its name is always exte rior It can t be renamed deleted It has no color and can t be shown in the slice view But it can be locked brush locked and selected The green button will transfer the selection to the selected material You must first select a material in the material list Each selected voxel will be labelled with the chosen material If a selected voxel is already labelled by an other material and if this material is locked then the voxel will keep its label and will not be transferred to the chosen material Fig 29 and 30 show how a selection in red crossing the skull material in green and the endocranium material in blue is added to a 3rd material named test in light purple while skull
3. o 6 10 Convert segment to 2 points 6 11 Point3Ds HMH Segment3D HMH value 6 12 Intersection between straight line and mesh 7 Creating a 3D path A Load Obj Spline yo jek ee se a n a a to a 7 2 Orthoprojection Path3D on plane Ta Resample Patki3D arco a ae dope BBA Ee wee Se ed 7 4 Intersection mesh plane o a 8 Creating a Plane SL Alignon mesh gyi60 eres Pb ES Sa Ho Oe Re eee 8 2 Make plane se s s sete 44054 tos ias Ee a a i 8 9 Mediumi plane se s 4 4 4 aoe 2 6 Baw alk ewe ee ES 8 4 Orthogonal plane from 2 planes through 1 point 8 5 Orthogonal to a plane including a straight line 8 6 Orthogonal segment 3D 8 7 Make an orthogonal point through 2 points 8 8 Parallel to straight line through 2 points 8 9 Shift plane toa 3D point s a s eos sacs csm 8 10 Bench Vice Mesh ocacion ane A Ra eS 8 11 Constrained Bench vice a Mesh o 8 12 Bench vice a limited mesh o 9 Creating a Segment 3D 9 1 Make 3D segment from 2 points o 9 2 Maximum distance from a 3D path toaplane 9 3 Minimum distance between 2 path3Ds 9 4 Shift along plane normal with ratio 9 5 Segment angle Spread o 9 6 Segment ladder ra s maiorra A A a ew has 10 Creating Data 10 1 Angle
4. Invert Normals Scale Scale factor Apply scale Optimize vertex use Point Spread specific Point Size 1 00 a e Resolution percent 100 00 v Color per vertex Figure 57 Mesh subwindow 23 Enhanced craniometrics Anthropologic measurements can me performed directly on the reconstructions Most landmark definitions need the skull to be oriented according to the Frank furt plane this section present the construction of planes and the positioning of some traditional landmarks Further examples of specific measurements are also described 23 1 Plane construction and landmark positioning Geometric landmarks are defined as the most superior or the most anterior point of structures This orientation is given by the Frankfurt Horizontal which definition is that of a plane passing through both porion most superior point of the external acoustic meatus and both infraorbitale most inferior point on the orbital rim As a plane passes through three landmarks we advise to create a medium plane based on those four points for a better accuracy 1 Using the 3D picking in the Point 3D subwindow place the right and left porion and orbitale on the reconstructed skull Figure 59 The nasion at the metting of the frontal and the internasal suture can also be placed for the further construction of the sagittal plane 2 The creation of the planes can be scripted Script menu Sta
5. to remove objectNamel objectName2 etc from the group named Group e g CMD study removeFromGroup P1 P2 88 CMD lt Group gt addToGroup lt string objectName1 gt lt string objectName2 gt to add objectNamel objectName2 etc to the group named Group e g CMD study addToGroup P1 P2 18 2 Commands to create objects Always begin with NEW followed by the type of object followed by the name of the new object to create followed by arguments if available Arguments are int for integer numbers float for floating point numbers and string for a sentence and displayed between lt and gt NEW Point3D lt string name gt lt float x gt lt float y gt lt float z gt to cre ate a 3D point at coordinates x y z e g NEW Point3D origin 0 0 0 0 0 0 NEW Segment3D lt string name gt lt float p1x gt lt float ply gt lt float piz gt lt float p2x gt lt float p2y gt to create a 3D segment from point xl yl z1 to x2 y2 z2 e g NEW Segment3D totalLength 1 0 0 0 3 5 8 6 0 0 5 2 NEW BoundingBox lt string name gt to create a new bounding box e g NEW BoundingBox my_roi NEW Path3D lt string name gt lt float x gt lt float y gt lt float z gt to cre ate a 3D path containing 1 point at coordinates x y z e g NEW Path3D perimeter 8 5 3 7 2 9 NEW GenericInt lt string name gt lt int value gt to create an integer num ber e g NEW GenericInt examCount 3 NEW GenericFloa
6. 78 Figure 44 Segmentation fill holes OfMthe top the original selection and on the bottom all holes have been filled Figure 45 Segmentation lasso Parts of drawing are made by free hand and others by lines 80 Figure 46 Segmentation Magnetic lasso 1 Angle 45ij 4 and Area 10 2 Angle 101 5 and Area 10 3 Angle 101 5 and Area 5 4 Angle 451 5 and Area 5 The Angle tolerance in degrees determines how the lasso will stuck to the shapes The area width is the area where the HMH is computed Big values will detect greater contrasts while small values will follow light shapes see fig 46 17 What can I do with a segmentation After editing a segmentation you will get a 8 bits depth 3D image where grey level 0 zero is not a region and others values are different regions From this 3D image you can use every plugins which use a 8 bits 3D image as input The most probable use should be the surface extraction of a region to get a 3D 81 mesh This can be done by using the HMH surface plugin see 5 5 This plugin can use a 8 bits 3D image as a binary image to extract the surface The HMH Surface plugin does not support segmented images with materials but it is able to extract the surface of non zero voxels set in the 8 bits image So if you made a segmentation with only one material this material will be reconstructed as a 3D mesh If your segmentation contains more materials they all will
7. Remove small components Max gnali component volume voral count Angie tolerance 12 C Aravada Ip Figure 74 Magnetic lasso usage crtl click to close the magnetic lasso Name Col Lek Brh Del Sel shy 10 Exte BX xk 21 mene JO ke 32 maxillary Brxr o als 19152x 276 147 862 Z 772113 El zoom auto ax Size Bi 5 boli key or rubber ESTA ax Fl Zoom Auto Kors e Max gnali component volume voxel count 3D 4 0 0 0 ES a Cl left ciek to close sel an v 212 area wet a Ip Figure 75 Add the selection to the maxillary material WD Mainwindow Dockable windows Materials EX slice view Name Col Lek Brh Del Sel m A x 10 Ene OX x 21 mae MOI ke 32 maxillary OxXxre als Add new material 17200x 181 264 401 2 66 7081 El zoom auto x See Da Hold AR key or rubber bi E Zoom Auto ca E Hold Ak key to proceed curan slice nly Hold Shi key to add to selection EME 4 10 4 Remove small components Max call component volume vonal count 3D 4 0 0 Wig Ange tlerace 12 L area neta E Figure 76 Use the brush to draw on remaining maxillary parts 114 File Plug in Script Option Deploy Shite t Window me customs organismon cesado Save to default Jf Load defoult
8. there are 3 materials 0 exterior 1 mandible and 2 maxillary You can close the segmentation editor To extract the surface of the mandible and the maxillary we will use the HMH surface plugin But this plugin uses a binary image Our segmented image is not a binary image because it contains values 0 1 and 2 If you use the segmented image as a binary image for the HMH surface extraction the plugin will extract the surface of non zero voxel values So it will construct the surface of the mandible and the maxillary merged In order to have 2 distinct meshes we need to call the HMH surface on each material 1 Call the plugin image3D double threshold 2 Set the input image to your segmented image 109 Loa al BY or Mavxre Figure 69 Magic wand usage in 3D 3 Set Gray value 1 and gray value 2 to 1 it means that all voxels which value is 1 will be set to 255 and all others voxels will be set to 0 The binary image will contain only the mandible 4 Set a name for this binary image e g mandible_binary 5 Call again the plugin image3D gt double threshold 6 Set the input image to your segmented image 7 Set Gray value 1 and gray value 2 to 2 The binary image will contain only the maxillary 8 Set a name for this binary image e g maxillary_binary 9 Create a surface on each binary image using the HMH surface plugin menu plug in mesh gt HMH Surface 2 Setup entries a
9. 0 e FOV field of view It is the horizontal angle of the camera e Near and far the near and far planes are orthogonal planes to the camera In front of the near plane and behind the far plane objects are not drawn You can use this to virtualy cut objects increase near plane Note that the 3D picking accuracy is linked to the distance between near and far plane So be careful if you increase the far plane too much the 3D picking will not be accurate e Stereo the 3D view will generate an image for each eye You must have a NVidia Quadro display card or any display card compatible with opengl quad buffered stereo e Environment controls lighting and background color 3 2 Image 3D Is a stack of classical 2D images Often it corresponds to a medical scanner exam e Slice scroll bar lets you navigate in slices e Info gives you the image dimensions and some DICOM informations if available e Resolution allows you to read and modify the voxel resolution As given in DICOM files TIVMI distinguishes Z voxel resolution and space be tween slices but for all treatments only space between slices is taken into account e windowing controls the contrast and brightness with a window on data Center and width are equivalent to the double horizontal slider under the image histogram Usefull for 16 bits images e You can show or hide the image bounding box e Segmentation You can use the button to convert a 8 bits
10. 2 planes saco rada e e a Re amp a eee eve 10 2 Angle 3 paintis 20 0 ed eb a de ee Si ecg ee ae Gs 10 3 Height of triangle sa se aowi m iane aiia a ie ee 10 4 Perimeter of a shape in a binary slice 10 5 Volume from VOXe S o 002 2 eee 10 6 Weight of all materials in a 3D image 11 Creating Straight Lines 11 1 Make straight line from 2 planes o 11 2 Make straight line from 1 segment 11 3 Shift a straight line to a 3D point s ss ecr pedi gaui tea 12 Output to file 12 1 Reslice and save to radio tiff a 3D image 12 2 Project each point of a mesh into an image 12 3 Dave Path 3D to SUE a ee e Ew ee we i A 12 4 Save Image3D to analyze img and hdr files 12 5 Save Image3D to amira mesh file format 58 12 6 Save segmented Image3D to amira mesh file format 59 12 7 Dave Mesh torob 2 osea si Ble Haw ads 59 12 9 Save path 3d tobi cercas d eR ew a ee ee a 59 12 9 Save mesh to ply 446 6 ha eed RAW Dawe ee eA 60 12 10Save Image 3D to one radio tiff file 60 12 11Save Image 3D to tEn e i oss reso ee a we Ke ee ae 60 12 12 Save an object tO SO s s ak ea aa eA a aE aa 61 12 13Save Image 3D to VEFE e occiso a 61 13 Creating any object 61 13E Load A deg a ee fe oe Od bo amp ah Soa ee ef av eray ers 61 V Segmentation 62 14 Creating a segmentation 62 MT From Scratch te wn 2 4 bha
11. Figure 33 Material lock scenario 3 selection crossing skull and endocranium WD Mainwingow To a mal Dockable windows Materials 2 stce view No teot ax Name Col Lek Brh Del Sel SIm z gt R 1 Baer Br k 21 sail Harxre Brush ax 3 2 Endocranium JG Xk 43 tes B xXke on Hold Akt key for rubber Magic Wand ae bi zoom Auto ol at hay o proceed cren sic oniy old Shi key 10 ad o see con Selection menpaalon ae Remove smal components Max al component volume oe tourt 100 E 70 0 x x x x x x E x 0 968252 2928192 241 ax Kiten ater Figure 34 Material lock scenario 3 selection crossing skull locked and en docranium locked added to the test material 70 16 3 Tools 16 3 1 No tool Click on the arrow button to unselect the last used tool This is usefull to disable the left click in the slice view 16 3 2 Brush Select the brush shape by hitting one of both buttons and set up the size with the slider On the slice view the mouse will appear as a blue brush Note that the brush is drawn with the real Image 3D pixel size With non isometrics voxels on orthoslices the brush is drawn with rectangular pixels see fig 35 If you move the mouse the brush will move only on the Image 3D pixels So if you zoom a lot the brush will be displayed aliased and will moove jerky Left click and hold left button to draw The blue brush will disappear during move
12. Reserved to advanced use of some plugins 11 3 7 Mesh 3D Is a polygonal mesh composed of points and faces TIVMI is able to compute normals per face or normals per vertex and invert them It is also possible to scale the mesh and to optimize the vertex use delete duplicates Color opacity and shininess are also customizable TIVMI is able to manage point clouds i e meshes without faces You can rebuild normals if the illumination is bad Normal per vertex will smooth visually no degradation of data Normal per face will show you the reality of the mesh but it may slows the 3D view and the rendering of the mesh will not look pretty 3 8 Plane Is a 3D plane using the equation ax by cz d 0 It can be displayed as dif ferent colors and thickness Its normal can be displayed Even if the plane is shown you need to constraint it to a specific object because a 3D plane is by definition infinite and TIVMI needs to know where to draw it So choose a target and apply the constraint You can set a thickness in the normal way It applies in real time This is usefull to simulate a parallel plane without creating it 3 9 Straight line Is an infinite line TIVMI uses a system of 2 planes equations to store a straight line It corresponds to the intersection of 2 planes It can be displayed as different colors Use as plane see 3 8 3 10 Bounding box Bounding box is usefull to crop a 3D image in order to save memory e g befor
13. Se am R O Estena xX R neat ho 6 2i mae BGK e ho mamy PO xe Hold Ak kay for rubber Magie Wand E Zoom Asto Hold Ak key to proceed current slice only Hold shit key ta add o selection El Remove small components Max cll component volume voral court 1 00 bi 16176 X 276 Y 203 359 Z 94 0044 A l 6 3 Cl left ciek to cose selection 5 irl At left clk to close and substract selection PZ magnetic Angie tolerance 12 m E l zoom auto maws Figure 72 Magnetic lasso usage for a non trivial interface 112 P Dockable windows Materiais Name 1 21 mandible 32 maxillary Add new material ee leva Ex x ooo eon teams i vad bie E zoom Auto Hold ak key to proceed aten sce aniy Hola Shet key to add to selection AEE pa Selection manipuistion ax Loo Laso 2 Ctrl left ciek to close selecson Ctrl At left ciek to close and substract election Z Magnetic Ange tolerance 12 L mawana D Figure 73 Magnetic lasso usage hold mouse left button to use it as a classical lasso Dockabie windows Matenas Name 10 Etter 21 mandible 32 maxillary EE D en Size Bi 5 Hold AR key for rubbar EA bie Hold Ak ke to proceed current slice nly Hald shift key to add to selection Selection manipulston CCT ESO
14. Segment3D_MinDistance_2Path3Ds Makes a new 3D segment where the starting point is a point from the first 3D path and the ending point is a point from the second 3D path and where the segment length is the smallest of all possible combinations 48 9 4 Shift along plane normal with ratio e Input 1 3D Segment 2 Plane 3 Ratio e Output 1 Name of 3D segment e Callable name in scripts Segment3D_Shift_Segment3DPlaneNormalRatio Makes a new 3D segment parallel to the given one moved in the same direction as the plane normal at the distance of the specified input ratio the ratio is applied to the normalized normal 9 5 Segment angle spread e Input 1 Point 1 axis 2 Point 2 from 3 Point 3 to 4 Angle step in degrees 5 Number of segments from and to included e Output 1 3D segment prefix e Callable name in scripts Segment3Ds_AngleSpread_3Points Makes a serie of segments where the starting point is always the point 1 Ending points are spread between point 2 and point 3 In the case of an angle step un unknown number of 3D segments are created and the angle with the previous segment is always the same The one but last 3D segment may touch the point 3 and the last segment will but the angle will not be respected see fig 17 In the case of a number of segments the angle with the previous segment is unknown but always the same The last segment will touch the point 3 This number should be greater t
15. The new image is 8 bits depth and keeps the position orientation and voxel size of the input 3D image 4 2 Simple threshold e Input 1 3D image 2 Grey value e Output 15 Original 3D Image 16 bits per pixel Binary image Threshold on bones Figure 1 Thresholded 3D image only one slice shown 1 Name of new 3D image e Callable name in scripts Image3D_SimpleThreshold_Image3D For less than the grey value grey level 0 is stored more or equal to the value the level 255 is stored see figure 1 The new image is 8 bits depth and keeps the position orientation and voxel size of the input 3D image 4 3 Double threshold e Input 1 3D image 2 Grey value 1 3 Grey value 2 e Output 1 Name of new 3D image e Callable name in scripts Image3D_DoubleThreshold_Image3D Less than the value 1 and more than the value 2 grey level 0 is stored and between or equal to the two values 255 is stored see figure 2 The new image is 8 bits depth and keeps the position orientation and voxel size of the input 3D image 4 4 Crop a 3D image e Input 1 3D image 16 Original 3D Image 16 bits per pixel Binary image Threshold on soft tissue without bones Figure 2 Double thresholded 3D image only one slice shown Original 3D Image and a bounding box centered on the mandible Original 3D Image and the croped new one Figure 3 Crop a 3D image using a bounding box 2 Bounding Box e Output 1 Name of
16. data was recorded on 12 bits and the 3D image was scaled to 16 bits use 16 as factor to divide the grey level by 16 before the weight computa tion BE CAREFUL this plugin works fine only if the slope and intercept are correctly provided by the scanner manufacturer in the Dicom file Our exper imentation shows that it is never the case In fact the reconstruction method of images changes the Hounsfield scale and the slope and intercept are not up dated 11 Creating Straight Lines 11 1 Make straight line from 2 planes e Input 1 Plane 1 2 Plane 2 e Output 1 Name of straight line e Callable name in scripts StraightLine_Construct_2Planes Creates the straight line at the intersection of both specified planes Planes must not be parallel 11 2 Make straight line from 1 segment e Input 1 Segment e Output 1 Name of straight line e Callable name in scripts StraightLine_Convert_Segement Creates the straight line containing the segment 55 11 3 Shift a straight line to a 3D point e Input 1 Straight line 2 Point 3D e Output 1 Name of straight line e Callable name in scripts StraightLine_Shift Point Creates the straight line parallel to the given one and containing the 3D point 12 Output to file 12 1 Reslice and save to radio tiff a 3D image e Input 1 Image 3D Ze 3 Pixel dimension Plane e Output 1 filename e Callable name in scripts ResliceAndSaveTo
17. es E sa 4 5 Crop a 3D image with a bounding sphere 4 6 Erase out of a bounding sphere 00 A Gaussian DUE 2405 4 6056564 4 Fa 8 Stee ee eas ALB Ortho slices sd ae oe eh ee ee ER EER RE AO Merges si ce tik bd a Me EO we Ree ol od ed A AQ Reslic ica eae ee Sk ee ee Bead Wa eae wads 4 11 Voxellize a mesh soser ae i i a DA Re ee eS 4 12 Load Analyze Img and Hdr ANS Load DICOM ute se ee e e He BG Se eee ees et 414 Load PGND risa bh aS Be oe ii ee eres 4 15 Load PNG series s cor e 4405 2 bb ddd ee Be ee bbe es 4 16 Load RAW usas ba keane dod dew ee is e AAG Load VEF oie be BEARS oR eR eM 5 Creating a Mesh 5L Load Pis 203 dea wie he ea Aw Al ee ara 0 2 Load OD e coss ea Oe a e oe oA Ba haw ae ee RS d ee Load Stl ls de Ade a HY oe Seer eg ee S4 Load Doris ak ke woe a A A da HMA Suttace 2 ba we ee be a ee DO VOR hanes lis lara cada da Ba ME oe Roe ke RTS 6 Creating a 3D Point 6 1 Intersection plane and straight line 6 2 Orthogonal projection point on plane 6 3 Orthogonal projection point on straight line 6 4 Make a 3D point on a 3D segment from a ratio 6 5 Barycenter path SD nie eee AS ade Ee ee are sds 6 6 Shift a point along the normal of a plane 6 7 Skeleton using region growing e 6 8 Skeleton using 2D region growing on all slices 6 9 Convert path3D to points o e
18. if needed see fig 25 The slider below let you navigate in slices The histogram modulates the windowing of the parent image and works as the histogram in the Object Control pannel Image 3D tab Mouse controls e pointing move the mouse on the slice 1 in fig 26 and see below the slice the grey level and 3D coordinates of the voxel targeted 2 in fig 26 A vertical red line shows the grey level in the histogram in real time 3 in fig 26 64 Figure 24 Configuration of segmentation GUI customized for dual screens Slice view 52 X 256 Y 473 039 Z 74 4546 F Zoom Auto Figure 25 Rectangular pixels on the segmentation slice view 65 2508 X 256 Y 460 497 Z 77 501 o Y Zoom Auto Figure 26 Voxel informations in the segmentation slice view Name Col Lck Brh Del Sel shu Figure 27 Material list for segmentation e Hold right button and move up or down to zoom or unzoom TIVMI will center the zoom on the mouse pointer e Hold middle button and move up down left or right to move the slice e The left button is used by tools 16 2 Materials list This list contains materials Each material is a label from 0 to 255 and this value is shown in the first column See fig 27 and 28 for columns details The first column is the label number of the material This is not editable e The second column is the name of the material Double click on it to edit the name
19. mesh but HMH computation is respected Use this setting for simple surfaces e mode 1 limit to voxel Vertices are free to move inside their own voxel This corrects topological troubles but restrict HMH computation Use this setting for complex surfaces like trabecular bones e mode 2 no HMH Vertices are located at the voxel border There is no HMH computation Grey threshold is for automatic threshold on the 3D image All voxels over this value will be part of the reconstructed mesh Fill with 0 if you want to use your own binary image last argument Grey min and gray max are thresholds to limit segments for HMH computation If a segment cross those values it is stopped Fill with respectively 0 and 2 1 where bpp is bit per pixel e g 255 for 8 bits per pixels or 65535 for 16 bits per pixel HMH Max length is a limitation for the HMH segment Fill with 0 for an automated computation of this value This will be 10 diagonals of a voxel Binary image is taken into account if threshold is 0 All non zero voxels will be used for the surface reconstruction 31 5 6 Morph mesh e Input 1 Mesh 1 2 Mesh 2 3 Percentage 4 Tech e Output 1 Name of new mesh e Callable name in scripts Mesh Morph Meshs This will create a new mesh which vertices position is a ratio from the mesh 1 to mesh 2 The percentage argument is the ratio to apply 0 is the mesh 1 position and 1 is the mesh 2 position The tech argumen
20. new 3D image e Callable name in scripts Image3D_Crop_Image3D Crop the image and only keep the voxels inside the bouding box see figure 3 If a voxel is cut by the bounding box it is kept If the new image has odd dimensions width height or slice count a column a line or slice is added to make a 3D image with pair dimensions The new 3D image is located and oriented as the original one 17 4 5 Crop a 3D image with a bounding sphere e Input 1 3D image 2 Bounding sphere radius e Output 1 Name of new 3D image e Callable name in scripts Image3D_CropBoundingSphere_Image3D The sphere is decribed by the second input a 3D segment The first point of the segment is the sphere center and the second point is on the sphere surface The new image has the dimension of the smallest bounding box containing the sphere If the new image has odd dimensions width height or slice count a column a line or slice is added to make a 3D image with pair dimensions The new 3D image is located and oriented as the original one This plugin can be combined with the erase out of a bounding sphere plugin see 4 6 4 6 Erase out of a bounding sphere e Input 1 3D image 2 Bounding sphere radius e Output 1 Name of new 3D image e Callable name in scripts Image3D_EraseOutOfBoundingSphere_Image3D Sets to 0 all voxels which geometric center is outside the bouding sphere see fig 4 This plugin is useful to limit a study t
21. number of available cores on your system in the task manager e BackgroundColor you should not modify this here but in the camera and environment window see 3 1 14 Part IV Plugins Each plugin has input s and output s Generally outputs are names of new objects to create or prefix for multiple results It can be also a filename for the output to file plugins Inputs are existing objects in TIVMI or numerical values It means that an input object can be a hidden object When you run a plugin you will always have the same window e on the left input objects You must chose the adapted object in a combo list For numerical values you will find a text input to fill and a combo list The combolist contains numerical values in TIVMI memory You can choose a numerical value here but if you fill the input text the combobox value will be ignored e on the right output names to fill with unique names or filename to browse Keep in mind that plugins will never alterate input objects They always create new objects and don t modify existing objects 4 Creating a 3D Image 4 1 Automatic threshold e Input 1 3D image e Output 1 Name of new 3D image e Callable name in scripts Image3D_AutomaticThreshold_Image3D Computes the mean between the minimum and maximum grey levels of the input image and thresholds the image Under or equal to the mean grey level 0 is stored and over the mean a lavel of 255 is stored
22. plugin an idea of the plane to compute see fig 12 The plugin will start to compute the plane including the 3 align points Then it will look for the farthest vertex of the 39 Quadrant 3 Quadrant 4 Align point 3 Align point 1 Align point 2 Quadrant 1 Quadrant 2 Figure 12 3 align points defined on a mandibule splitted into 4 quadrants mesh on a side of this plane and the farthest vertex of the mesh on the other side It will also compute the vertex count on both sides of the plane Then it will keep the vertex on the side containing the smallest vertex count as a new align point This new align point will replace one of the 3 align points and for that it will choose the nearest align point from the new align point This is an iterative process so it is computed until there is no mesh vertex on one side of the plane It means that the plane will move in the direction of the smallest part of the mesh Quadrants allow to limit movements of align points It consists in 2 planes that split the mesh into 4 parts Each point must be in a dinstinct quadrant the quadrant 1 is defined by the align point 1 quadrant 2 by the align point 2 and quadrant 3 by the align point 3 The last quadrant is quadrant 4 see fig 12 Align point 1 and align point 2 will move only in its quadrant while the align point 3 will be allowed to switch between quadrant 3 and quadrant 4 see fig 13 40 Figure 13 Plane aligned on mandibule
23. run Plugin Mesh_HMHSurface_Image3D Input Output Image 3D scan2 x Name of mesh to create bone Mode O free 1 Iimit to voxel 2 no hmh 0 Gray threshold O binary image 21299 Gray min 0 Gray max 65535 HMH max length 0 auto 3 Binary image if threshold 0 scan Figure 55 Setup of the HMH Surface Plug in 9 Once the reconstruction is done TIVMI indicate the potential errors and memory amount allocated for the operations Figure 56 Message from plug in Memory amount 174228828 Harlequin patterns 627 AN Taux HMH rat s 0 Limitation rat O Figure 56 Automatic message after a successful HMH surface reconstruction 10 Use the Show Hide toolbox to show the mesh created 11 The color mesh can be changed in the Mesh subwindow Figure 57 and the light can also be modified for better visualization in the Camera and Environment subwindow The same operation can be performed by changing the threshold to obtain the surface of the skin Furthermore in the Mesh subwindow the last surface displayed can be made transparent by changing its opacity Figure 58 If any problem hide all meshes and show them in order the last being the first visible layer 99 Mesh Ga El lt Ed Mesh bone vertices 744192 Faces 922961 Color Opacity Shininess T Normals Normal per face Re Build Normals Normal per vertex smooth Show
24. scan2 s Sice J 2 Sice J 29 Resolution Resolution Voxel width 0 265625 voxel width 0 265625 Voxel Height 0 265625 Voxel Height 0 265625 Voxel Thickness 1 a Voxel Thickness 1 Space between slices 0 599976 Space between slices 0 599976 Apply changes Apply changes J Window Center A Figure 54 Manual visualization of threshold unit in case of different tissues 2 The HMH reconstruction can be performed through Plug in Mesh HMH Surface Specify the Image3D that will be used to calculate the HMH interfaces in 3D 3 For medical exam we advise to use the free mode 0 Gray threshold is the value previously recorded to aim a particular density 98 5 Gray min and max can be used to avoid the recosntruction of material of exterme density artifacts By default enter respectively 0 and 65535 6 HMH max length must be at least equivalent to twice a voxel diagonal in order to cover at least 2 voxels in each direction when measuring the HMH for a voxel of 0 3 x 0 3 x 1 the 3D diagonal averages 1 08 so the segment should be superior to 2 16 putting 3 is a wise choice 7 The Binary image is to be used only if such an image has been previously created in this example it is not used 8 Finally name the mesh to create Figure 55 Calculation of the surface can be more or less time consuming depending on the DICOM resolution and the exam size Setup and
25. slice begins Each voxel is stored on used bits Typically it is 8 or 16 Allocated bit is useful for the plugin to allocate a smaller image if necessary if allocated bits is 16 and used bits is 8 the plugin will generate a 8 bits image and read the file as 16 bits per voxel Big endians is a switch to read data as big endian if set to 1 or little endian if set to 0 The shift data option is used to convert signed data to unsigned data See plugin loadAnalyze 4 12 for more details Positionning the first slice is centered on the world origin and parallel to the X Y plane and next slices are set along the Z axis 4 17 Load VFF e Input 1 Filename e Output 28 1 Name new 3D image e Callable name in scripts LoadVFF Open the VFF file given as first argument VFF is a file format used by the MicroView software 5 Creating a Mesh 5 1 Load pts e Input 1 Filename e Output 1 Name of new mesh e Callable name in scripts loadpts Open the file given as input PTS design ASCII file containing a point cloud This plugin is able to open and detect automatically various ways for describing those points It will try to read each line as given in the ordered list below No headings of comments are supported Each line must end with a CR carriage return or LF line feed character 1 XYZnXnYnZrgb 2 XxX YZnXnYnZc XYZrgb XYZc oo p o XYZ 6 else ignore Where X Y and Z are floating points numbers designi
26. the pixel containing the start point This is the grey reference Then it will look around this pixel on the same slice using a region growing algorithm based on 4 connectivities and will stop when a grey value is different from the grey reference Then the mean of all pixels visited is computed and the point is created This plug in computes a kind of centroid for a given 2D shape It should be used on a binary image For processing multiple slices see 6 8 6 8 Skeleton using 2D region growing on all slices e Input 1 Image 3D 2 Start point e Output 1 Name prefix of new 3D Points e Callable name in scripts Point3Ds_Skeleton2D5_Image3D The plugin computes a first skeleton point on the slice containing the given point see 6 7 for more details The skeleton point is shifted to the next slice and to the previous slice and a new skeleton point is computed And so on until there is no slice to proceed or the grey level of the pixel is different from the reference Be careful this plugin does not compute a real skeleton on 3 dimensions It computes a list of 2D skeletons 6 9 Convert path3D to points e Input 1 Path 3D e Output 1 Prefix e Callable name in scripts Point3Ds_Explode_Path3D Each point of the 3D path is created as an independant 3D point 35 6 10 Convert segment to 2 points e Input 1 Segment3D e Output 1 name of first 3D point 2 name of second 3D point e Callable name in scripts Point
27. 1 Name of plane e Callable name in scripts Plane_Orthogonal_PlaneStraightline Creates a plane that is orthogonal to the plane given as input and that includes the straight line That means that all points on the straight line are on the computed plane The straight line must not be orthogonal to the plane 8 6 Orthogonal segment 3D e Input 1 Segment 2 Point e Output 1 Name of plane e Callable name in scripts Plane_Orthogonal_Segment3D Creates a plane that is orthogonal to the segment 3D given as input and that includes the point 8 7 Make an orthogonal point through 2 points e Input 1 Plane 2 Point 1 3 Point 2 e Output 1 Name of plane e Callable name in scripts Plane_Orthogonal_Through2Points Creates a plane that is orthogonal to the plane given as input and that includes both points Both points must not describe an orthogonal segment to the input plane 43 8 8 Parallel to straight line through 2 points e Input 1 Straight line 2 Point 1 3 Point 2 e Output 1 Name of plane e Callable name in scripts Plane_Parallel_StraightLine2Points Creates a plane that is parallel to the straight line given as input and that includes both points Both points must not describe a parallel segment to the straight line 8 9 Shift plane to a 3D point e Input 1 Plane 2 3D Point e Output 1 Name of plane e Callable name in scripts Plane_Shift_Point Creates a plane that is parallel to the g
28. 18 1 9 AFA3D CMD lt Afa3D gt setSkullVisible lt true false gt to show or hide the skull mesh e g CMD specimen setSkullVisible true CMD lt Afa3D gt setSkullPointsVisible lt true false gt to show or hide 3D points of the skull mesh e g CMD specimen setSkullPointsVisible true CMD lt Afa3D gt setTargetedPointsVisible lt truelfalse gt to show or hide 3D points of the targeted face e g CMD specimen setTargetedPointsVisible true CMD lt Afa3D gt setComputedFaceVisible lt truelfalse gt to show or hide the computed face mesh e g CMD specimen setComputedFaceVisible true 87 CMD lt Afa3D gt setComputedPointsVisible lt true false gt to show or hide 3D points of the computed face e g CMD specimen setComputedPointsVisible true CMD lt Afa3D gt setOriginalMeshColor lt int red gt lt int green gt lt int blue gt to set the skull mesh color Red green and blue are 3 integers from 0 to 255 e g for white CMD specimen setOriginalMeshColor 255 255 255 CMD lt Afa3D gt setSkullPointsColor lt int red gt lt int green gt lt int blue gt to set the 3D points color of the skull Red green and blue are 3 integers from 0 to 255 e g for red CMD specimen setSkullPointsColor 255 0 0 CMD lt Afa3D gt setTargetedPointsiColor lt int red gt lt int green gt lt int blue gt to set the class 1 3D points color of the targeted face Red green and blue are 3 integers from 0 to 255 e g for dark red
29. 3 Point 3 e Output 1 Name of angle e Callable name in scripts Data_Angle_3Points Computes the angle between 3 points where the point given as first input is the summit of the angle 10 3 Height of triangle e Input 1 Point 1 summit 2 Point 2 basis 3 Point 3 basis e Output 1 Name of height e Callable name in scripts Data HeightOfTriangle_3Points Computes the height of a triangle where the point given as first input is the summit of the triangle 52 Figure 19 Perimeter computation of a 2D shape 10 4 Perimeter of a shape in a binary slice e Input 1 Binary Image3D 2 Point3D e Output 1 Name of perimeter e Callable name in scripts Data_Perimeter_Image3DPoint3D Computes the perimeter of a shape The 3D point gives the slice to proceed and must target the shape The plugin will start from this point and look for the shape border When found it will follow the 8 connectivity border of the shape The final length is the sum of segments linking the center of pixels inside the shape see fig 19 10 5 Volume from voxels e Input 1 Image 3D 2 Grey value from 3 Grey value to e Output 1 Name of volume e Callable name in scripts Data_VolumeVoxels_Image3D Computes the volume as the sum of all voxel volumes which grey value are between the specified grey value from included and the grey value to included 10 6 Weight of all materials in a 3D image e Input 1 Original 3D
30. 3D image to a segmentation when needed and start the segmentation GUI see V 3 3 Point 3D Is a point in 3D space with coordinates x y and z The point can be displayed in different shapes sizes and colors e Z Slice Style is a special shape for 3D points picked on 3D images where image stack is oriented on Z It consists in 2 squares on each side of a slice connected by a sgement crossing the slice exactly at the point coordinates The ball style is more conventionnal e Coordinates let you convert world coordinates of a 3D point to local coordinates of a 3D image where Z is the slice number ans X and Y are coordinates in the 2D image Coordinates and size are writable and can be validated by the button apply 10 e 3D picking chose an object that will intercept the click on the object reference combo list Click on pick new or shortcut key p and click on the object in the 3D view You will be prompted for a name The 3D point will be automatically shown you don t need to click on show hide Use pick move each time you want to move the selected point Note that hitting space will reiterate the last action performed this can be useful when the point needs to be moved several times or if numerous point must be places in a row keeping your eyes on the 3D view e copy to clipboard copy ALL 3D points in the clipboard and not only the 3D point selected Then you can paste in Excel to get all coor din
31. 3D view 2 In the object control windows hit on the Edit a new segmentation button see fig 65 WW tiv 21 License expires in 334 day sre file Plugin Ser ipt Option Diay ox PLL e x o le Bren Bess Prono P semma Bronze W irage i gi Figure 65 Open a 3D image and create a new segmentation 3 Create a new material by hitting the add new material button see fig 66 4 Rename the material double click on the name 5 Choose a color click on the color square We suggest you to choose a color different from a grey levels used to display CT scans and red used to display current drawings see fig 67 6 Use the magic wand to select a bone see fig 68 and 69 a Select a range on the histogram to keep only high values of grey level b Click on the magic wand icon c Hold alt key and click on a bone in the image to proceed on the current slice only d Move the histogram range to adjust the threshold Computation is in real time because the last click was on current slice only e Click again on a bone in the image to proceed for all slices 106 Materials ax Name Col Lck Brh Del Sel shw 10 Exterior Es Je R 2 11 Unnamed m 6 Xk oe Figure 66 Add a new material f You can move again the histogram range to adjust the threshold but the result is updated only when you release the range because the last click was on
32. 3Ds_Explode_Segment Create both points of a 3D segment as new 3D points 6 11 Point3Ds HMH Segment3D HMH value e Input 1 Image 3D 2 Segment 3D 3 HMH value e Output 1 name prefix of new points e Callable name in scripts Point3Ds_HMH_Segments3DValue Computes a HMH on the 3D segment using the 3D image as reference If not equal to zero the HMH value is used Else it is computed automatically The output can be one or more 3D points 6 12 Intersection between straight line and mesh e Input 1 Straight line 2 Mesh e Output 1 name prefix of new points e Callable name in scripts Point3Ds_Intersection_StraightLineMesh Computes the intersection of a straight line with a mesh as new 3D points This plugin could be very slow on big meshes It is still in developpement it craches on complex meshes 36 7 Creating a 3D path 7 1 Load obj spline e Input 1 Filename e Output 1 Prefix of new 3D path e Callable name in scripts Load0bjSpline Opens an obj file containing lines The obj file should contain a list of vertices v lt x gt lt y gt lt z gt and a list of lines 1 lt vertex_index 1 gt lt vertex_index 2 gt 7 2 Orthoprojection Path3D on plane e Input 1 Path3D 2 Plane e Output 1 Name of 3D path e Callable name in scripts Path3D_OrthoProjection_Path3D0nPlane Creates a new 3D path where each point is the corrsponding point in the original 3D path orthogonaly projecte
33. 6 Segment 3D CMD lt Segment3D gt setColor lt int red gt lt int green gt lt int blue gt to set the segment color e g for dark green CMD headWitdh setColor 32 64 32 CMD lt Segment3D gt setSize lt float size gt to set the segment size balls e g CMD headWitdh setSize 4 5 CMD lt Segment3D gt setPointiPosition lt float x gt lt float y gt lt float z gt to set the position of point 1 e g CMD headWitdh setPointiPosition 28 10 38 61 30 62 CMD lt Segment3D gt setPoint2Position lt float x gt lt float y gt lt float z gt to set the position of point 2 e g CMD headWitdh setPointiPosition 39 27 61 95 50 51 18 1 7 Straight line CMD lt StraightLine gt setConstraint lt string object gt to set limita tions to an object for the plane display Object can be an image3D a mesh a boundingbox or a path3D e g CMD rotationAxis setConstraint head CMD lt StraightLine gt setColor lt int red gt lt int green gt lt int blue gt to set the line color red green and blue are 3 integers from 0 to 255 e g for pink CMD rotationAxis setColor 255 127 127 CMD lt StraightLine gt setSize lt float size gt to set the line size e g CMD rotationAxis setSize 3 18 1 8 Path 3D CMD lt Path3D gt setColor lt int red gt lt int green gt lt int blue gt to set the path color Red green and blue are 3 integers from 0 to 255 e g for blue CMD perimeter setColor 0 0 255 CMD lt Path3D gt showPointNum
34. CMD specimen setTargetedPointsiColor 127 0 0 CMD lt Afa3D gt setTargetedPoints2Color lt int red gt lt int green gt lt int blue gt to set the class 2 3D points color of the targeted face Red green and blue are 3 integers from 0 to 255 e g for dark green CMD specimen setTargetedPointsiColor 0 127 0 CMD lt Afa3D gt setComputedFaceColor lt int red gt lt int green gt lt int blue gt to set the computed face color Red green and blue are 3 integers from 0 to 255 e g for skin CMD specimen setComputedFaceColor 255 244 231 CMD lt Afa3D gt setComputedPointsiColor lt int red gt lt int green gt lt int blue gt to set the class 1 3D points color of the computed face Red green and blue are 3 integers from 0 to 255 e g for red CMD specimen setComputedPointsiColor 255 0 0 CMD lt Afa3D gt setComputedPoints2Color lt int red gt lt int green gt lt int blue gt to set the class 2 3D points color of the computed face Red green and blue are 3 integers from 0 to 255 e g for green CMD specimen setComputedPoints2Color 0 255 0 CMD lt Afa3D gt movePoint lt int index gt lt float x gt lt float y gt lt float z gt to set the index point position index is an integer between 0 and 77 x y and z are floating point numbers e g for the Nasion CMD specimen movePoint 4 10 5671 25 4713 5 8417 18 1 10 Group CMD lt Group gt removeFromGroup lt string objectName1 gt lt string objectName2 gt
35. MI This operation is indicative l 2 Menu Plug in Plot Plot profile on 3D segment Select the target Image 3D and the Segment 3D on which the profile will be measured Name the plot to create In the Plot subwindow Figure 49 select the plot created and show it The first point of the segment corresponds to the beginning of the plot the end being point 2 Tha variation in density can be observed through soft tissues and bone Figure 50 The interface between 2 tissues can be manually calculated by selecting two extreme densities on the plot and by clicking on HMH The Y value expresses the density in Hounsfield units 94 we T a Export Figure 49 Plot subwindow Figure 50 HMH profile led on a segment passing through the cranial vault 21 4 Automatically compute the interface 3D points on a 3D segment with the HMH protocol The previous operation can be automatically performed and the interface 3D points placed with reproducibility on a segment 1 2 Plug in Point3D Point3Ds HMH Segments3D HMH Value Select the Image and Segment 3D on which the HMH will be calculated Enter a HMH value 0 for automatic HMH calcuation is advised If there are several tissues and the user want to target a specific one he cen enter the corresponding HMH value previously evaluated in a plot Finally name the prefix of the points to be created
36. NE a Veraces 72957 Faces 148046 Normal per face Normal per vertex smooth El Show Twent Normals sae Saeta O e Optimize vertex use Point Spread spetic ott See 100 ecion ercer 100 00 og elton percent 100 Color per vertex c a eel Bror Beso Brno Bso Woro W mem W camera andtewtrenment ae Figure 77 3D Meshes of a mandible editor and a maxillary set by the segmentation 115 Tos Bounding Box bbox PERS Image 30 scend EEK sosna ABR O Mesh mandible SEXO maay SEXO A
37. O Color New 3D Picking Choose a 3D Object reference al Pick Corner 1 Pick Corner 2 Figure 52 Bounding Box subwindow 4 Scroll the exam up to the slice where the opposite corner of the box will be set 5 Place the second corner by clicking on Pick Corner 2 in the Bounding Box subwindow The bos is created Figure 53 Figure 53 Bounding box created 6 Change the color of the created box if the visibility is not good and change slices to check if all the region of interest is into the bounding box The two opposite corners can be moved by repeating the operation Pick Corner to adjust the box 97 7 A new scan can be cropped from the scan according to the bounding box Reconstruction of surfaces from this new scan will be faster Use Plug in Image3D Crope a 3D Image select the image the box and name the new scan 22 2 Reconstruct HMH surfaces In the case of medical exam and presence of tissues of different densities we can manually find an optimal threshold for each material 1 In the Image 3D subwindow with a Window width set at 0 the user looks for specific values in Hounsfield units until only the wanted structures are visible Figure 54 This subjective phase of choosing threshold will not interfere with the reproducibility of the reconstruction as the algorithm uses the HMH protocol Image 3D Image 3D EJ Image 30 scan2 w Image 30
38. Point3D_Ratio Segment3D Compute the position of a 3D point on the 3D Segment according to a ratio Ratio is a floatting point number Zero represents the first point of the segment 1 represent the second point of the segment A ratio between 0 and 1 will place the point on the segment proportionnally to the segment length Less than zero or more than 1 will place the point repectivelly before or after the segment on a virtual straight line including the segment e g 33 e Ratio 0 5 the middle of the segment e Ratio 1 the mirror of point 2 compared to point 1 e Ratio 2 the mirror of point 1 compared to point 2 6 5 Barycenter path 3D e Input 1 Path 3D e Output 1 Name of new 3D Point e Callable name in scripts Point3D_Barycenter_Path3D Compute the barycenter i e the centroid of all points defining the given 3D path 6 6 Shift a point along the normal of a plane e Input 1 3D point 2 Plane 3 length e Output 1 Name of new 3D Point e Callable name in scripts Point3D_ShiftOnPlaneNormal_Path3D Duplicates the point given as first argument and shifts it using the normal of the plane given as second argument The length between the origin and the new point will be the length given as third argument 6 7 Skeleton using region growing e Input 1 Image 3D 2 Start point e Output 1 Name of new 3D Point e Callable name in scripts Point3D_Skeleton_Image3D 34 The plugin records the grey value of
39. RadioTiff This plugin was provided to save memory when computing a reslice to be saved as radio tiff Now we suggest you to reslice your 3D image using the reslice plugin see 4 10 and use the save to radio tiff plugin see 12 10 12 2 Project each point of a mesh into an image e Input 1 Plane Thickness Pixel size aoa e Ww N Mesh Point diameter 56 Figure 20 Point cloud projection on 2D image e Output 1 filename e Callable name in scripts SaveMeshProjectionToPng This plugin is used to perform an orthoprojection of a point cloud The plane represents the 2D image The thickness the the volume from the plane to a distance of thickness where points are taken into account The 2D image has white background The more the point are close to the plane the more it is black and the more the point are far the more it is white The pixel size is the real size of the new image pixel in the 3D world You should choose a value near the distance between 2 neighboor mesh points The resulting image looks like embossed see fig 20 Measurements are possible because you know the pixel size The point diameter is ignored 12 3 Save Path 3D to Svg e Input 1 Path 3D or group 97 2 Xup 1 Yup 2 Zup 3 auto 0 e Output 1 filename e Callable name in scripts SavePath3DToSvg Svg is a 2D vectorized file format This plugin is useful to import TIVMI path 3D into graphic software The 3D path or
40. TIVMI V2 1 USER MANUAL Bruno Dutailly and Pierre Guyomarc h Universit Bordeaux 1 CNRS UMR 5199 PACEA F 33405 Talence Cedex France b dutailly pacea u bordeaux1 fr pierreguyo gmail com November 19 2012 Contents I Introduction 5 II Graphical Interface 7 1 The menu bar 7 AAA es Ey a Bet T L2 Plugin ee anneme e e D e eee ee EA 7 1 35 CMP we 4 4 as ik ee fe ech ae dl BO eam 7 14 Options 224400 en Geb ea Ske See et eee ee 8 2 3D layout 8 Dele SIDPVICW so iB a Se ee ee BG Sh A owe Gla Ae 8 DoD OOS a SoG a a ee a A ye we oe ae 8 221 Maim behavior s s lt i ie pon 4d ab eee da 8 QD GIOUPS dea ea da a A wR ee a ag 9 3 Objects control 9 3 1 Camera and environment se ae bet poto nm t dve hira 9 32 AIMS BONN a kt BG Be a i e Bios tt de dk ta Bea ay or vt te 10 AA 10 34 Geement Ds saeia aese Aa A Ae 11 Seo A A OR Ba te ese od 11 B10 BasisidlD a o ee Gee BGS ee aa we Ae 11 3T Mesh SD cc shed bk ed ec ako ae Pooh a RRR 12 39 Plame 27208 as eed eee on oe we he rere ale es 12 29 Straight line so ns picada gag b SY Aad Bo eM eee es 12 3 10 Bounding POX kan se ct ee ee a pAr a we G 12 SILPI sce evs hh A e B oe a BS amp A ek Bre ete a 12 el DAG Ns 2 eos a fee A A RN 12 III Options IV Plugins 4 Creating a 3D Image 4 1 Automatic threshold o 00020 e 4 2 Simple threshold 4 466 44544040 6 ee ne a 4 3 Double threshold ssri 4 2 ee eo SAG Band Ewe Ee ae 4 4 Crop a 3D image 20 ace le oe ee a De
41. The points are created make them appear in Show Hide Point3D Fig ure 51 95 Image3D E v point_interface_01 egment3D v point_interface_02 Straight line Plane gt Mesh Bounding Box Basis 3D po Path3d A r Tools Figure 51 Automatic placement of interface landmarks blue on a segment defined by the red landmarks 22 Reconstruct two surfaces from two different densities Craniometrics imply landmarks that cannot be spotted on 2D slices and repro ducible surface reconstruction based on the HMH protocol can be done from medical CT scan This scenario develop the different steps to reconstruct hard and soft tissues of the face from a medical exam 22 1 Select the region of interest Depending on the virtual memory available surface reconstruction may be time consuming and it is not always necessary to render the whole exam when only a region is studied In this cases the user can define a box around the interested zone and reconstruct only that zone Also this is faster than the slice by slice segmentation process 1 Once the exam is loaded and displayed in the 3D view select the slice where the first corner of the bounding box will be set 2 Create the bounding box from the specific subwindow Figure 52 3 Once the new box is named place the first corner by clicking on Pick Corner 1 then clicking on the target zone in the 3D view 96 Bounding Box Founding ox
42. a group of 3D paths should be included in a plane or several parallel planes The second argument will force the path to be oriented with a chosen up axis The up axis will be the canvas height in the svg Auto will let TIVMI determine the best orientation In all cases the 3D Path is projected on a plane and exported as a 2D shape 12 4 Save Image3D to analyze img and hdr files e Input 1 Image 3D e Output 1 filename e Callable name in scripts SaveToAnalyzeImg Save a 3D Image to the Anayze file format This format will lose the image 3D position in the 3D space and additional information read in DICOM for example 12 5 Save Image3D to amira mesh file format e Input 1 Image 3D e Output 1 filename e Callable name in scripts SaveToImage3DAmiraMesh Save a 3D Image to the Amira Avizo mesh file format am This format will lose the image 3D position in the 3D space and additional information read in DICOM for example 58 12 6 Save segmented Image3D to amira mesh file format e Input 1 Image 3D e Output 1 filename e Callable name in scripts SaveToImage3DLabelsAmiraMesh Save a 3D Image to the Amira Avizo mesh file format am The image must have a 8 bits depth This format will lose the image 3D position in the 3D space 12 7 Save mesh to obj e Input 1 Mesh e Output 1 filename e Callable name in scripts SaveTo0bj Save a mesh to the obj file format wavefront 12 8 Save path 3
43. ad PNG serie e Input 1 Path e Output 1 Name new 3D image e Callable name in scripts LoadPNGSerie Open all files in the given path Files are taken in the order given by the system It is often alphabetically sorted so be careful with file numbering with no 0 zero fillings e g imagel png image2 png image10 png will be opened in this order 1 10 2 3 etc Rename to image001 png image010 png The voxel size is set to 1 by 1 by 1 and is customizable in the TIVMI GUI see 3 2 Positionning the first slice is centered on the world origin and parallel to the X Y plane and next slices are set along the Z axis 27 4 16 Load RAW e Input Filename Size X Size Y Size Z Voxel size X Voxel size Y Voxel size Z Allocated bits Used bits Big endians 11 Shift data oO On nw A wo Ww Ep o e Output 1 Name new 3D image e Callable name in scripts LoadRAW Raw file format as no official specification The simplest way to store a 3D image as raw is to write sequentially all voxels in the file This plugin opens the file given as first argument This file is supposed to contains a 3D image in 1 dimension Voxels are sorted as slices rows and finally columns That mean that the first voxel is located at 1st slice 1st row 1st column The second is located at 1st slice 1st row 2nd column and so on When a row is complete the next row begins When the slice is complete the next
44. ae ea gd 90 18 8 Call a plug in 2 o eG e Re Ww Re a 90 19 Script generation 91 VII Scenarios 92 20 Open a DICOM exam and place 3D points on slices 92 21 Create a segment and find the HMH interface between two tissues 93 21 1 Create a new segment 93 21 2 Create a segment from 2 existing 3D points 94 21 3 Evaluate the density profile on a segment 94 21 4 Automatically compute the interface 3D points on a 3D segment with the HMH protocol 95 22 Reconstruct two surfaces from two different densities 96 22 1 Select the region of interest o 00004 96 22 2 Reconstruct HMH surfaces o 98 23 Enhanced craniometrics 100 23 1 Plane construction and landmark positioning 100 23 2 Measurement in projection o 103 23 3 Measurement of soft tissue depth 104 24 Segmentation of a 3D image basic threshold 106 25 Advanced segmentation of a 3D image 108 Part 1 Introduction TIVMI standing for Treatment and Inscreased Vision for Medical Imaging is a software developed in the PACEA laboratory UMR 5199 of CNRS Univer sit Bordeaux 1 and Minist re de la Culture It is designed for the need of anthropology researchers for accurate and reproducible measurements in 3D of medical imaging material when other software does not respond to this goal It also has been extended to mesh and point cloud manipulation and h
45. all slices 7 Click on the bone material in the material list see fig 70 8 Click on the green button to add the selection to the bone material see fig 70 9 Close the segmentation window 10 You can see a new 3D image in the object list named seg followed by the name of the original 3D image see fig 71 11 Create a surface on the segmented image using the HMH surface plugin menu plug in mesh gt HMH Surface 2 Setup entries as follow a b Mode 0 c Gray threshold 0 because you will use the segmented image to define the object to extract Image 3D the original 3D image the CT scan d Gray min 0 e Gray max 65535 for a 16 bits CT scan see 5 5 HMH max length 0 g Binary image choose the seg 3D image previoulsy created 107 Materials Gx Figure 67 Rename and choose a color for the new material The surface extraction works on non zero voxels of a binary image The segmented image containing only one material as this scenario creates is con sidered as a binary image If you want to create 2 or more materials and extract surfaces of those materials see the scenario 25 25 Advanced segmentation of a 3D image We assume that you already know basic segmentation as described in the sce nario 24 We start from the scenario 24 where a mandible and a maxillary are in a ma terial named bone We will try to create a material for th
46. ally be averaged between those two 5 The third plane the Mean Sagittal can be constructed simply by creating a plane orthogonally to MT and MC passing through the nasion Plug in Plane Orthogonal Plane from 2 planes through 1 point Figure 61 Figure 61 Mean planes yellow mean transverse green mean coronal red mean sagittal with normal displayed 6 Color thickness and position of the planes can be modified in the Plane subwindow 102 7 For the positioning of geometric landmarks as the glabella most anterior point of the cranial vault between the supraorbitary arches the MC can be shifted or thickenned until delimiting the targeted zone Figure 62 Figure 62 Plane assisted positioning of the glabella with the MC and zygion with the MS 8 This methodology can be adapted to all geometrically defined traditional landmarks It significantly enhances the repeatability and reproducibility of anthropometric protocols 23 2 Measurement in projection TIVMI proposes basic geometric operations that can be used to perform specific measurements Mastoid height or orbital height in example are measurements that are not strictly defined by two landmarks As those were created to be taken with a sliding caliper it requires more than one step to record them 1 For mastoid height MDH the most inferior point of the mastoid process mastoidale can be positioned by thickenning the MT up to its very po sition I
47. as met needs of archaeologists This help is designed to beginners and advanced users Paragraphs in bold are simple descriptions and explainations the rest being more detailed Part II Graphical Interface 1 The menu bar 1 1 File to load or save states It is an internal file format of TIVMI You can save all objects and re open them It creates a tsf file tsf is for TIVMI Script File and a directory with the same name without tsf All objects are stored in the directory and the tsf file contains instructions to open objects files If you want to share data with another computer copy the tsf and the corresponding folder with the same name Objects in the folder are saved as tso files tso is for Tivmi Serialized Object It consists in a binary format of the object In the future state file format will evolve to a gzip file containing xml and binary files to make interoperability easier with others softwares 1 2 Plugin contains features that allow to create new objects from other objects You will find a description of all plug ins on the website Plug ins in this menu are sorted by the object type they produce e g if you want to create a plane go to the plane submenu and select the desired operation to create a plane e g if you want to open DICOM files that means you want to create a 3D Image etc To export objects use the output to file submenu Plugins are dll files for Windows and so files for linux Th
48. ates Be carefull numbers are written with a floating point On french Excel you will have to replace by to be able to manipulate those entries as numbers e export copy the selected 3D points in a textfile with a specified sepa rator We suggest you to use the easier copy to clipboard button 3 4 Segment 3D is an association of two 3D points connected TIVMI gives the Euclidian dis tance between the 2 points which is the length of the segment It can be displayed as different sizes and colors A color gradient from one point to the other gives the order between points 3D picking works like 3D point but you need to click 2 points The name will be asked between the 2 clicks in the 3D view You can rotate the object and pick move point 2 if you need to pick a non visible position 3 5 Path 3D Is a path of 3D points connected like a chain of segments An option can close the path The lock action checkbox allows you to click more than one time in the 3D view to pick new points Check this box and click on Insert after then click click click in the 3D view When finished or if you want to rotate or navigate uncheck the box change the view recheck the box and re enter pick new This can be used to collect outline data explore the Path submenu in plug ins for further treatments 3 6 Basis 3D Is a 3D orthonormal basis It is used to compute basis changes on 3D point coordinates
49. be merged into one To extract only one material you must use the plugin double threshold see 4 3 on the segmented image and set the label number of the chosen material as grey value 1 and 2 and create a new 8 bits 3D image Then use this new image as the binary image needed by the HMH surface plugin More information are avalilabale in the scenarios 25 It is planned to update plugins in order to support segmentations 82 Part VI Scripts 18 Scripting language The scripting language is basic and allows to reproduce all actions of the inter face The best way to learn scripting language is to record yourself while using TIVMI and edit the script file with an ASCII text editor 18 1 Commands on objects Always begin with CMD followed by the name of object to target followed by a command keyword and arguments if available Arguments are int for integer numbers float for floating point numbers and string for an object name and diplayed between lt and gt 18 1 1 Image 3D CMD lt Image3D gt setCurrentSlice lt int num gt to set the displayed slice to num e g CMD scan setCurrentSlice 3 CMD lt Image3D gt setVoxelDimensions lt float width gt lt float height gt to change voxel dimension e g CMD scan setVoxelDimensions 0 25 0 25 0 5 CMD lt Image3D gt updateSlicesPositionsFromVoxelResolution lt float to update slices position In fact the voxel thickness is not necessarily the space between sl
50. ber lt true false gt to swho or hide point number in the 3D view e g CMD perimeter showPointNumber true 86 Q MD lt Path3D gt setSize lt float size gt to set the path size balls e g CMD perimeter setSize 2 CMD lt Path3D gt setStyle lt 0 1 gt 0 to display points as balls or 1 to dis play points as squares on screen e g CMD perimeter setStyle 1 CMD lt Path3D gt setClosed lt truelfalse gt false to keep the path open true to close it e g CMD perimeter setClosed true CMD lt Path3D gt addPointAfter lt int position gt lt float x gt lt float y gt lt float z gt to add a point which coordinates are x y z after the point position Po sition of point in a 3D path starts from 1 e g CMD perimeter addPointAfter 5 3 6 1 8 5 2 CMD lt Path3D gt addPointBefore lt int position gt lt float x gt lt float y gt lt float z gt to add a point which coordinates are x y z before the point position Po sition of point in a 3D path starts from 1 e g CMD perimeter addPointBefore 1 2 3 4 6 1 8 CMD lt Path3D gt deletePoint lt int position gt delete the point at the specified position e g CMD perimeter deletePoint 2 CMD lt Path3D gt movePoint lt int position gt lt float x gt lt float y gt lt float z gt to move the point at the specified position to the specified coordinates x y z Position of point in a 3D path starts from 1 e g CMD perimeter movePoint 1 2 0 4 9 7 8
51. d on the plane note that the equidistance if the 3D path was resampled will not be respected on the 2D projection See fig 10 7 3 Resample Path3D e Input 1 Path3D 2 Point count 3 Precision e Output 1 Name of 3D path e Callable name in scripts Path3D_Resample Path3D 37 Figure 10 Orthoprojection red of a 3D path green on a plane Creates a new 3D path where distances between two neighboor points is always the same Point position is interpolated The process is iterative until the last point matches the original last point re garding the precision It results in a kind of smoothing and produces equidistant landmarks usable in geometric morphometric analyses See fig 11 7 4 Intersection mesh plane e Input 1 Mesh 2 Plane e Output 1 Prefix name of 3D path e Callable name in scripts Path3Ds_Intersection_MeshPlane Creates new 3D paths on the intersection between the plane and the mesh 38 Figure 11 Original path green containig 13 points resampled to a path red with 20 points 8 Creating a Plane 8 1 Align on mesh e Input 1 Point 1 Point 2 Point 3 Mesh Use quadrants Quadrant plane 1 NO oO FP W DY Quadrant plane 2 e Output 1 Name of plane e Callable name in scripts Plane_AlignOnMesh_3Points3D This plugin will look for the plane laying on the mesh regarding specific constraints The 3 points given as input named align points will give to the
52. d to obj e Input 1 Path 3D e Output 1 filename e Callable name in scripts SaveTo0bjSpline Save a 3D path to the obj file format wavefront It consists in a list of vertices v lt x gt lt y gt lt z gt followed by a line 1 lt vertex_index gt lt vertex_index gt vertex_index This is usefull to load a 3D path in Autodesk 3DSMax for example 59 12 9 Save mesh to ply e Input 1 Mesh 2 Binary e Output 1 filename e Callable name in scripts SaveToPly Save a mesh to the ply file format stanford It can output binary set to 1 or ASCII set to 0 12 10 Save Image 3D to one radio tiff file e Input 1 Image 3D e Output 1 filename e Callable name in scripts SaveToRadfioTiff Collapses all slices of the 3D image to one and averages all grey levels It results in a radiography like 2D image The tiff file format allows to keep the 16 bits depth if needed 12 11 Save Image 3D to tiff e Input 1 Image 3D e Output 1 filename e Callable name in scripts SaveToTiff Save each slice into a tiff file The tiff file format allows to keep the 16 bits depth if needed If pixels are not square see 4 8 the plugin will resample each slice to fit to square pixels The pixel dimension will be the smallest dimension of the original pixel 60 12 12 Save an object to tso e Input 1 Object e Output 1 filename e Callable name in scripts SaveToTso The tso file format is for Ti
53. e 3D reconstruction To create it click on new and click 2 opposite corners in the 3D view on the reference object 3 11 Plot Is a 2D plot serie using 2 axis The plot can be displayed as an histogram or a curve and mathematical functions can be applied to enhance the curve LOG square root etc Used for segment profiles or 3D Image histograms 3 12 Data Data contains numerical data produced by some plugins e g volume compu tation 12 Part III Options In TIVMI options are saved into the tivmi ini file located in your home directory in a folder named TIVMI On Windows and linux platform folders starting with a dot are hidden If you want to browse these folders you must setup your file browser to let you navigate inside TIVMI has a little graphical interface to setup the configuration file without editing directly the tivmi ini file In the menu bar click on option and then edit e folders Contains a set of 4 folders that TIVMI uses to store the information about different objects and actions Exports when using the export button in the Point 3D of Segment 3D object controls see 3 3 and 3 4 Scripts when loading or recording scripts see 1 3 States when loading or saving states see 1 1 Swap when swapping objects see 2 2 e license This contains a reference to the network card needed for the license check ing You shouldn t need to modify
54. e glabella we will project it according to the MC Figure 64 Figure 64 a Bony glabella positioned b Segment created from the projected bony glabella along the normal of the MC plane c STD at the glabella between the bony glabella and the projected interface between skin and air calculated by HMH 3 First get the point out of the bone in order to avoid the bone density to bias the further HMH calculation Use a ratio of 0 5 units are in mm as DICOM are most of the time in mm and name the point glabellal 4 Then repeat the same operation but make sure that the second point crosses the skin Use a ratio of 30 and name the point glabella2 5 Create a 3D segment from glabellal and glabella2 and name it glabseg 6 Let TIVMI find automatically the HMH interface between skin and air by performing the calculation on the glabseg segment Plug in Point 3D Point3D HMH Segment 3D HMH Value Let 0 for automatic HMH and name the interface glabellasoft 7 Make appear the created interface point Show Hide Point 3D glabella soft interface 01 Delete the glabellal glabella2 and glabseg they won t be used anymore 8 Create a segment between the bony glabella and the soft glabella name it glabellaSTD You can also erase now the interface point Stop recording the script here The STD can be checked in the segment subwindow 105 24 Segmentation of a 3D image basic threshold 1 Open a 3D image and show it in the
55. e image will have rectangular pixels In TIVMI orthoslice images are stored as squared pixels but displayed as rectangular pixels The more you zoom on an orthoslice the more you will see those rectangular pixels Computations on orthoslices are perfectly equivalent to the same computations on the original data set Be careful with the storage classical file formats for images like jpeg png tiff etc support only square pixels TIVMI will compute a new image resampled to store in those file formats The pixel size will be the smallest side of the rectangular pixel In the internal file format of TIVMI tso file format TIVMI keeps the information of rectangular pixels and the image will not be resampled 4 9 Merge e Input 1 Image 3D reference 2 Image 3D to add 3 Use 3D positionning e Output 22 1 Name of new 3D image e Callable name in scripts Image3D_Merge_Image3D Merge two 3D images into one If use 3D positionning is set at 0 the new 3D image dimensions are herited from the ref image and the slice count is the sum of slices of both images If images cross themselves slices are intercalated If slices of the image to add are shifted compared to the the reference image the shift will be kept If the option is set to 1 the plugin will look at the exact position of slices in 3D space and compute a bounding box containig both images This bounding box defines the new image dimensions If the image to add is shifted and
56. e mandible and another for the maxillary 1 2 Create a new material named maxillary Rename the bone material to mandible matreial Set the exterior material to drawing disabled Choose a slice orientation to see the fusion between the mandible and the maxillary sagittal view for instance On each slice use the magnetic lasso to draw a line between the mandible and the maxillary We recommand to set the area width and angle tolerance to a small value in order to help the HMH computation to find the interface near the yellow line of the lasso see fig 72 Hold the left mouse button to roughly select the maxillary then ctrl click to close it see fig 73 and fig 74 Tt doesn t matter if you don t select all the maxillary on the slice especially if you zoom a lot so the maxillary is partially hidden we will correct this latter Note that the 108 Loa ea Figure 68 Magic wand usage on current slice only exterior material is set to drawing disabled so the selection in red is not set on the exterior 7 Add the selection to the maxillary material see fig 75 8 Now we need to complete the maxillary with remaining parts owned by the mandible material use the brush and paint roughly on those remaining parts on each slice Note that the brush will not affect voxels owned by the exterior material see fig 76 9 Add selection to the maxillary material Now
57. e planes 8 12 Bench vice a limited mesh e Input 1 Mesh 2 Straight line 3 Plane 1 4 Plane 2 e Output 1 Prefix for 3D planes e Callable name in scripts Planes_LimitedBenchVice_StraightlineMeshPlanes Creates 2 planes like a bench vice as the plugin bench vice see 8 10 but only vertices on the same side of the planel normal and on the same side as plane 2 normal are tested This is the same as the bench vice plugin on a sliced mesh 46 Figure 16 Constrained bench vice on a mandibule top limit to 1 cm and bottom limit to 0 ignore mesh under the ground plane Impact points are highlighted 47 9 Creating a Segment 3D 9 1 Make 3D segment from 2 points e Input 1 Point 1 2 Point 2 e Output 1 Name of 3D segment e Callable name in scripts Segment3D_Construct_3Points Makes a new 3D segment where the starting point is point 1 and the ending point is point 2 9 2 Maximum distance from a 3D path to a plane e Input 1 Path 3D 2 Plane e Output 1 Name of 3D segment e Callable name in scripts Segment3D_MaxDistance_Path3DPlane Makes a new 3D segment where the starting point is a point from the 3D path and the ending point is the orthogonal projection of the starting point on the plane The chosen point on the 3D path is the farthest one from the plane 9 3 Minimum distance between 2 path3Ds e Input 1 Path 3D 1 2 Path 3D 2 e Output 1 Name of 3D segment e Callable name in scripts
58. ey are stored in the plugins directory and loaded dynamically when TIVMI starts Live update can replace or add plug ins without modifying the TIVMI program 1 3 Script let you record and replay scripts tsf files The created file is plain text so you can easily edit those Generate and execute is useful to repeat the same commands several times e Iterate will repeat the command written in the text area and replace all d occurrences by the number between from and to e g if a plug in generates 10 3D points and you need to show them type Show p d and fill from 1 and to 10 This will generate 10 lines SHOW p1 SHOW p2 Show p10 and execute them e regular expression to learn what is a regular expression we invite you to read the wikipedia article about it http en wikipedia org wiki Regular_expression In the text area type the command and add inside the command a regular expression between two All objects names matching the regular expression will be played in the command e g to show all ob jects which a name beginning by p and followed by a number type Show p 0 9 It means show all object beginning 7 by a p fol lowed by a digit from 0 to 9 at least one time with nothing else See 18 and 19 for more details about available commands syntax and genera tion 1 4 Options is a basic graphical interface to read and edit the TIVMI configurat
59. han 2 In all cases all segments are included into a plane and have the same length computed as the biggest length between the point 1 to point 2 segment and the point 1 to point 3 segment This plugin can be used for the computation of a bisector of an angle 49 Figure 17 Segment 3D angle spread plugin difference between setting up angle left 7 degrees and segment count right 10 9 6 Segment ladder e Input 1 Point 1 summit 2 Point 2 base 3 Point 3 base 4 Number of segments base and summit included e Output 1 3D segment prefix e Callable name in scripts Segment3Ds_Ladder_3Points Makes a serie of segments parallel to the base segment point 2 to point 3 segment contained in the plane including the 3 points The distance with the previous segment is unknown but always the same The first segment is the base and the last includes the summit see fig 18 10 Creating Data 10 1 Angle 2 planes e Input 1 Plane 1 2 Plane 2 50 Figure 18 Segment 3D ladder example ol e Output 1 Name of angle e Callable name in scripts Data_Angle_2Planes Computes the angle between 2 planes in degrees There are 2 solutions The plugin computes the angle between the two normals so only one solution is found To find the other solution you can invert the normal of a plane or compute manually the complementary angle to 180 degrees 10 2 Angle 3 points e Input 1 Point 1 angle 2 Point 2
60. ices Use this command to setup new location of slices eg CMD scan updateSlicesPositionsFromVoxelResolution 0 25 CMD lt Image3D gt mirrorX to invert x positions of voxels CMD lt Image3D gt mirrorY to invert y positions of voxels CMD lt Image3D gt ShowBoundingBox to show the bounding box of the 3D Image CMD lt Image3D gt HideBoundingBox to hide the bounding box of the 3D Image 83 lt float thickness gt spaceBetweenSlices gt 18 1 2 Point 3D CMD lt Point3D gt setColor lt int red gt lt int green gt lt int blue gt to set the 3D point color red green and blue are 3 integers from 0 to 255 e g for orange CMD P1 setColor 255 127 0 CMD lt Point3D gt showName lt truelfalse gt to show of hide the nam of point in the 3D view e g CMD P1 showName false CMD lt Point3D gt setSize lt float size gt to set the point size e g CMD P1 setSize 1 2 CMD lt Point3D gt setStyle lt int style gt 0 for z slice 1 for ball e g CMD P1 setStyle 1 CMD lt Point3D gt setPosition lt float x gt lt float y gt lt float z gt to set the position in the 3D space e g CMD P1 setPosition 0 0 10 0 2 5 CMD lt Point3D gt setLocalPosition lt float x gt lt float y gt lt float z gt lt string reference same as setPosition but using the basis of object reference e g set postion of P1 to the voxel 10 15 3 of the 3D image scan CMD P1 setPosition 10 15 3 scan 18 1 3 Plane CMD l
61. ientation e Fill holes looks for small sets of unselected voxels closed inside selected voxels and select them if count is lower or equal to the max hole volume or if all holes are targeted see fig 44 This can be done in 3D on current slice or on all slices reagrding the selected slice orientation 16 3 5 Lasso Click on the lasso button to select this tool On the slice view hold left button to make a free hand drawing Release left button and move the mouse A yellow line shows the next segment in real time Left click to validate this line see fig 45 To close the lasso and fill interior hold the Ctrl key and left click anywhere This click will not be a part of the lasso When closing the lasso you can hold the Alt key to substract lasso to selec tion rather than adding it Magnetic the magnetic option customisable with the 2 sliders Angle toler ance and Area width will use the parent image to make local HMH compu tation in 3D and attract the lasso on shapes When you move the mouse the lasso drawn in red will be validated by the next click while the yellow segment helps you to find the good shape to follow 76 Figure 42 Segmentation grow selection top before growing and bottom after growing 77 Figure 43 Segmentation removes small components On the top the original selection and on the bottom the small components which volume was lower or equal to 2 voxels are removed
62. image Segmented 3D image Slope from dicom tags Intercept from dicom tags o Ae Ww N factor e Output 1 Prefix name of data to output e Callable name in scripts Data Weight MaterialImage3D This plugin is avaliable only on segmented images You can convert a 8 bits image to a segmented image by clicking the convert to segmentation button in the Image3D object control window group box segmentation see 3 2 Note that your image must be shown and must be a 8 bits depth image A material is a set of voxels with the same grey level in the segmented image For example 0 black is the air 1 is the soft tissues and 2 is the bone The plugin will look at the grey value of each voxel in the original 3D image and use the Slope and Intercept inputs to compute the Hounsfield value of each voxel Voxel_houns field grey value slop You can find the slope and intercept values in TIVMI in the user interface of 3D image see 3 2 This information are provided only if the 3D image has been loaded by the load dicom plugin Then the weight of the voxel is computed 54 Vorel_weight_cm3 Vovel houns field 1 0 3 voxel It is scaled to the real volume of a voxel This weight is given for a 1 cm Vorel_weight pie Vozxel_weight_cm3x A hes 2istance petwcen slices Then all voxel weights are summed to get the material weight The factor is used in the case of scaled grey levels on the original 3D image if the original
63. ion file Use ful if you need to change default folders for states or setup proxy informations for live update if tou are behind a proxy see III 2 3D layout 2 1 3D view e left mouse button and movement rotation e middle mouse button and movement pan translation parallel to the point of view e right mouse button and movement up and down or forward and back ward zoom in and out e TIP if you want to rotate the object in a clockwise way from the point of view use the left mouse button and draw small counter clockwise circles e Hold Ctrl key and click on an object to center the view on the targeted point e see 3 1 for more customization of 3D view 2 2 tools Tools are a tree containing all objects in the TIVMI memory They are sorted by type The first column is the name of the object and next to the name you will find actions 2 2 1 Main behavior 1 Name of the object a double click on it will bring up the object control window and select the correct object in the list 2 Eye show or hide the object 3 Hard drive swap the object It writes the object to the hard drive to save memory You can unswap it by clicking again on it 4 Red cross delete the object 5 Pencil rename the object 6 Target center the camera point of view on the object This is equivalent to go to the camera and environment window control select the object and set target see 3 1 You can select m
64. is locked and endocranium is unlocked The skull in green is not modified Fig 31 and 32 show how a selection in red crossing the skull material in green and the endocranium material in blue is added to a 3rd material named test in light purple while skull is unlocked and endocranium is locked The endocranium in blue is not modified Fig 33 and 34 show how a selection in red crossing the skull material in green and the endocranium material in blue is added to a 3rd material named test in light purple while skull and endocranium are locked Neither the skull nor the endocranium are modified The red button will set all selected voxels to the label 0 zero As the button locked materials are not affected No material needs to be selected before The Add new material button will create a material with a generic name and a random color 67 DB Mainwingow To a la Dockable windows ee 2 shoe view No tool ax Name Col Lek Bih Del Sel shw R 1 a7 K 2 Moix xi ES 22 Endocr ES X R e 43 test Brxrkr o Remove smal components Max smali component volume e 3D 4 S Da D EE a new materiai Figure 29 Material lock scenario 1 selection crossing skull and endocranium Wins Doctable windows Name Cl ck Dal Se tw 5 a mb entocanar T a a Brush ax Hold At key for rubber 1 3 4 Magic Wand ax roed are
65. its location in the 3D space is correct the new computed image should not reproduce the shift This plugin is usefull if you need to join two different DICOM sets of a unique object splited in different series 4 10 Reslice e Input 1 Image 3D to reslice Use basis 3D Basis 3D Plane of cuts Number of cut Space between cuts Pixel subdivision Ol E bai Joo Ee Pixel size e Output 1 Name of new 3D image e Callable name in scripts Image3D_Reslice_Image3D Compute a new 3D Image with slices parallel to a plane of cut or aligned to the x y plane of a given basis The second input is 0 or 1 1 means yes for using a 3D basis 0 means yesfor using a plane of cut Input 3 is the basis if you fill 0 in the second input you can let this combo list empty or with any 3D basis The plugin will ignore it If you fill 1 in the second input you must choose a 3D basis as input 3 Input 4 is the plane of cut If you fill 0 in the second input you must choose a plane as input 4 If you fill 1 in the second input you can let this combo list 23 Figure 8 Head resliced empty or with any plane The plugin will ignore it Input 5 is the number of cut to process This will be the slice count of the new 3D image If you fill with 0 the plugin will compute as many slices as needed for reslicing all the input image Input 6 is the space between cuts of the new image It will be also the new voxel thickness Input 7 is a
66. iven plane and that includes the point 8 10 Bench vice a mesh e Input 1 Mesh 2 Straight line e Output 1 Prefix for 3D planes e Callable name in scripts Planes_BenchVice_StraightlineMesh Creates 2 planes like a bench vice where the screw is the straight line see fig 15 This plugin also creates the 2 contact points This is usefull to compute the distance between the two planes 44 Figure 15 Making a bench vice around a mesh 45 8 11 Constrained Bench vice a mesh e Input 1 Mesh 2 Ground plane 3 Parallel straight line 4 top limit 5 bottom limit e Output 1 Prefix for 3D planes e Callable name in scripts Planes_ConstrainedBenchVice_PlaneStraightLineMesh Creates 2 planes like a bench vice Both planes are orthogonal to the ground plane and parallel to the straight line see fig 16 The contact point is taken only if its distance to the ground plane is less or equal to the top limit on the same side as the ground plane normal and less or equal to the bottom limit on the ground plane on the other side For limit inputs you can set 0 if you want to take into account only one side of the ground plane or 1 if you want to ignore limitation Both contact 3D points are also created Be careful created planes are infinite planes as all planes in TIVMI If you use the limit inputs you mean that you want to create half planes or a kind of stripe plane but TIVMI will display them as full infinit
67. l open file as big endians Try this option if the opened scan looks like snow The shift data option is used to convert signed representation of pixels in the file to unsigned representation used by TIVMI In the case of signed data the black area will look like grey white will look like black grey will look like white and the histogram is splitted see fig 9 Set 1 to the shift data option to get a correct image 4 13 Load DICOM e Input 1 Path e Output 1 Name prefix of new 3D image s e Callable name in scripts LoadDicom Open all files in the given path To avoid unwanted messages or troubles make sure that only DICOM files are present The plug in will analyze all DICOM files and try to recognize different studies if available Thats why the output parameter is a prefix In fact if the plug in detects more than one study 26 it will name the studies using the prefix and adding a count This plugin uses the DCMTK library 4 14 Load PGM3D e Input 1 Filename Conform to Voxel width Voxel heigh Voxel thickness Voxel corner 1 to 4 X Y and Z DO oo A Ww N e Output 1 Name new 3D image e Callable name in scripts LoadPGM3D Open the filename given as first argument Image dimensions are given in the file Voxel dimension and 3D positionning are unknown To setup voxel di mensions and 3D positionning you can use a 3D image as the second argument or fill in all following arguments 4 15 Lo
68. lar pixels bottom regarding slice orientation on non isometrics voxels 72 Figure 36 Segmentation brush tool draws or erase a selection Brae Name Gol Lek Brh Del Sel sw ES g nents 2903 321V 226 782 11 E n Figure 37 Segmentation magic wand tool in 3D The selection grows and stops when the voxel grey level is outside the range chosen in the histogram The propagation is in 3D 73 lola et Figure 38 Segmentation magic wand tool on current slice The selection grows and stops when the voxel grey level is outside the range chosen in the histogram 16 3 4 Selection manipulation Invert invert selection on the 3D Image Hold Alt key to invert current slice only see fig 39 Clear sets all voxels as unselected Hold Alt key to clear current slice only Horizontal mirror makes the symmetry of the selection along a vertical axis On XY view or XZ view this will make a X mirror On YZ view this will make a Y mirror see fig 40 Vertical mirror makes the symmetry of the selection along an horizontal axis On YZ view or XZ view this will make a Z mirror On XY view this will make a Y mirror Move moves the selection in 3D see fig 41 If a part of the selection is out of the image dimensions it will be kept during the move but lost when the mouse button is released Grow grows the selection in 3D Each unselected voxel next to a se
69. lected voxel in 6 connectivity will be selected see fig 42 Shrink shrinks the selection in 3D Each selected voxel next to an unse lected voxel in 6 connectivity will be unselected 74 gt ai Dockable windows Name Col Lck Brh Del Sel shw R A Ds d m TZ zoom Auto Hold ak key to proceed current sce only Hole She key ro ada to selection SIC 10 i Remove small components ax sll component volume 3D J Sd Cdl Edl C left eto dose selection Cir A left ck to dose and subsractselecnan Magnetic chad el eae leer Area with 10 Add new materiel Figure 39 Segmentation inverted selection all is selected but the bone previ ously selected kea i T Ds d E 7 Size Q 5 Hold AR kay for rubber Magic Wand ax Saiz 7 e Minor Let Right Li ox 510 771 293 1372 11 irl left eli to dose selection Cri A left eck to dose and substract selecnon Magnet Angle tolerance 45 Area wath 10 Figure 40 Segmentation horizontal mirror of a selection 75 BD Mainwindow TT elt Figure 41 Segmentation move selection e Remove small components looks for small sets of selected voxels and unselect them if count is lower or equal to the max small component volume see fig 43 This can be done in 3D on current slice or on all slices reagrding the selected slice or
70. mals e g CMD head showNormals true CMD lt Mesh gt invertNormals to invert normals e g CMD head invertNormals CMD lt Mesh gt setPointSize lt float size gt to set the size of vertices only for point cloud e g CMD timeOfLightScan setPointSize 3 CMD lt Mesh gt setResolution lt float resolution gt to set the display res olution of point cloud Resolution is a percentage from 0 excluded to 100 included e g CMD timeOfLightScan setResolution 50 CMD lt Mesh gt setLDResolution lt float resolution gt to set the low def inition display resolution of point cloud The low definition resolution is a percentage from 0 excluded to 100 included used when moving the camera in the 3D view e g CMD timeOfLightScan setLDResolution 10 CMD lt Mesh gt setColorPerVertex lt 0 1 gt 1 to use the color per vertex if available 0 to use the general mesh color e g CMD timeOfLightScan setColorPerVertex 1 18 1 5 Bounding Box CMD lt BoundingBox gt setColor lt int red gt lt int green gt lt int blue gt to set the bounding box color e g for red CMD roil setColor 255 0 0 85 CMD lt BoundingBox gt setCorneri lt float x gt lt float y gt lt float z gt to set the coordinates of corner 1 e g CMD roil setCornerl 25 34 62 56 12 45 CMD lt BoundingBox gt setCorner2 lt float x gt lt float y gt lt float z gt to set the coordinates of corner 2 e g CMD roil setCorner2 23 92 20 41 72 12 18 1
71. ment to let you see the image 3D parent behind Hold the Alt key to transfrom the brush to a rubber and erase the selection see 36 16 3 3 Magic wand From a clicked voxel the magic wand will grow while the grey level of neighbor is inside the range chosen on the histogram To use the magic wand you should first select a range of grey values in the histogram click on the magic wand button and then click a voxel in the slice view see fig 37 The growth is computed in 3D Hold the Alt key to proceed with the current slice only see fig 38 If a selection is already set it will be erased and replaced by the magic wand computation To keep the selection and add the magic wand computation hold the Shift key You can hold Alt and Shift keys to use the magic wand many times on the current slice After a voxel click in the slice view you can change the grey range on the histogram If you do so there are 2 scenarios e The last magic wand computation was in 3D the computation will be updated only when you release the histogram range slider e The last magic wand computation was on current slice only the com putation will be updated in real time while moving the histogram range slider This is due to the computation time needed by the 3D growth A real time update would have slow dramatically TIVMI 71 Figure 35 Segmentation brush tool shown in blue with square pixels top and rectangu
72. n this case it is important to keep the original position of the MT as MDH is the direct measurement from the tip of the mastoid process to the Frankfurt Horizontal 2 Start recording a script here The mastoidale can thus be orthogonally projected on the MT with Plug in Point3D Orthogonal Projection Point On Plane Select the mastoidale and the MT and name the projected mastoidale 3 Create a segment between the mastoidale and the projected mastoidale Plug in Segment3D Make 3D segment from 2 points and name it MDH The projected mastoidale will not be used anymore it can be deleted Stop recording the script here MDH can be consulted in the Segment subwindow Figure 48 Orthogonal projections are also used to record the orbital height OBH which is the projected measurement vertically between the superior and in 103 ferior orbital rims The most superior suprakonchion and most inferior in fraorbitale landmarks of the orbital rims are however not aligned vertically a point to point direct measurement will not give the traditional OBH as if it was recorded with a sliding caliper 1 Position the most inferior and superior landmarks of the orbital rim visual positionning is sufficient for small structures as orbits 2 In order to record a straight projected measurement of OBH it is necessary to project the landmarks both on MS and MC Start recording a script now if you want to further automatise those operatio
73. nal So the new Y axis will correspond to the old Z and the new Z will correspond to the old Y The second image is oriented with the Y axis unchanged It means that in the new image X axis will correspond to the old Z the Y is unchanged and the Z will correspond to the old X If the original image is an axial view and the lateral axis of the specimen is the X axis in the image the the first orthoslice will be a frontal view and the second will be a sagittal view Otherwise if you make a mistake you can rename any object in TIVMI see 2 2 Created images are correctly located and oriented The most important is to note that in the case of non isometric voxels new images have rectangular pixels see figure 7 An isometric voxel has the same length width and height In most medical data set it is not the case DICOM images have square pixels 20 Original 3D Image zoomed on soft tissues Gaussian blured image Teta 1 NJ A Gaussian blured image Teta 2 A Figure 5 Gaussian blur on a 3D image with 2 different values of theta Original axial 3D image and Sagital and frontal orthoslices Original 3D Image axial slices Figure 6 Orthoslices 21 Rectangular pixels on orthoslices Square pixel on orginial 3D Image Slices intersections Figure 7 Zommed view of orthoslices on non isometrics voxels but the distance between slices is different and often greater than the pixel size An orthoslic
74. ng the coordinates of a vertex in the space nX nY and nZ are floatting points numbers designing normals Normals must be normalized r g and b are integers from 0 to 255 included designing the color of the vertex c is an integer from 0 to 255 included designing the grey value Indexed colors are not supported in TIVMI 29 5 2 Load obj e Input 1 Filename e Output 1 Name of new mesh e Callable name in scripts loadobj Open the file given as input TIVMI does not support materials and groups yet 5 3 Load stl e Input 1 Filename e Output 1 Name of new mesh e Callable name in scripts loadstl Open the file given as input TIVMI supports ASCII and binary formats 5 4 Load ply e Input 1 Filename e Output 1 Name of new mesh e Callable name in scripts loadply Open the file given as input TIVMI supports only mesh and point cloud formats 30 5 5 HMH Surface 2 e Input 1 Image 3D Mode Gray threshold Gray min Gray max HMH Max length Binary image ND om BP WwW WY e Output 1 Name of new mesh e Callable name in scripts Mesh_HMHSurface2_Image3D Creates a mesh from a 3D image using the HMH surface algorithm The first version of HMH Surface is not supported anymore Please use the HMH Surface 2 plugin instead Mode defines the way to compute vertices e mode 0 free Vertices are free to move in spage along the HMH seg ment This causes topological troubles on
75. ns 3 Project the landmarks on the MS Plug in Point 3D Orthogonal Pro jection Point on Plane Project those projected landmarks on the MC Figure 63 Figure 63 a Most superior and inferior landmarks of the orbital rim b Pro jection of both landmarks on the MS c Projection of the projected landmarks on the MC d Shifted segment equivalent to the traditional measurement OBH 4 Make a 3D segment from the last projected landmarks and name it OBH Plug in Segment3D Make 3D segment from 2 points Delete all pro jected landmarks Stop recording the script here OBH length can be consulted in the 3D segment subwindow 5 For a better visibility the 3D segment can be shifted Plug in Segment 3D Segment 3D Shift Segment 3D Along Plane Normal with ratio It creates another segment the original one can be deleted 23 3 Measurement of soft tissue depth Since both hard and soft tissues can be reconstructed with medical CT scans the soft tissue depth STD can be measured at specific landmarks To enhance 104 the repeatability and reproducibility of such measurements projection and au tomatic determination of the interface between skin and air can be computed in TIVMI 1 The glabella has been positioned using the MC plane Start a script here 2 Use the projection of point following the normal of a plane Plug in Point 3D Shift point along the normal of a plane In this case we want to measure the STD at th
76. nt see only add o selection Remove smal components Max sal component volume vone count 100 3D Sa x Figure 30 Material lock scenario 1 selection crossing skull locked and en docranium unlocked added to the test material 68 DB Mainwingow To a la Dockable windows Name Oa Lek Brh Del Se Sm TE By x 21 sai Harxre ar ax 3 Endocanium IO XR e a3 he B X ro on A ey rer aoa halle pa eee GL ree as Remove small components Figure 31 Material lock scenario 2 selection crossing skull and endocranium D MairWindow To a mal Dockable windows stele E aov Mo teal ax Name Col Lek Bih Del Sel hw R 1 Erte B7 K 21 sail Ho xr e E ax 32 Endocranium JG Xk as tet B7 Xk e on Hold At key for rubber Magic Wand ax proceed current sie oniy 1 add selection ax Remove sat comporcers Max al component volume oe tourt 100 E 0 0 0 x x x x x x le Lasa ax ed ne ater Figure 32 Material lock scenario 2 selection crossing skull unlocked and endocranium locked added to the test material 69 BD Mainwinaow To a la Dockable windows ET mm tm ieee aS 10 Exe Or R 23 ull marxre aa ae 3 Endocanium OX e as BX ke on ae a gt hadita 7 fal ae haere ile eee e A me DEREI el as e x 3 3 mE came
77. o a sphere volume like volume computa tion tissues analysis etc 4 7 Gaussian blur e Input 1 3D image 2 Teta e Output 1 Name of new 3D image 18 Figure 4 Voxels out of the sphere are set to 0 19 e Callable name in scripts Image3D_GaussianBlur_Image3D Compute a 3D mask of 6 round theta 1 size Each cell of the mask contains a value computed using a gaussian function Considering that mask dimension is always odd and the center of the mask has coordinates Cs 0 cy 0 cz 0 the value stored in a cell x y z has the value 1 22442422 Cita ab T2 theta Fe 2theto This plugin is not equivalent to a 2D gaussian blur on each slice It is a real 3D gaussian blur Then each voxel of the new image is the original voxel convolved by the mask scaled to a ratio of 1 The new image has the same depth position orientation and voxel size of the input 3D image This plugin can be used to reduce noise on images Complexity is exponential This plugin is multi threaded but it still can take a while even on a powerfull computer 4 8 Ortho slices e Input 1 3D image e Output 1 Name of first new 3D image 2 Name of second new 3D image e Callable name in scripts Image3D_OrthoSlice_Image3D Compute 2 new images orthogonally to the original one see figure 6 The first image is oriented with the X axis unchanged It means that in the new image the X axis will be the same as the origi
78. ore than one object using a multiple selection shift and or control click and click on an icon to apply the action to all selected objects 2 2 2 Groups You can group several objects in a group even if objects are not of the same type This is useful to collapse a group of objects and save space in the tree and also to hide or show all objects without a tedious multiple selection Right click on an object or on a multiple selection and click on add to group New group Give a name and click on OK You can also add objects to an existing group through the same menu A right click on an object inside a group will offer you to remove the object from the group Very few plugins use groups but this will evolve later 3 Objects control Each sub window contains on the top a combo list of available objects All controls will apply to the selected object chosen on this list If the list is empty it means that there is no object of this type OR the object is hidden Show it see 2 2 and it will appear I will describe only some features I let you discover others You also must know that EVERY object must be named with a unique name 3 1 Camera and environment e set target centers the camera on the selected object Useful to rotate around easily or simply recover it in the viewing space e g a DICOM file contains a 3D location and TIVMI respects this information So the DICOM slices may appear far from the origin 0 0
79. rt record Create four planes passing by both porions and left infraorbitale both porions and right infraorbitale both infraorbitale and right porion both infraorbitale and left porion Use the Plug in Plane Make plane and 100 Mesh skin Vertices 701284 Faces 825170 m ES g Figure 58 Transparency of mesh Figure 59 Placement of the infraorbitale and porion name them FH1 to FH4 As objects the planes must be displayed Show Hide Plane and applied to a specific constraint image 3D or mesh through the Plane subwindow Figure 60 Each pair of plane can thus be used to create a mean plane Plug in Plane Medium plane and the two resulting mean planes can be aver aged together to get the final Mean Transverse MT plane When using medium planes the user must be careful to orient the normal of each plane in the same direction The normal of the planes can be displayed and inverted in the Plane subwindow Figure 60 The frontal or coronal plane can be constructed by creating a plane or thogonal to MT and passing through both porion another one passing through both infraorbitale Plug in Plane Make an orthogonal plane thru 101 Plan Frank Y Color Constraint target of constraint bone v Apply constraint Z Show Normal 1 E Plan thickness ba E Figure 60 Plane Subwindow 2 points The Mean Coronal MC plane can fin
80. s follow a Image 3D the original 3D image the CT scan b Mode 0 c Gray threshold 0 because you will use a binary image to define the object to extract a Nw Gray min 0 Gray max 65535 for a 16 bits CT scan see 5 5 HMH max length 0 _a a gt O s 110 Loa lea Figure 70 Add a selection to a material g Binary image choose the mandible_binary 3D image previoulsy created and maxillary binary for the second call 10 You can delete both binary images 11 Show both meshes and choose a color see fig 77 The HMH surface plugin will evolve to create automatically a mesh by material The binary image in input will be replaced by a segmented image 111 File Plug in Seript Diay Bounding Box ATT pie LEX Image 3D tomatic organisation Cascading J scan2 eex o i Seve to default al Lood default segs REX aMesh bone sgx 0 Veriss 179940 Faces 380040 calor Opady a Di shinies torna nomal per foe crepes horma per vertex sooth E show a sce Saktan O epic pame venere Pairt Sprei peiie ponese 100 Resolution percent 100 00 Moving resolucion percent 1 00 EZ color per vertex PEI Bror Bena Brno Breno Boro Winns Peres n Figure 71 Create a surface from a segmented 3D image Doctable windows Materiais E i tio toot Name Col Lek Bh Del
81. see 3 2 select the parent image in the list In the segmentation box a list of potential segmentation is available This list is filled with 8 bits 3D image which have the same dimension as the parent image Choose a segmentation in this list then click on Edit fig 22 16 The segmentation GUI The GUI starts with a default placement the material list is on the left 1 on fig 23 The slice view associated with the image histogram is centered 2 on fig 23 and tools are on the right 3 on fig 23 63 BD Mainwindow ren Dockable windows hotels E Stes vew Mo tal pla 7 A eon 1 2 ES ni se page Add new material Figure 23 Default configuration of segmentation GUI The Material list and tools are dockable windows and can be moved out of the segmentation window This is useful to maximize the slice view surface on dual screens see fig 24 The main goal of this GUI is to help you to set a label on voxel This means set a voxel as a material It consists in selecting voxels with tools and add the selection to a material You can select any voxels even if they are labelled or not 16 1 Slice view This part of the GUI displays the parent image with the segmentation as an overlay 3 buttons on the top change the slice orientation XY is the default 3D Image slice orientation YZ and XZ are orthoslices As in the 3D view of TIVMI non isometric voxels are displayed as rectangular pixels
82. subdivision control 1 means that only one measurement is done in the original image to compute the grey level of the corresponding voxel in the new image The position of the measurements are determined randomly for each voxel A regular sample brings fringes Random samples will automati cally smooth those fringes like a low frequency filter The computation time is multiplied by this parameter A good value is between 4 and 8 Input 8 is the target pixel size Big values will give less informations and the image will be less accurate Small values will give big images and big memory comsuption and fringes can appear A value near the voxel size of the original 3D image is a good choice If the number of cuts is different from 0 the first slice of the new 3D image will be located exactly mingled to the plane of cuts or to the x y plane of the 3D basis All next slices will be computed in the way of the plane normal or in the way of the Z axis of the 3D basis The new 3D image is a resample of original image so it is recommended to 24 reslice only original data and not reslice a reslice Reslicing an orthoslice is possible because TIVMI don t resample on orthoslice see 4 8 This plugin use multithreads so comuptation time can be seriously reduced if multithread is available 4 11 Voxellize a mesh e Input 1 Mesh Voxel width Voxel height Voxel thickness Bits per pixels must be 8 or 16 a oF uN Margin e O
83. surface in the 3D view From the Segment 3D subwindow Figure 48 click on Pick new and click on the target landmark location Give a name segl The next click on the 3D view will place the second landmark of the segment and create the segment If one of the point is not well positioned select the segl segment in the combo list and click on Pick move point 1 or 2 to change the location of the landmark and length of the segment The coordinates of the 2 landmarks along with the length of the segment can be exported or copied to the clipboard from the Segment 3D sub window 93 Segment 3D DDR Segment 3D segl v Color Size 0 2 Apply size Length 20 2123 3D picking Choose a 3D object reference scan Pick new Pick move point 1 Pick move point 2 Export Copy to clipboard Figure 48 Segment 3D subwindow 21 2 Create a segment from 2 existing 3D points 1 2 oe Ae o Go to menu plugin segment 3D make a 3D segment from 2 points Input In the first combo list choose the first landmark In the second combo list chose the second landmark Output give a name seg2 Click on show hide segment 3D segplp2 In the Segment 3D subwindow the length of the segment is specified the unit is the one by default in the DICOM file usually mm 21 3 Evaluate the density profile on a segment The HMH profile can be observed on a segment in TIV
84. t lt string name gt lt float value gt to create a floating point number e g NEW GenericInt supposedVolume 563 98 NEW GenericString lt string name gt lt string value gt to create a sentence Double brackets are optional e g NEW GenericString readMeFirst Look at the front side of this bone NEW Afa3D lt string name gt lt string originalMeshName gt to create an Afa3D object If provided the Afa3D object will be based on a mesh e g NEW Afa3D specimen aSkullMesh NEW Group lt string name gt lt string objectName1 gt lt string objectName2 gt to create a group named name containing objectNamel object Name2 etc e g NEW Group study myMesh aPointi aPoint2 aSegment 89 18 3 Regular expressions Always begin with RE followed by the string containing commands and regular expression e g RE Show point 0 9 18 4 Delete objects Always begin with DELETE followed by the name of object to delete e g DELETE P1 18 5 Show objects Always begin with SHOW followed by the name of object to show e g SHOW P1 18 6 Hide objects Always begin with HIDE followed by the name of object to hide e g HIDE P1 18 7 Rename objects Always begin with RENAME followed by the name of object to rename and fol lowed by the new name e g RENAME Pi P2 18 8 Call a plug in Always begin with CALLPLUGIN followed by the name of the plugin see chapter IV and followed by input list and o
85. t Plane gt setConstraint lt string object gt to set limitations to ob ject to display the plane Object can be an image3D a mesh a bound ingbox or a path3D e g CMD frontal setConstraint head CMD lt Plane gt showNormal lt 0 1 gt 1 to show normals 0 to hide the normal e g CMD francfort showNormal 1 CMD lt Plane gt setColor lt int red gt lt int green gt lt int blue gt to set the plane color red green and blue are 3 integers from 0 to 255 e g for purple CMD frontal setColor 127 95 127 CMD lt Plane gt invertNormal to invert the normal e g CMD frontal invertNormal CMD lt Plane gt shift lt float distance gt to shift the plane along its nor mal If distance is negative the plane will be shifted backward the normal e g CMD frontal shift 42 67 84 18 1 4 Mesh CMD lt Mesh gt setColor lt int red gt lt int green gt lt int blue gt to set the mesh color e g for bone color CMD head setColor 235 235 220 CMD lt Mesh gt setShininess lt 0 1 gt 1 to enable the shininess 0 to disable it e g CMD head setShininess 1 CMD lt Mesh gt buildNormals lt 0 1 gt 0 is normal per face 1 is normal per vertex e g CMD head buildNormals 1 CMD lt Mesh gt scale lt float factor gt to scale the mesh e g CMD head scale 10 CMD lt Mesh gt optimizeVertexUse to delete duplicates vertices e g CMD head optimizeVertexUse CMD lt Mesh gt showNormals lt true false gt to show or hide nor
86. t can be displayed by TIVMI in the 3D view as a grey level 3D image like other 3D images but a specific interface is provided to create and edit a segmentation Each label can be named and has a color A segmentation is always associated to a 3D image the parent image This parent image is a 8 bits or 16 bits 3D image like a CT Scan 14 Creating a segmentation 14 1 From scratch To create a segmentation you need the parent image to be displayed in the 3D view Then in the Object Control pannel in the Image 3D tab see 3 2 select the parent image in the list fig 21 step 1 and click on the button Edit a new segmentation fig 21 step 2 A new 8 bits 3D image si created with the same dimensions and position in 3D as the parent image The name is automatically set to the parent image name 62 oo Coe oe Peo Figure 22 Create a segmentation from a 8 bits 3D image with the seg prefix 14 2 From a 8 bits 3D image If you own a 8 bits 3D image imported from another software you can convert it to a segmentation Display the 3D image in the 3D view then choose it in the image list and click on convert this image to a segmentation 8 bits image only The 3D image will be tagged as a segmentation image and will appear in the segmentation list below 15 Editing a segmentation To edit a segmentation the parent image must be displayed in the 3D view in the Object Control pannel in the Image 3D tab
87. t will define how the computation is done e O index Mesh 1 and Mesh 2 should have the same number of vertices The new position of the nt vertex is the ratio applied between the nt vertex of mesh 1 and the nt vertex of mesh 2 e 1 euclidian The Mesh 1 is duplicated to create the new mesh and each vertex is moved to the nearest vertex found on mesh 2 The method can take a while to compute 6 Creating a 3D Point 6 1 Intersection plane and straight line e Input 1 Plane 2 Straight line e Output 1 Name of new Point 3D e Callable name in scripts Point3D_Intersection PlaneStraightLine Compute a point at the instersection of a plane with a straight line If the straight line is parallel to the plane the plugin will not create the point 32 6 2 Orthogonal projection point on plane e Input 1 Plane 2 3D Point e Output 1 Name of new 3D Point e Callable name in scripts Point3D_Intersection PlaneStraightLine Compute the orthogonal projection of the point to the plane 6 3 Orthogonal projection point on straight line e Input 1 3D Point 2 Straight line e Output 1 Name of new 3D Point e Callable name in scripts Point3D_OrthoProjection_PointOnStraightLine Compute a point following an orthogonal projection of the point on the straight line 6 4 Make a 3D point on a 3D segment from a ratio e Input 1 3D Segment 2 Ratio e Output 1 Name of new 3D Point e Callable name in scripts
88. this e live Contains informations for the live assistant The live assistant will replace the live updater and will provide a graphical interface to manage the license You shouldn t need to modify this e mdiDisplayConfiguration This contains the configuration of mdi windows Mdi windows are the window system of object control You shouldn t need to modify this The only option you can edit is the docked one Set it to true to dock the mdi window inside TIVMI Else set it to false This is useful if you use dual screens In this case the object control window should be on the second screen If you go back to a single screen configuration the object control window is lost Set the docked option to false close TIVMI and restart it e updater Contains informations for the live update This will be replaced by the live section 13 proxy let you configure the updater to use a proxy connection first setup the enable switch to true Then fill host password port and username autoUpdate this switch enable set to true or disable set to false the updater at each TIVMI startup Directory do not modify Server do not modify e AllowedThreadCount is the number of thread that TIVMI is allowed to use on multithread processings Yous should set it to the core count of your system minus 1 to let you use your system during a computation You can find the
89. ts Use the mouse left button down in the 3D view to rotate around the image 3D In the Point 3D subwindow Figure 47 click on the pick new button in the 3D picking group don t use the HMH 3D picking group Click on the wanted structure in the 3D view to create the point The location of the landmark must then be visualized prior to clicking on pick new Give a name pl Each landmark should be given a specific and unique name if scripts are to be computed In the Point 3D subwindow it is possible to change the style to ball and change the size and color 92 21 Point 3D color Style Z slice Coordinates X Y 2 World Local Image3D Point 3D TBIR x Size apply Coordinates and size 30 picking Choose a 3D object reference v Pick new Pick move HMH 3D Picking Reference Mesh v Reference Image 3D HMH Y Automatic Manual value Segment length V Automatic Manual value L _ Pick new Pick move Export Copy to clipboard Figure 47 Point 3D subwindow Create a segment and find the HMH inter face between two tissues There are two ways to create segments Use a plugin to create a segment based on two existing landmarks or create directly a segment 21 1 Create a new segment L Localize the position of the first landmark beginning the future segment on the slice or
90. utput 1 Name of new 3D image e Callable name in scripts Image3D_Voxellize Mesh Compute a grid of voxels oriented as the world basis Each slice is parallel to the plane X Y The new image dimension is computed taking into account the bounding box of the mesh and margins The result is a binary 3D image which depth is specified in input If the geometric center of a voxel is inside the mesh the voxel will have a grey level of 255 for 8 bits image or 65535 for 16 bits image Else 0 is stored If you want to simulate a simple CT Scan acquisition use the gaussian plug in to blur the binary image This plug in will improved the image since the border of the mesh will be represented as melted grey levels Be careful the algorithm is dependant on the mesh s face count So computation can take a very long time on big meshes 4 12 Load Analyze Img and Hdr e Input 1 Hdr filename 2 Big endians 3 Shift data e Output 1 Name of new 3D image e Callable name in scripts LoadAnalyze 25 File Object Plugin Script Option Help Deploy Vin Bren Wess Brno Bisogno Brora W mem W camer anewrenment 4 gi Figure 9 Signed data opened as unsigned data issue Open the hdr file given as argument and automatically deduce the img filename by replacing hdr by img Setting 0 to the big endians option will suppose that the file has little endian encoding most of computers 1 wil
91. utput list Input and output lists are lists of arguments separated with space Each argument of input list is prefixed by in Each argument of output list is prefixed by out After the use object names numbers or strings e g CALLPLUGIN Image3D_DoubleThreshold_Image3D in scan in 10534 in 38610 out binaryScan 90 19 Script generation The Script menu contains the Start record command that begins the gen eration of the script User must use specific object names to make them recog nizable for further use of the script in other TIVMI states i e saves 91 Part VII Scenarios 20 10 11 12 13 14 15 16 Open a DICOM exam and place 3D points on slices Menu plugin Image3D load dicom Input browse a folder containing a list of dicom files Output give a name scan for example If the load dicom plugin detects multiple series it will create more than one image3D and number them Click on OK Click on show hide image 3D scan In the camera and environement subwindow the top combolist will contain scan Click on set target The image3D scan will appear in the 3D view Use the mouse right button down to unzoom the 3D view if the scan is not visible In the Image 3D subwindow move the scroll bar slice to navigate into slices In the Image 3D subwindow move the scroll bar window width and window center to change the contra
92. vmi Serialized Object It consists in a binary version of the object writable in a file The object type is stored in the file so TIVMI is able to read it and create a well typed object see 13 1 This plugin is used by the save state menu 12 13 Save Image 3D to VFF e Input 1 Image 3D e Output 1 filename e Callable name in scripts SaveToVFF Save a 3D image to the VFF file format VFF is a file format used by the MicroView software 13 Creating any object This section contains plugins that are able to create any kind of object in TIVMI For the moment there is only one of those 13 1 Load tso e Input 1 Filename e Output 1 Name of object to create e Callable name in scripts LoadTso The tso file format is for Tivmi Serialized Object It consists in a binary version of the object writable in a file The object type is stored in the file so TIVMI is able to read it and create a well typed object This plugin is used by the Load state menu 61 eana image 3D scan eex o Mesh ibe Figure 21 Create a new segmentation Part V Segmentation The segmentation consists in labelling voxels of a 3D image A label is a number between 1 and 255 All voxels with the same label is a part of the same material or region A voxel cannot be tagged by 2 or more labels The label 0 zero is used for non tagged voxels The segmentation is stored as a 8 bits depth 3D Image I
93. w ae dS ane Bae AR 62 14 2 From a8 bits 3D image oee soy kat teatea avt w aia 63 15 Editing a segmentation 63 16 The segmentation GUI 63 GUSTO VIEW a ted di a A Rak wy ate at 64 16 2 Materials St ergi ka ere e aid la as a 66 16 3 Tool ciao ar a Be io a n 71 16 34 NOOO 2200340 24 feed oe as ss id x 71 16 32 Brusk 00 0 a E A is Wha 71 16 3 3 Magic wand 0d hee Oe ake ae a 71 16 3 4 Selection manipulation 74 16 3 0 ASSO iair e e o a eee ed aed 76 17 What can I do with a segmentation 81 VI Scripts 83 18 Scripting language 83 18 1 Commands on objects s ice a iera s kawot aoda 83 18 1 1 Image 3D m asi 40d ha g e aa ma God Ego we ee AA 83 181 2 Pont 3DU soga ea E BR oe eek vain a 84 US dS Plane Ds tisk ee eg eh of ae A RA 84 SAA Mest tico ee et ee gp eR e o ee ee 85 18 15 Bounding Box sisi core emana doran ia EE aa 85 181 6 Sement BD ia Sis aw a ae Oe a 86 18 1 f Straight lines essc coe 645 4 204 SA ee ea eed 86 18128 Path GID ona vow aoe ee ae ee ge ay Eo donate ee a GOK 86 13159 CAPAS 02 sea e a dt eee Bae Bak egies a 87 ISSO Groupies fo eee a Boe ee PS Oe ree Be E SE 88 18 2 Commands to create objects o 89 18 3 Regular expressions ws secs e A a ee E a 90 18 4 Delete objects 2 4 i wom to ee e a eR ee A 90 18 5 Show ODJEGUS p scra aca ack ee ae Oa eek eae a 90 18 6 Hide objects i 2 e toe i ee eee ee Kee ad 90 18 7 Rename Objects seoce m s rias BH Do oe e

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