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CardioViz3D : Cardiac Simulation Data Processing - GForge
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1. Size 80 x 80 x 103 mm o Data Manager View Port atlastmri v Mame O oO o Data Attributes Sequence No attribute v Sil Figure 2 10 left In the information toolbox you will find the save button allowing you to save currently highlighted dataset at any time into a specified file right From the main toolbar you can save the entire data manager with the save button Note that this action might take some time for large sets of data At any time you can save the currently imported data in CardioViz3D As shown in section the imported data is summarized in a dedicated window Select highlight a specific dataset here From the information toolbox you can save this dataset in a desired file see Fig 2 10 Note that the extension given by the user will be determinant for the writing process However if no extension is given then the dataset is saved in a default format TIP Ctrl S when a dataset is highlighted will pop up a save dialog In case the dataset you want to export is a sequence process the same way unless you will be asked for a export directory in it is a mesh sequence In this case CardioViz3D will save a serie of VTK files or Analyze dor images corresponding to all frames of the selected 18 sequence In case of image sequence CardioViz3D is able to read and write 4D image files Note that for that specific case of image sequence you will need a file format that supports 4D images W
2. _ Value Hue Saturation IO 7 Opacity Line Width 100 2 Tes salid Gouraud Attributes mapping Mot available E Bar Figure 3 4 This figure shows the mesh visualization parameterization being used You can set its color some light effects surface representations wireframe surface etc On the right is shown a mesh rendered in the 3D view 23 a specific attribute of the currently selected mesh see Sect 2 5 Note that you might en counter some known issues when you try to transfer a mesh from a view port to another you loose the attribute visualization properties you might have set befor ethe transfer Scalars are mapped in the mesh representation s Linear interpolation is done between values Note that interpolation is not done in case the scalars are associated to triangles or any other cell type You can choose the color map to associate to the currently visible scalars and you can display the corresponding scalar bars in the views TIP sometimes the lighting settings can affect the colors In case scalars are mapped to the mesh disable any light by setting the color value down to zero 3 3 Snapshot and movie exports 0 0700 0 0350 Snapshot Handler Camera 0 00 Number of frames 186 Previews Create INRIA 2007 CardioViz3D Figure 3 5 From the main toolbar you will find the snapshot movie export button In case of
3. As INRIA INRIA Sophia Antipolis Research Project Asclepios CardioViz3D Cardiac Simulation Data Processing and Visualization User Manual Nicolas Toussaint April 28 2008 INRIA Sophia Antipolis Research Project ASCLEPIOS 2004 route des Lucioles BP 93 06902 Sophia Antipolis Cedex France Contents 5 De beee ee E eee reese ee ee ee eee ees 5 ee ee re ee 5 EA AAA AA 6 ETE EEE 6 LAA WINDOWS 2 20 errores AAA 7 pana AAA E A ee ee E ee ee ee ee T Lo Cod gt rento desa eee ERE eGR eee ee EG T 2 Data management 9 aa woe eee eee DA ARA 10 2 1 1 Supported and unsupported configurations 11 AA 12 E RD DD AAA 13 oo oe oe Asas res mesa ee 14 Hoe eee ee eae eee Eee eee ewe ee he ee eS 14 fee E EE eee eee Re eee a 15 2 0 1 Static mesh attribute 2 ee 15 ee ee ee ee 17 FREE 18 2 6 1 Exporting a DICOM exam 2 04 19 3_ Generic vizualization tools 21 AAA AA 21 3 2 Mesh vizualization oa a a a a a a 22 RARE asa E Ss Rd eae eee eee 24 324 Timetables s ao ona ee brisa EPA ES 25 3 4 1 Landmark follow up 0 0 0 0 00 cee eee ee 25 3 4 2 Global parameter evolution follow up 26 yee ee eee eee ea ean eee ee E A E 21 29 Pe eee eee yp eee ee ee ee ee na 30 pe be ee eee et ene ee eee ase ne eee a eae 30 See SAM Pa eee ee ea ee Oe eee A eee pe ee 30 bee kent ESSAS ea eeeeaeheeee enue E E 31 eb eeeuereee ep E Seen eee Gee
4. From this link you will find 1 More screenshots amp tutorial videos 2 Some example data links to the heart anatomical atlas as well as the DTI heart atlas 3 Online html documentation 4 forums and user mailing lists feel free to let any comments on CardioViz3D forums 5 News about future feature and recent releases 6 etc 41 A2 Bibliography 1 http www itk org 2 http www kwwidgets org 3 http www vtk org 4 R Deriche Recursively implementing the gaussian and its derivatives Technical report INRIA 1993 5 G Turk and J O Brien Variational implicit surfaces Technical report Georgia Institute of Technology 1999 43
5. activate the cropping box control the windowing etc The image vizualization parameters allow you to set the color map of an image Fig Volume rendering mode is available You can also activate the shading effects on the volume rendering from the visualization toolbox Note that volume rendering is not supported by all graphic cards Note also that the shading effects dramatically slow down the rendering time The windowing feature consists on a range that you can control either with the mouse or with the corresponding minimum and maximum value entries Note that the range is synchronized 21 with the mouse interaction in the 2D views There is an interesting feature that allow you to see all your imported images and image sequences in a same page the Preview Page see Fig 3 2 Activate Deactivate this feature with the View Menu Application Settings CardioViz3D settings ROSAS Sees 0_20060103_MR_ tfisdy2ci1 Figure 3 2 The preview page summarizes all imported volume images If sequences have been imported they will be played also here You can activate and deactivate this feature through the Application Settings panel View Menu you will find the corresponding checkbox Note that user interactions are all synchronized in this page You can also visualize a specific user defined plane from an image For that in the 3D view of the desired image press P A plane will appear in the center of the image Shrink o
6. be oe Da 31 5 Mesh processing tools 5 1 Mesh projection 9 2 Mesheropping lt lt c secaressa EDR eee ERE DE AA E 5 3 Interactive mesh moving tool 0 0 2 0 0 eee eee 5 4 Surface extractor tooll s 6 aa a bo a ee RSD EERE ER ERE GO 5 5 Orientation vector 5 6 Anatomical fibers 6 Segmentation tools 6 1 Surface generator 7 Conclusions 33 33 34 34 39 39 37 39 39 Al Chapter 1 Introduction 1 1 About CardioViz3D CardioViz3D is a free software available at http www sop inria fr asclepios software CardioViz3D dedicated to the visualization and processing of 4D medical data and espe cially cardiac imaging and simulation data Besides its capabilities in terms if static image and mesh visualization CardioViz3D offers adapted tools for visualizing and processing dy namic data i e that integrate a time dimension Such time sequences are easy to import visualize in real time and process DICOM exams import is provided and supports time se quences directly CardioViz3D uses the Visualization ToolKit VTK 3 as its base framework The user interface uses KW Widgets library 2 Some image processing tools use the Insight Toolkit ITK 1 1 2 CardioViz3D feature overview 1 2 10 11 Static and dynamic image support Static and dynamic surfacic and volumic mesh support Image visualization color map changing window level changing zoom effect multi
7. have to detect what kind of time sequence you have in the DICOM exam by looking at the preview window and pressing interactive Note that an imperative condition to a good ending of the sequence import is that the time instance images have exactly the same dimension and spacing Several scenari are possible detailed as followed 1 N volumes i e lines in the DICOM importer represent N time instances of the same object This is an easy one Remove all additional volumes of the list In the 3D 4 Sequence panel indicate that these volume represent a sequence by validating the corre sponding checkbox Then indicate the sequence duration Note that if any information concerning the cardiac cycle duration is found in the DICOM flags CardioViz3D will detect 1t and automatically preset the right duration 2 One and only one volume contains all the 3D t information This means that when you have a look on the preview window of this volume and when you navigate in the volume slices you detect that several instances of a 3D object are actually incorporated in this big volume First remove all the other volumes or press select to only select currently highlighted volume then use the Split button in order to separate time instances You should then see several volumes in the list Each volume representing a single time instance of the object You can now follow scenario 1 3 One or several volumes in the list represent
8. means that the spacing in x y and z is adapted to match the mesh real 33 size This also means that distances visualized in the 2D views are real distances You have access to some sample data via vtkINRIA webpagd 5 2 Mesh cropping Figure 5 2 The crop tool allows to control a cropping box in the 3D view left This results in the cropping of the selected dataset synchronized in the 2D views right TIP You can use this tool with some mesh sequence as input For the user convenience this tool allows to crop any surface or volume mesh or sequence of those thanks to the control of a box widget in the 3D view see Fig 5 2 This tool does not affect the structure of the mesh but only its visualized representations on the 2D amp the 3D views Note that you can disable the cropping box widget visibility throught the dedicated checkbox Known limitation When cropping a mesh some of the visualization parameters such as a scalar color map can be lost However it can be retrieved easily through the visualization toolbox see Sect 3 2 5 3 Interactive mesh moving tool This feature proposes to interactively move a surface volume mesh in the 3D view Thus all points of the dataset will be transformed according to the user defined movement see Fig 5 3 First select the desired mesh or mesh sequence in the manager then click ion the move mesh button A dialog will raise to help you in this step You c
9. movie export choice this movie exporter will raise to help you exporting 3 types of movies The slice type will explore all slices of a 2D view The camera type will allow you to control camera movements of a 3D view Finally the time type will snap through time the current 2D 3D view In the main toolbar the screen like button annouce the possibility to export a snapshot of the current full screen view However you can drop down a menu to choose to export a movie out of the current view Fig 3 5 Different types of movies can be exported 1 Slice Considering a 2D view you can use this export type to snap each available slices into a movie Note that the number of output frames can be set 2 Camera Use this export type if you want to control a 3D camera for your movie Move the sliders according to the desired path 24 3 Time This type allows you to export your sequence s as a movie It will take the current view and snap it while time is evolving By default the best amount of frame is set corresponding to the finest time resolution TIP 1 You can choose to let the cross visible or not during export in the Application Settings Panel of the View Menu TIP 2 The scalar bar visibility can be set to ON see Sect ES Sect 3 4 Time tables 3 4 1 Landmark follow up INRIAViZ4D 1 0 mm ae AE HR Figure 3 6 This is the time table of a specific mesh sequence Available scalars are shown on the right click on the
10. plave views user event synchronization volume rendering volume cropping box user defined plane intersection shading effect etc Mesh visualization color chaging light opacity effects surface representations surface Gouraud interpolation scalar mapping plane intersections DICOM exam import DICOM flags overviews dynamic DICOM series support 2D t and 3D t DICOM exam export DICOM flags editing etc Dynamic sequence creation and export Dynamic scalar field visualization on meshes Magnified snapshot export 2D and 3D movie export of static or dynamic objects Dynamic point of interest follow up on meshes Mesh projection on 2D slices mesh cropping m CardioVizsD c INRIA 2008 ADECHEQ TT PLUS Data Manager Al Preview ER atlasmri Name B lt Inncige Size 256 x 256 6 x 256 A Voxel Size 0 3125 x 0 3125 mm e MA iS a Rt ar a Er APB VAN f y a DEEE COOK Visualization tools atlasgeometry a atlasmri E A ar AN als Ls gt ma My PRESA AA rah ait Mesh x Value Hue Saturation ra ez 4 tat SND PO Material INS 4 P RIA ioViz3D acao Tracer OM nag 6x 128 Slic 2 e Voxe 125 x 0 8125 mm Opacity Line Width Wind l 100 2 4 Pi Wireframe v Gouraud v Attributes mapping Not available ER Bar fe Image X INRIA 2007 CardioViz3D TAO INRIA 2007 CardioV
11. processing features proposed in this toolbox 29 4 1 Arithmetic operations As shown in Fig the arithmetic operations allow you to compute the sum multiplica tion etc of one or two input images Several operations are available and will act on the currently selected set of image s Some operations need only one input image This is the case of the NOT and the INV operations However all other arithmetic operations will take two input images Note that all operations are 4D compatible This means that if the dataset s currently selected are image sequence s then CardioViz3D will reflect this by performing the desired operation frame by frmane between the two sequences Note that this sequence processing operation is only possible if the two inputs have exactly the same amount of frames There is no time interpolation 4 2 Convolution process This button just proposes a convolution of the input image or sequence using the recursive gaussian approach proposed by Deriche 4 with o of 2 0 See Fig At current stage of developement there is no parameter available for the gaussian convolution Figure 4 2 On the left the input image here an anatomical atlas of the heart On the right the result of the convolution process 4 3 Clipping planes This feature allows the user to to define a plane in the 3D view in order to clear the image above this plane When you click on the dedicated button a dialog raises to explain y
12. will see the Sequence Importer button a dialog will show up to help you in the sequence construction Fig 2 5 Load the different files corresponding to the different frames of your future sequence Note that the order is important You can add several files at the same time About the attribute loading please refer to Sect Several kinds of data sequences can be constructed 1 Image sequence If you want to create a sequence from a DICOM exam please refer to Sect On the other hand if you want to create a sequence from several image files 2D or 3D images representing the same object at different time steps make sure that they match in terms of image size and spacing 13 2 Surface Volume mesh sequence You will have to make sure that the different mesh files are consistent together i e all surface meshes OR all volume meshes Press the same topology checkbox if you are sure that the different meshes have the exact same topology links between points This is for memory saving purposes Note The sequence duration setting 1s predominant against the frames time flags Press return key to update time flags according to the duration just set 2 3 Playing a sequence Data sequencer a 00 ki duration s 2 gt Real Time mw Ne Name Time s Cuad 1 Pei e start time 0 1 01 gipl gz 0 066667 speed 9 100 2 02 gipl gz 0 13333 jr Same Geometry 3 O3 gipl gz 0 2 El gt gt 4 04 gi
13. 00601 O3_MR_ted LA ae Field of View m 81 25 Pixel Bandwidth DS 930 Device Serial Number LO 21166 Software Versions s LO syngo MR 2004A 4VA25A Type A Image Data Protocol Name LO tf2d11_2chamber Trigger Time DS 12 5 ja Nominal Interval IS 736 a Cardiac Number of Images IS 13 ize 323 x 390 x 19 mm A md Table Height DS tf2d11_2chamber k Date of Last Calibration DA 20051125 y Figure 2 4 Recover the DICOM information of a specific image select it in the data manager after the import process by clicking on the DICOM information button in the information toolbox Left the corresonding information dialog will pop up right 2 2 Importing a sequence E Sequence Importer x He Name Time duration s 4 o ga E start time 0 1 01 gipl gz 0 066667 2 02 gipl gz 0 13333 jm Same Geometry 3 03 gipl gz 0 2 4 04 gipl gz 0 26667 5 05 gipl qz 0 33333 6 06 gipl gz 0 4 T OF gipl qz 0 46667 amp O8 gipl qz 0 53333 9 09 gipl qz 0 6 Reset 2 OR Cancel Figure 2 5 The Sequence importer allows you to construct a sequence of data from one or several dataset files Import file s with the Open button Import some attribute files with the attribute button Set the sequence duration edit the time step flags if needed then press OK The sequence will be built and added to the Data Manager CardioViz3D is able to construct some data sequences and play them From the main toolbar you
14. 1 01 N gt sY0YU0Y y wNNN EP O OOOO OO O O 26 To load this file just select the desired sequence in the data manager Then in the In formation toolbox there is a load attribute button see Fig 2 1 Click on it and load the global parameter file Once this is done go back to the sequence toolbox From there you can click on the Global Parameters button see Fig 2 6 It will pop up a time table with all previously loaded global attributes The result is shown Fig TIP 1 the number of lines in the global parameter file does not have to match the number of frames of the sequence All 1D curves are stretched to match the sequence time size TIP 2 The global parameter file extension has no influence on the read ing Process 3 4 3 Other time table properties TIP 1 RightClick in the time table window to zoom in amp out through out the graph TIP 2 MiddleClick in the time table window to navigate translate in the graph Time table graphs are perfectly synchronized with the sequence toolbox Hence you can play the sequence Fig 2 6 you will see the scalar evolving according to time A vertical bar is also shown to remind the current time You might want to export this data this can be done by several ways 1 You can export a screenshot of the current field of view or export a movie with the snaphot export button see also Sect 3 3 2 The save data button will write a s
15. 1 Model resolution this slider allows you to define the surface resolution It is in percent of the resolution of the underlying image 2 Add boundary constraints automatically adds outside control points at the image corners to further constraint the 3D surface With O divisions one control point at each corner of the image is placed With 1 division control points are placed at the corner plus the middle of the faces and edges of the image when seen as a cube and so on 3 Save implicit function the implicit function used to create the 3D surface is saved when clicking on OK 4 Save ROI a binary mask corresponding to the inside of the 3D surface is saved when clicking on OK When you have finished the segmentation click on OK to save it into the data manager 40 Chapter 7 Conclusions CardioViz3D is a software dedicated to dynamic medical data visualization and processing Even it is still at an early stage of developement it already provides potential users with simple and easy to use features A large range of data is supported including DICOM for mat An effort has been made to adapt all features to a dynamic data level This means that image mesh sequences are easy to import or build and that image and mesh processing and visualization tools can be applied to sequence of data CardioViz3D is freely available For more information please visit our website www sop inria fr asclepios software CardioViz3D
16. 2 for specific imports such as DICOM or sequences The second set of buttons are dedicated to user interactions choices in the 2D views Assuming you are visualizing an image in CardioViz3D this image is represented in 3 perpendicular plane sections axial coronal and sagittal views and a 3D representation of it In the 2D views you have several kinds of mouse interactions that are possible 1 the arrow allows to navigate between slices in the different views 2 The orange color map button allows you to change the window and the level of the image Note that these parameters are also available from the visualization toolbox see Sect 3 1 3 The zoom button allows to zoom in and out in the xurrent image slice Press Shift to translate the visualization TIP Press Shift when the zoom interaction 1s ON to translate the current slice Chapter 2 Data management CardioViz3D is able to read several types of image and mesh data here is a non exhaustive list of supported formats 1 Static i e 2D or 3D and dynamic i e 2D t or 3D t image file support Ana lyze hdr NIFTI nii nii gz MetaFile mhd mha DICOM format dcm NRRD nrrd GIPL gipl gipl gz VTK image format vti vtk PNG png JPEG jpg jpeg TIFF tif tiff Inrlmage inr gz 2 Surfacic and volumic mesh support VTK polydata and unstructured grid format vtp vtu vtk HomeMade formats tr3D atr3D tr trian noboite mesh
17. IP When a dataset is highlighted Crtl D to remove it from the Data Manager 2 1 Importing a DICOM exam a DICOM importer x E e Reset Remove Split Select Volume Size Sequence 2D t A 0 20060103 MR tfis 256x256x3 1 20060103 MR tfis 208x208x6 a 2 20060103 MR tfis 224x224x5 Interactive E 3 20060103 MR tfis 256x256x5 a 3D T Sequence v 4 20060103 MR tfis 224x224x12 o 20060103 MR tfiZd 208x208x13 a 6 20060103 MR tfiZd 208x208x20 20060103 MR tfiZd 208x208x20 pg 8_ 20060103 MR tfiZd 256x256x20 9 20060103 MR tfiZd 256x256x20 f OK Cancel Figure 2 2 The DICOM importer helps you in importing a DICOM exam as easily as possible Double click on a volume to show a list of available DICOM flag information indicate when you detect 2D t or 3D t image sequences then click OK to import all volumes First click on the Import DICOM exam button on the main toolbar a cd like button A dialog pops up Fig 2 2 From here you will be able to reconstruct volumes construct 4D sequences etc You have basically two different options 1 First you can import the exam from its root directory path CardioViz3D will scan recursively this directory and reconstruct all available volumes The scan process might take a few minutes for large exams 2 Second you can import manually one or several DICOM image files Each f
18. an now follow the instructions to move your mesh in the 3D view downoald sample data http www sop inria fr asclepios software vtkINRIA3D 34 IRIA 2007 CardioViz3D 07 CardioViz3D Figure 5 3 The interactive moving tool allows the user to drag a selected mesh in the 3D view and drop it at a specific location All points coordinates of the dataset will be replaced by transformed ones This tool is also avaliable in 4D In this figure you can see on the left the 3D view of the input situation and on the right the resulting situation after interactive moving has been performed At any moment you can cancel the step by pressing cancel When you have finished moving the mesh press OK The mesh will update according to the affine matrix defined by the user movement you can now save your resulting mesh see Sect 2 6 TIP this process is available in 4D simply move the currently displayed frame the entire set of frames will be transformed according to the affine matriz All other parameters are kept 5 4 Surface extractor tool The next tool acts on volume meshes to extract the surface geometry of it Simply click on the button while the desired volume mesh is selected in the manager an output mesh is created under the name of inputmeshname_sur face See Fig 5 4 TIP this process 1s available in 4D simply move the currently displayed frame the entire set of frames will be transformed according
19. attributes consist on a list of files describing the evolution in time of any scalar vector field associated to the mesh points cells This of course includes the point positions File header is slightly different a file is needed for each frame and for each scalar field Let us go back to our previous example We want the color field to change during time We need to build some file describing this evolution At each frame we need to indicate in the file an additional parameters the frame number the scalars will be associated to Then our previous tetrahedroncolors cucolor will be turned into tetrahedroncolors_t cucolor Point_Color 1 17 411i 1 0 4 0 3 2 2 7 37d line number of scalars scalar dimension cycle number frame number By replacing with the frame number and replacing the scalars by some that evolve in time we will be able to construct a time sequence Sect 2 2 In the sequence importer just import our base geometry tetrahedron vtk Then asso ciate scalars directly from here with the load attributes button Load all previously created tetrahedroncolors_i cucolor Set the sequence duration and press OK This example files and output video is available from CardioViz3D website TIP If you save the mesh sequence in a set of VTK files scalars will be incorporated into the outout files 2 6 Exporting your data Data Infonnation File View Window Help script Name atlasmri e sm sm am
20. aving Cardio Viz3D 2 5 Mesh attributes system 2 5 1 Static mesh attribute You can easily attribute some data to a surface or volume mesh This data can be scalars vectors or higher order objects ten sors etc associated to the points or cells i e triangles tetrahedra of the mesh Let us take a foo example Consider a surface mesh made of 3 triangles the VTK file woud look like tetrahedron vtk vtk DataFile Version 3 0 vtk output 15 Figure 2 8 3D view of the resulting tetra hedron ASCII DATASET POLYDATA POINTS 4 float 000 1 O O O e O O 0 1 POLYGONS 4 16 3012 w w Ww O 1 O 2 1 2 w w Ww Resulting surface mesh is shown Fig Let s consider we want to associate scalars to each of the points of this surface mesh CardioViz3D has its own attibute file system The idea is to have a unique file describing the data associated to a specific geometry Several parameters can be set 1 A single description name string 2 A flag describing to what the data will be associated 1 for points 2 for cells 3 The dimension of the data 1 for scalars 3 for vectors etc 4 The number of data number of points or number of cells Now we can build our own file describing a scalar on each point of the tetrahedron tetrahedroncolors cucolor Point_Color 1 4 1 1 0 4 0 3 2 2 7 1 1 line the description name 2 271 line association flag 1 for points 2 for cells 3 37
21. ctually save each volume into a set of 2D image files You can set a prefix for the output image files Note Image that have not been imported directly from a DICOM exam don t have any DICOM information However some default DICOM flags are set during the writing process After all parameters are set press OK You will be asked for an output directory Note that the writing process can take some time in case of large exams 19 20 Chapter 3 Generic vizualization tools To each independent dataset listed in the data manager you can apply some vizualization parameters Tuning some parameters will act on the currently selected highlighted object s on the data manager and only on this these one s As said before an image or an image sequence has its own tab in the main window On the other hand meshes are incorporated in these tabs You can create an empty tab by pressing Ctrl T The visualization toolbox is obviously dedicated to visualization parameter tuning Se lect the desired dataset s in the data manager the corresponding specific parameters will raise in the toolbox 3 1 Image visualization Image E Rendering Mode Cropping box acalar bar 20 windowing 155 Shading Figure 3 1 This figure shows the image parameters being tuned You can set a color map associated to the currently selected image or image sequence Access to the 3D rendering mode
22. e recommend the NIFTI format nii However no extension information from the user will directly take this option 2 6 1 Exporting a DICOM exam fa DICOM exporter j 3 20060103 MR thseg2d1 DICOM Data W Select All protocol A Selected Name Type AN Hame Type Value N a sequence Sequence Percent Phase Field of View DS 187 5 Device Serial Number LO 21166 0_20060103_MR_ tfiseg2d1 ImageData z Software Versions s LO syngo MR 2004A 4VA25A Lal 1_20060103_MR_ tfiseg2d1 ImageData Protocol Name LO trufi 4 chamber 42 20060103 MR tfiseg2di ImageData Trigger Time DS 567 5 ii Nominal Interval IS 810 3_20060103_MR_ tfiseg2d1 ImageData Cardiac Number of Images IS 1 Date of Last Calibration DA 20051125 File prefix IMG Time of Last Calibration TM 134444 000000 r OK Cancel OK Cancel Figure 2 11 left The DICOM exporter dialog You can select the images you want to export in the exam click on the CD button to have access to the highlighted image DICOM flags information right The DICOM flags window You can edit the flags by double ckicking on one of them The DICOM importer button on the main toolbar can drop down a sub menu allowing the user to open the DICOM exporter dialog see Fig 2 11 From there you can select a set of images you want to export Note that CardioViz3D will also export image sequences as a set of volume images The process used for writing uses an external library to a
23. ed tab TIP Ctrl T creates a new empty tab Useful to separate several im ported meshes After the import data are listed by name in the Data Manager on the left of the window Fig right Select one of them by clicking on its corresponding line the system will automatically switch to the corresponding tab A checkbox allows you to control its visibility Cardioviz3aD c INRIA 2008 File View Window Help Script Coe S masa Data Manager Al z ag 2 Preview atlasqeometry allasmri Mame Ei mage Sie 256 x 256 A Vowel Sre 0 3125 x 0 3125 mm o atlasgeometry a atlasmn NA Pad UF E E ar APAC aa Y REBEL a Yana Figure 1 2 This zoom points out the principal structures of CardioViz3D The main toolbar on the top of the window gathers the most important functions of the software such as the open button to import any data the DICOM import button the sequence import button etc You can see on the upper left corner the Data Manager that summarizes all imported data At the bottom of it you see a set of buttons Each button represents a toolobx the first and second ones rely to general purposes NOTE Each action you might do in the toolboxes acts on the currently selected dataset s and only on it them In the main toolbar Fig 1 2 you will find the most important functionnalities of CardioViz3D The first set of buttons rely on data import and export please refer to Sect
24. ed will help you defining the parameters of the extraction Fig 4 4 You can define a threshold value or a iso value with respect to the currently highlighted image on the data manager You can see the resulting surface mesh in Fig Here are some brief explanations about the parameters provided by the dialog 31 1 Name the name of the output image No Threshold iso value You can define a threshold value a The algorithm will then separate the input image in two regions lt a and gt a On the other hand you can define a iso value 5 the algorithm is the same but it interpolates the value between pixels to have a subpixel resolution mesh 3 Decimate You can choose to decimate the output mesh The decimation algorithm used is from VTK 4 Target reduction This parameter will define the spatial resolution of the output mesh It represents a percentage of the input image finest spacing resolution 5 Smooth You can also smooth the output mesh vtk filter this is actually recom mended Note this feature is not available for image sequences Extract Iso surface Name outputname Threshold 00 Decimate the mesh a Wes No Target reduction 0 60 m smooth the mesh se YES No Figure 4 4 Left The surface extractor provides a quick algorithm to extract a surface mesh from an input image A dialog allows to set some extraction parameters Right Here is shown the resul
25. ge this color by double clicking in the corresponding color square 20 3 4 2 Global parameter evolution follow up Figure 3 7 The global parameters file system allows you to visualize in real time the evolution of some global scalar among the time line of dynamic sequence Here a synthetic sequence is shown in the 3D view see Sect 2 5 2 to which a global parameters file has been loaded INRIAVIZ4D c INRIA 2007 O Bie View Window Help Egas O al gt Data Manager Li Preview tetrahedron D BEE Ed Real Time m Speed 100 le gt dl Time cursor in seconds 0 10 0 900 el eco E os ei ei aj aj ecg par Click on the global parameter follow up button to raise the time table CardioViz3D also has a sequence global parameters file system The idea is to follow 1D scalars among the sequences These scalar values are not associated to any specific point or cell or position of the dataset A typical example would be the electro cardiogram associated to a cardiac dynamic sequence The file system is quite simple The idea is first to provide a set of strings that explain the different scalar curves and then list the data Here is a simple example file ecg par Time Phase ECG 0 O OOOO OOOO O OMAN OTF WN BE 0 01 02 03 03 02 01 00 01 0
26. he 2D views some control points that define the oe 6 inside on and outside regions of your surface To this aim navigate into the image and place the cursor where you want to add the control point Then click on the outside on or inside buttons of the dialog window to actually add it figure 6 1 As you add points the 3D surface is created interactively in real time The underlying algorithm is based on the variational implicit surfaces proposed by Turk et al 5 39 To easily create the surface first place one or two inside points then draw the surface by placing the on points Use the three 2D views to help you in the 3D design To create concave curves you can use outside points The closer they are to the actual surface the more control you have on the local curvature You can select a control point by middle clicking on it You can then move it by drag and drop or delete it by pushing the appropriate button in the dialog window Then click on the refresh button to rebuild the 3D surface If you want to restart from scratch click on the reset button to destroy all the control points The control points can be saved and reloaded through the dialog window Finally the name of the 3D surface as it is showed in the data manager can be edited in the related textbox Several advanced options are available to further tune the delineation process
27. hile Z axis oriented vector are shown in blue The surrounded box displayed around the vectors can be manipulated by its control spheres to crop the vector field interactively The Checkbox next to the button controls the cropping box visibility Figure illustrates this specific visualization process TIP The orientation vectors button is a toggle Press it a second time to hide the vector field Note that in case of a mesh single topology sequence the vector field being associated to the points or the cells of the sequence vectors will follow the points in their displacement during time 5 6 Anatomical fibers si fe IR 2007 HE Fic Yew Winiow Hel Script BASS AS OQADO Data Manager Gomera Mew Proview atins HRA 2007 CordiavizsD Figure 5 6 This screenshot shows the CardioViz3D 3D view where the anatomical MRI atlas of the heart is being displaed as well as a setlection of a corresponding fiber field coming from a DTI sequence ex vivo and a fiber tracking process All data can be downloaded from this adress http www sop inria fr asclepios data heart Another type of data can be visualized in CardioViz3D anatomical fibers Indeed fiber fields coming from a DTI exam and a fiber tracking algorithm for instance can be represented as continuous lines e g polylines color coded once again with their unsigned orientation see Sect 5 5 This data can be imported a
28. iguration after loading a DICOM root for instance 2 1 1 Supported and unsupported configurations CardioViz3D supports most of the DICOM exam configurations The volume images are re constructed from the slice files using the DICOM series flag In some cases a single DICOM series flag can have several volumes for example in case of interlaced T2 proton density acquisition Detect these non coherent volumes by looking at the preview window inter active button has to be pressed Press split to un interlace these volumes CardioViz3D uses the patient position DICOM flag to distribute slices between instances This interlace configuration case also appear in some Diffusion Weighted MRI acquisitions but splitting using this button reconstructs the volumes correctly TIP double click on a volume to pop up a window listing all visible DICOM flags for this volume Fig 2 3 However there are some known configurations that are not handled by CardioViz3D DICOM RT format for instance is not yet supported We also encontered problems recon structing some 3D and 3D t UltraSound data 11 2 1 2 2D 4t and 3D t configuration The specificity of CardioViz3D in terms of DICOM import is the capability of constructing directly from this dialog one or more sequence s of images However this tool needs some user interaction to well define sequence parameters There are two different kinds of time image sequences You
29. ile will be considered as a volume 10 Note that importing a DICOM exam from a root directory overwrites the previous set of volumes Each line of the list corresponds to a volume i e a volumic image a volume can actually contain only one slice Select one or several volumes to act on it them The preview window shows the middle slice of this volume Note that there is no 3D reconstruction yet to fasten the process Press interactive to see the entire volume playing TIP double click on a volume to pop up a window listing all visible DICOM flags for this volume Fig 2 3 oO 5_20060103_MR_tfi2d1_17 DICOM Data protocol Name Type Value Percent Phase Field of View DS 61 25 Pixel Bandwidth DS 930 Device Serial Number LO 21166 Software Versions s LO syngo MR 20044 4VA25A Protocol Name LO tf2d11_2chamber Trigger Time DS 12 5 Nominal Interval IS 736 Cardiac Number of Images IS 113 Table Height DS tf2d11_2chamber Date of Last Calibration DA 20051125 Figure 2 3 Double click on a desired volume from the importer to show this information box It shows all available DICOM flags from the DICOM series corresponding to the selected volume such as pixel type protocol patient information but also heart rate etc You will find a search box to help you find a specific DICOM information TIP At any time of the DICOM import process you can press reset to go back to initial conf
30. ir respective checkboxes to visualize them Export a movie or a table file containing all visible values Act on the zoom buttons to adjust the field of view Contraction fj o Potential o Contraction m 0 036455 Potential DO o Contraction f 0 046738 F al 2 A Y A It is sometimes interesting to follow a scalar evolution among a time sequence of meshes for example This can be done by the landmark follow up feature First select a sequence in the data manager then in the sequence toolbox press the point follow up button This will pop up a landmark manager dialog see Sect 2 4 You can load a previously saved set of landmarks Save the set of landmark before clicking OK to be able to retrieve this landmark set TIP An easy way to add landmarks can be done by pressing Shift Right Click on the 3D view Then a landmark is added at the mouse position on the surface of the first mesh encontered Once all desired landmarks have been set clcik OK to validate The time table will raise see Fig 3 6 You will see on the right a list of the available graphs that you can display Click on the their eye checkbox to visualize them Each graph represents the evolution during the time sequence of a specific scalar at the specific position given by the previously defined landmark Note that the graph s color corresponds to the landmark color However you can manually chan
31. iz3D a File Figure 1 1 This is a screenshot of CardioViz3D showing the MRI atlas of the heart and a volume mesh geometry segmentation of the ventricules 12 Interactive dynamic mesh manual registration 13 Vector field visualization on meshes 14 Interactive surface mesh generation DO oe 1 3 System Requirements CardioViz3D is available for Microsoft Windows XP x86 and x64 LINUX x86 and x64 Fedora Core 7 and MAC OS X Tiger and higher At least 1GB of memory is required as well as a powerful processor P4 2GHz AMD FX 3800 or later Also a powerful graphic card is recommended You may experience difficulties to visualize images with volume rendering technique using an ATI card this is a known issue CardioViz3D is multi threaded thus optimaly using multi core technologies 1 4 Installing Cardio Viz3D CardioViz3D software is available from this webpage http www sop inria fr asclepios software CardioViz3D You will find a lot of useful information screenshots tutorials links testing data online documentation etc 1 4 1 Windows From the webpage download the installer CardioViz3D X X X win32 xX X exe correspond ing to your architecture x86 for 32 bit processors x64 for 64 bit ones Execute it It will overwrite any previous installation of CardioViz3D you might have on your computer 1 4 2 Mac OSX From the webpage download the package installer CardioViz3D X X X macOSX Unive
32. line number of scalars Dimension of the data 4 4 line actual data 1D scalars Resulting tetrahedron is shown Fig where you can see the corresonding color map The extension has no influence on the reading process However the description name is quite important Indeed this name will result in the attribute list on the information toolbox Fig 2 1 It will also be listed in the visualization toolbox as possible data to be visualized Sect 16 mage Size 128 x 128 mage Size 128 x 128 Voxel Size 0 078125 x 0 078125 0 Vo Zi Size 0 078125 x 0 078125 mn INRIA 2007 Cardioviz3D mage Size 128 x 128 Voxel Size 0 078125 x 0 078125 mn INRIA 2007 Cardio Viz3D aa INRIA 2007 CardioViz3D Figure 2 9 2D and 3D views of the tetrahedron example to which scalars have been associated to each of its points Access to the scalar visualization in the visualization toolobx see Fig 34 3 2 Note in the actual data scalars are separated by a space TIP If the description name is Position and the scalars are actually vectors associated to the points of a mesh then Cardio Viz3D will take the data as real coordinate positions and overwrite current mesh positions with it TIP If you save the resulting mesh in a VTK format scalars will be incorporated into the outout file 2 5 2 Mesh sequence attributes Extending the last section CardioViz3D has a file reading process for sequence attributes Se quence
33. n Ims 2 You can click on the Add button CardioViz3D will add a landmark in the current position of the current view Note that the freshly added landmark will be displayed in a random color However you can change this color in the landmark dialog 14 atlasmri Landmark Manager x ee EELEE p Landmark 3 selection Properties H 5 Value Hue Saturation scaling O m Figure 2 7 The landmark system allows you to define points of interest Control each land mark parameters in the landmark dialog left After adding landmarks they are displayed in all available views right 3 On a 2D view Shift RightClick will add a landmark to the current mouse position 4 On a 3D view Shift RightClick will add a landmark to the current mouse position at the first intersection with the surface of the selected dataset only available for mesh data TIP 1 To translate a landmark in a 2D view LeftClick on it and drag it until desired position TIP 2 Double LeftClick on a landmark to make the cross position match the landmark position At any moment you can save the current set of landmarks default extension is Ims The Remove button will remove the currently selected landmark while the Remove All button will remove all landmarks from the views In the landmark dialog you can choose the color and size of a specific landmark Don t forget to save your landmarks before le
34. ou how to control the plane position and orientation This is done in the 3D view moving the plane is synchronized 30 with the other image views Once this is done press OK the input image will be transformed so that the part above the plane will be cleared with zero values Careful the input image is altered by the process there is no output image derived from this process unless the binary mask defining the operation 4 4 Crop image Figure 4 3 The crop image function allows to place a box in the 3D view thanks to control points CardioViz3D will create an output image corresponding to the inside of this box On the left you can see the box being placed in the input image On the right the result of the cropping The crop image button will act on the currently selected image or image sequence Click on it a box will appear on the 3D view Fig 4 3 Place it and size it with the dedicated control points then click OK An output image or image sequence will be created under the name of extractor_output taking the size of the user defined box limited by the input image dimensions TIP this feature is available in 4D Simply select your image sequence and crop it The output will be an image sequence of cropped frames All other parameters will be kept 4 5 Surface extraction From any image you can extract a surface mesh This can be done by the last button of the toolbox The dialog rais
35. pl gz 0 26667 5 05 gipl gz 0 33333 Time cursor in seconds e Degiplg Da 0 00 7 O7 gipl gz 0 46667 8 08 gipl gz 0 53333 9 O9 gipl gz 0 6 y Reset enel all al x e o x ma Figure 2 6 The sequence toolbox will help you to play pause your imported sequence s Press the Manage Sequence button to set parameters of the currently highlighted sequence You can tune the speed with the dedicated spinbox The sequence toolbox is announced by the play button The Play Pause button will act on all imported sequences see Fig 2 6 You have access to the currently highlighted sequence s parameters such as its duration with the Manage Sequence button In case the sequence s are not cyclic you can act on the play mode toggle button to play sequences in a go and back way When real time is activated sequences actual durations will match their duration parameter with a risk of frame skipping i e a 2 0 seconds sequence will actually last 2 0 seconds When this mode is deactivated then the sequence is rendered frame by frame at maximum time resolution 2 4 Landmark system You can associate some landmakrs i e points of interest the currently displayed view port i e tab For that click on the Manage Landmarks button in the main toolbar A dialog will raise see Fig 2 7 There are several ways of defining landmarks 1 You can load a previously saved set of landmarks default extensio
36. preadsheet file csv this file will contain semi column separated values for all currently visible graphs 27 28 Chapter 4 Image processing tools IMPORTANT Toolboxes contain image mesh sequence processing al gorithms These algorithms are beta versions and should not be consid ered otherwise At the current stage of developement v1 4 0 most of the toolboxes are still work in progress Some of the provided features are relatively stable and there 1s no warranty concerning their efficiency Image toolbox fm Arithmetic operations 2 4 Arithmetic Operations x x Arithmetic operations Image 1 oz yy Convolution process Image 2 11 y Output name sum SY Image clipping plane Operation Select an operation e y ar Image NOT a AND a CIR nin Extract iso surface oK XOR T IRES Figure 4 1 The Image processing toolbox left allows the user to apply simple filters to images On the right an example is shown where an arithmetic operation is being applied to two input images e g Image Images All filters are applied to the currently selected image s The image toolbox provides some basic processing for images and image sequences Each of its buttons provides a specific treatment First select your image s or image sequence s of interest in the Data Manager then select the filter you want to apply to it The next sections explain briefly what are the image
37. r expand the plane thanks to the control points Change its orientation with the arrow You will see a dialog showing up while you manipulate this plane This dialog displays the exact intersection between the plane widget and the underlying image see Fig 3 3 TIP Clicking on the middle of the plane will translate it among the orientation axis Clicking on the arrow will rotate the orientation axis 3 2 Mesh vizualization Meshes are more versatile to render That is why the visualization tools are more complex Fig 3 4 You can set some light effects associated to the selected mesh If the mesh is projected in 2D views see Sect 5 then all visualization parameters are shared between the projections and the 3D object Another aspect of mesh visualization is related to their attributes Meshes can have scalar vector or tensor attributes associated to each of their vertices cells see Sect 2 5 In the case of scalar attributes they can be visualized on the surface or volume of the object In Fig 3 4 left the attribute mapping part has the aim of letting the user choose to visualize 22 atlasmri Figure 3 3 Press P in the 3D view to activate the plane selection feature Manipulate the plane widget with the control points and the arrow left The dialog displays the exact intersection between the image and the user defined plane Press P again to deactivate it Visualization tools Hesh
38. rsal dmg These are universal binaries and will suit for all macOS 10 Tiger and higher architecture Execute it it will also overwrite any previous installation of CardioViz3D you might have on your computer Note that you will need X11 environement installed on your computer see http www apple com support downloads x11formacosx html 1 4 3 Linux systems From the webpage download the dedicated tarball CardioViz3D X X X linux FCX xXX corresponding to your architecture x86 for 32 bit processors x64 for 64 bit ones Untar the file in a dedicated directory The binary is included in the output directory as well as the needed libraries You might need to add a line in your bashrc file to be able to execute the software Depending on your system this line should be something like in bash export LD_LIBRARY_PATH my_cardioviz3d_directory LD_LIBRARY_PATH in telsh setenv LD LIBRARY PATH my_cardioviz3d_directory LD_LIBRARY_PATH 1 5 Get started You will find test data tutorial and screenshots at this webpage http www sop inria fr asclepios software CardioViz3D First click on the Open file s button Fig left You can ask for opening several files at the same time See Sect 1 2 for a list of supported formats TIP Ctrl O directly opens the import dialog Each image will induce the creation of a new tab whose name corresponds to the image file name meshes will be incorporated to the currently open
39. s a VTK polydata file in the data manager hen in the mesh tool box you can indicate that this data corresponds actually 37 to anatomical fibres in order to have access to an interactive mode of fiber bundle selection When clicking on the anatomical fibers button with anatomical fibers currently selected you will see a cropping box surrounding the fiber field Manipulate this box with the control spheres Only the fibers that pass through the box will be displayed 38 Chapter 6 Segmentation tools The segmentation toolbox aims at providing advanced tools for the interactive and automatic segmentation of medical images So far only one tool is available the Surface Generator 6 1 Surface generator This tool allows the interactive creation of 3D surfaces To launch it select a tab con taining an image and click on the Surface Generator button The dialog window presented in figure 6 1 is then displayed providing the controls to personalize the manual segmentation Surface Generator Hame SurfaceNane Humber of constraints E a AE Display E Auto update E Surface E Constraints REEL Options Figure 6 1 Left Surface generator dialog window Right Example of interactive delin eation In blue the 3D surface in green an inside control point in red the on control points and in yellow the currently selected control point To create the 3D surface you have to place on the image in any of t
40. slice s of the 3D object moving in time i e some volumes are 2D t sequences If a set of these 2D t sequences putting them together make a 3D t sequence then refer to the 4th scenario On other cases just click on the 2D t checkbox of the corresponding volume line s sequence s will be well constructed and you will be able to set their parameters afterward 4 In this last scenario you have a set of 2D t sequences in the volume list representing a global 3D t sequence First make sure you have remove all additional volumes from the list Then click on the 3D t checkbox and set the sequence duration then click on any of the 2D t checkbox to indicate CardioViz3D that it is a set of 2D t sequences The software will construct the global sequence TIP the preview page Fig helps summarizing the imported data To activate deactivate it go to the Application Setting View menu Once you have imported your DICOM images and or sequences you can retrieve the DICOM flags of a specific data To do so select the desired image or image sequence in the Data Manager go to the information toolbox and click on the DICOM information button CD button the same information dialog will pop up see Fig 2 4 Note that you can open several of these dialogs corresponding to different images to compare the data 12 Data Information fa 5_20060103_MR_tfi2d1_17 EJ DICOM Data protocol By E Name Type Value Hame 6_2
41. t of a surface extraction thresholding at a specific value of the anatomical atlas The image color map chosen here is GE colors see section 13 1 The output surface mesh is shown in bright green 32 Chapter 5 Mesh processing tools Meshtools RR E Project mesh g Crop mesh Box Estract surface mesh etmerdecimate mesh Ai fibers m Box Figure 5 1 Left The mesh processing toolbox contains a few features to manage surface and volume mesh objects or sequence of those They act on the currently selected mesh or mesh sequence Right This image shows the result of the projection process of the atlasgeometry volume mesh The mesh processing toolbox proposes some simple algorithm for surface and volume mesh processing First select the desired mesh or mesh sequence in the data manager then click on the desired process Here are some brief explanations on how to use each of them 5 1 Mesh projection When opening a mesh file the mesh object is directly rendered in the 3D view One might want to have an insight in the mesh geometry slice by slice This can be done here by the projection tool see Fig 5 1 It simply consists on creating a bounding box corresponding to the bounds in real coordinates of the currently selected mesh The mesh is then projected in three orientation planes The resolution of the synthetic image is 128x128x128 respecting the real coordinates mesh bounds This
42. tet3D atet3D sm OBJ format obj Each dataset you might import is added to the Data Manager see Fig 1 2 on the left side Select a dataset to act on it through the toolboxes The checkbox aligned with the dataset controls its visibility Each dataset has its associated view port i e a tab where the dataset is drawn You can change a dataset view port through the Data Information toolbox see Fig 2 1 When you select dataset CardioViz3D automatically raises the correct tab where the dataset is currently drawn Note that you cannot change the view port of an image Data Information Name atlasmri Type ImageData Image Ske 256 x 256 Voxel Se 0 38125 0 3125 pam Size 60 x 00 x 103 mm View Port latlasmri Data Attributes No attribute g E Fi Figure 2 1 The information toolbox left allows you to act on the currently highlighted dataset You can remove it from the Data Manager save it into a file pop up some DICOM information see Sect 2 1 or show a histogram of its scalar information You can also change the view port tab of a specific dataset Tabs are shown on the right You can save a specific dataset into a file or remove it from the Data Manager and from the views through the information toolbox Note that removing a dataset from the Data Manager does NOT actually delete its corresponding file TIP When a dataset is highlighted Crtl S to save it into a file T
43. to the affine matrix All other parameters are kept 5 5 Orientation vectors Vector fields can be loaded as attributes of a mesh or a mesh sequence The file system is exactly the same as the scalar field attribute system see Sect 2 5 exept the dimension of the data is now 3 Vector can be affected to the points nodes of the mesh or to the cells triangles tetrahedra of the mesh In the mesh processing toolbox the orientation vectors 30 E a a A 1 E a Figure 5 4 The surface extractor tool just isolates the surface of a volume mesh and creates another mesh object with it On the left the input mesh projected in a 2D view on the right the result of the surface extraction The surface mesh is represented in red INRIA 2008 CardioViz3D Figure 5 5 This figures shows a snapshot of the CardioViz3D 3D view where an anatomical geometry atlas of the heart is being displayed A vector field has been provided to this geometry through the mesh attribute system In the mesh toolbox you can display the available vector field Vectors are color coded with their unsigned orientation A cropping box allows to select a area of interest of this vector field 36 button will scan the currently selected dataset to find some associated vector field Vectors are then normalized and color coded with an unsigned orientation lookup table X axis oriented vector are shown in red Y axis oriented vectors are shown in green w
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