DTIWEB - USER MANUAL
Contents
1. S uo Ogey DTIWEB USER MANUAL Loranhics The objective of this document is to present the DTIWeb platform and describe the main steps that have to be followed to obtain from a DTI data set a white matter fiber map grouped into anatomical bundles Figure 1 shows the main screen of the application This consists of a top menu area to select the different options a left menu to perform the main steps of the proposed technique and a main area to display the obtained results Sres Corrty vaie Meth let RE 1st Step sal Vode 2nd Step se Vee 3rd Step p Vere 4th Step Figure 1 Main screen of the DTIWeb application To obtain the automatic fiber reconstruction we have to apply the four following steps 1 Press Load Model button With this option the user accesses to the directory with the testing data sets and he has to select one of them It is important to remind the name of the data set it will be needed in the next step Once a data set is selected a progress bar appears see Figure 2 and then the axial coronal sagittal and multiplanar reconstructions of the selected data set are rendered in the visualization area see Figure 3 Reconstruction of the selected data set are rendered in the visualization area ist Step 2nd Step Jrd Step iota A 1st Step 2nd Steg Jrd Step 4th Step 2 Press Load Mask button With this option the background o2. see Figure 12 Figure 14 Seeding parameters window 8 Help menu This menu see Figure 15 has three options e Reset to reset and refresh the main visualization area e Help to open the user manual e About a little explanation about us Figure 15 Help menu options 9 Tab Visualization From this tab panel see Figure 16 we can modify the visualization options Wizard Visuakzation ROI i Bounding box visualization J Box Seeds Seeds visualization 1D Visualization v Activate 1D visualization FA Color gt Anisotropy measure 30 Visualization a Activate 3D visualization Fiber tracking algorithm Fiber primitive drawing type Start fiber tracking computation V X Piane Y Y Pane 2 Plane Activate view planes Alpha channel Transparency level for 1D visualization Figure 16 Detail of the visualization tab panel 10 Tab ROI This panel see Figure 17 provides all the operations needed to manipulate ROIs or VOls Wizard Visualization ROI ee eee 2 gt Type of ROI Execute the BSP Merge algorithm for automatic VOI detection Delete the last ROI manually drawn Save a Manually drawn ROI Save a group of ROIs Groups List of all the groups of ROIs Seti Y gt Open window for manual ROI edition see 11 Color Change the selected color of the group of ROIs FA Color gt List of textures for fiber tubes Fibers Tubs W Roi Visualize or not
3. steps considered to draw a fiber Parameters used as stop criterion Stopping value of the anisotropy index selected as stop criterion 0 0 1 0 Stopping value of angle 02 3602 degrees Assign a new random seed Seeding strategy used All brain whole brain seeding All ROIS seeds are placed in all voxels of each ROI First ROI seeds are only placed in the first ROI of each group of ROIs Special it follows the strategy presented in the Neuroinformatics paper Algorithm used for VOI detection Treshold 0 4 Value of stop criterion 0 1 for MIR and an integer for the number of regions Stop criterium MIR i Index used as stop criterion MIR or number of regions Region All brain 3D Region where the VOI detection algorithm is applied Mesure 1 Main Direct v First data set used for VOI detection Mesure 2 FA Second data set used for VOI detection Final regions 59 Number of final VOls the process could stop before if no more regions can be obtained Remove BSP 0 4 1 At the end of the BSP process regions with FA less than the selected value are removed Remove Merge 0 4 At the end of the merge process regions with FA less than selected value are removed Save result file Save the intermedium results using the Analyze format Seeding Parameters Planes 75 Percentage of seeding planes for each VOI Seeding rate 4 0 Seeds per voxel for the special seeding method presented in the Neuroinformatics paper 5
4. es seeds in the defined VOls and performs tracking By default the method uses the 75 of planes with 4 seeds per voxel The user can modify the tracking technique and the number of seeds following the indications of the Config menu described in Section 7 Once the parameters have been set a progress bar see Figure 7 appears and then the obtained fiber clusters are rendered in the visualization area see Figure 8 Fiber Tracing Tracking Corp Laue Oporad Figure 7 Progress bar of tracking computation TTW Gi Lyewerytat de an Scere Cpmig oven s lst Step 20i Mato and Step sed Vart Jrd Step 4th Step eer lroetry Figure 8 Visualization of obtained fiber clusters y imagmg e ADVANCED OPTIONS Granhics In this section we describe the advanced options supported by the DTIWeb application For each option we present the menu and the description of the main options 5 File menu The File menu see Figure 9 has the next options e Open with this option the user can access to the directory and select a data set for loading e Save the user can save the tracking results in the Fiber DTIStudio format or the anisotropy maps in the Analyze format e Snapshot this option is used to take snapshots of the different views e Exit this option closes the DTIWeb application Lae DTIWeb GILAS Universitat de Guon A File Scene Contig Open on ROL Save S
5. f the loaded data set is removed and a directory with the masks corresponding to each one of the data sets appears Select the mask of the data set and then a progress bar will appear When the process ends the axial coronal sagittal and multiplanar reconstructions without the background of the selected data set are rendered in the visualization area see Figure 4 Dive CILAO Lveweritat de Genre re p GE PO g ist Step n Paip Figure 4 Visualization of the loaded data set where the background has been removed Press Split and Merge button With this option the proposed approach with the default parameters is applied These parameters can be modified using the Config Menu described in Section 7 A progress bar appears to show the evolution of the BSP computation the Region removal and the Merge computation see Figure 5 When the merging phase is finished the obtained VOI decomposition with each VOI represented with a different color see Figure 6 is visualized At this step of the process the user has the option of editing the obtained VOls following the indications of Sections 10 and 11 3rd Step SpA Merge 4th Step Carsi per slar Figure 5 Progress bar of BSP computation Site Scere Contre rev eee ROI ist Step 2nd Step Srd Step 4th Sep Figure 6 Visualization of the obtained VOI decomposition 4 Press Tracking Computation The last step of the process plac
6. indow 12 Statistics This window provides information of the obtained VOls or fibers and represents it in a tabular mode or as a graph see Figure 19 The user can print export or make a snapshot of the obtained results noe lt gt i beep ee Set fet Peet Wet Wet Wee Peet er Bet et Bet IBst Wet Sch leet et Wet Iet Ww Por Histeoyeoe Sez 57 D IOR 4 0 7987 0 8275 0 33066 L i gt 0 02000 0 03000 0 00009 G GOIOT 2 02020 4 Sez 38 0 O623 0 81546 0 66344 0 35044 i257 gt 0 02030 0 02020 0 000093 G GOIO0OO gt 09090 Jez 59 D O3 L0 0 79722 0 45887 0 13369 1136 0 02030 0 03020 0 00009 G COI0O 2 09090 Sez J0 0 36742 0 694933 0 45936 0 09714 163 gt 0 02010 0 02020 0 00000 G c0000 gt 09090 Figure 19 Example of statistical results For more details or information about the application please contact with Ferran Prados at ferran prados udg edu
7. napshot 1 X ais Exit Y axis D a ans 3D 2nd Ste All views Load Mask Figure 9 File menu 6 Scene menu The Scene menu see Figure 10 has options to load or save ROIs or VOls Fibers or Masks e ROIS this option is used to load the file of ROIs or to save the ROIs that are shown in the main visualization area e Fibers this option can load fiber trackings or save fiber trackings e Load mask this option can load a binary file to remove the background of the loaded image h Fale Scene Config ROIS Load ROS Fibers i Save ROG Load maik Lood Model 2nd Step load Mas Figure 10 Scene menu 7 Config menu The Config menu see Figure 11 has options to set the parameters of tracking Binary Space Partition BSP merge and seeding algorithms For each option we present the different parameters that can be modified see Figures 12 13 and 14 I Fle Scene Contig Wierd Vig Tractang BSP Merge ist Seeding Load Model 2nd Step Tracking Configuration Seeds per voxel Start value Space between seeds Minimum length Stop criterion FA Angle Stop value Angle E Random seed Put seeds at Figure 12 Tracking configuration window Seeds per voxel when the seeding strategy is not the presented in the Neuroinfomatics paper Value of FA to put seeds to start fiber tracks 0 0 1 0 Number of voxels between two adjacent seeds gt 0 Minimum number of
8. the fibers tubes or ROIs of a selected group of ROIs RO Boolean operations between ROIs of the group Refresh boolean operations of the group of ROIs Del All Delete all ROIs and fibers Clear ROIS Visualize or not all ROIs Delete the selected group of ROIs Visualize or not all fibers ROI Group Set 1 gt Name of the selected group Save the name of the selected group RO v gt List of ROIs of the selected group Delete the selected ROI of the group Concatenate ROI Concatenate the selected ROI to the selected ROI group Set 1 List of destination of groups of ROIs to change a ROI Change the selected ROI of the group to the selected destination group Statistical data about ROI groups and fibers trackings Figure 17 Detail of the ROI tab panel 11 Manual editing ROIS From this window see Figure 18 the user can edit the voxels of each group of ROIs and can apply boolean operations between them such as union erasure or intersection Color Vowels Fibers fel 1099 o Remove voxels from the group of ROIs by manual drawing with the Add voxels to the group of ROIs by manual drawing with the mouse WH iso o Visualize or not fiber tubes Visualize or not fibers Set 10 a Number of fibers and voxels for a group of ROIs Number of fibers Name of the group of ROIs Visualize or not the group of ROIs Selected group of ROIs for boolean operations Figure 18 Manual editing ROIs w
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