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Surgical Planning Laboratory -1- Brigham and Womens Hospital Diffusion Tensor Imaging Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D.

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Presentation on theme: "Surgical Planning Laboratory -1- Brigham and Womens Hospital Diffusion Tensor Imaging Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D."— Presentation transcript:

1 Surgical Planning Laboratory -1- Brigham and Womens Hospital Diffusion Tensor Imaging Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D. National Alliance for Medical Image Computing

2 Surgical Planning Laboratory -2- Brigham and Womens Hospital Acknowledgments National Alliance for Medical Image Computing NIH U54EB Neuroimage Analysis Center NIH P41RR Laboratory of Mathematics in Imaging, Brigham and Womens Hospital Thanks to Carl-Fredrik Westin, Lauren ODonnell, Raul San Jose Estepar, Carlos Isorna, Maxime Boucher, Matthan Caan

3 Surgical Planning Laboratory -3- Brigham and Womens Hospital Material Slicer 2.6 DTI Sample Data Set Dwi-dicom.zip SlicerSampleDTI.zip

4 Surgical Planning Laboratory -4- Brigham and Womens Hospital Goal of this tutorial Guiding you step-by-step through the DWI data analysis capabilities of Slicer, including generation of tensors, calculation of scalar metrics and tractography tools. Final result of the tutorial

5 Surgical Planning Laboratory -5- Brigham and Womens Hospital Slicer DT-MRI Module

6 Surgical Planning Laboratory -6- Brigham and Womens Hospital Overview Part 1: Loading and Converting DTI Data Part 2: Computing Fractional Anisotropy Part 3: Generating Fiber Tracts Part 4: Selective Seeding Part 5: Clustering

7 Surgical Planning Laboratory -7- Brigham and Womens Hospital Diffusion Weighted Imaging (DWI) Diffusion Sensitizing Gradients Diffusion Weighted Images

8 Surgical Planning Laboratory -8- Brigham and Womens Hospital Diffusion Weighted Imaging (DWI) Example: Correlation between the orientation of the 11 th gradient and the signal intensity in the Splenium of the Corpus Callosum

9 Surgical Planning Laboratory -9- Brigham and Womens Hospital Loading DTI Data Slicer can load DWI Volumes ……………………. Tensors…………………………… Tracts……………………………… DTI Scenes ……………………….

10 Surgical Planning Laboratory Brigham and Womens Hospital DWI Training Dataset 1 2 Baselines and 12 Gradients

11 Surgical Planning Laboratory Brigham and Womens Hospital DWI Training Dataset 2 1 Baseline and 6 Gradients

12 Surgical Planning Laboratory Brigham and Womens Hospital Loading the DWI Training Dataset 1 Click on Add Volume to load the Dicom-DWI training dataset

13 Surgical Planning Laboratory Brigham and Womens Hospital Loading DWI data Select Nrrd Reader in the Properties field The Props Panel of the module Volumes appears.

14 Surgical Planning Laboratory Brigham and Womens Hospital Loading DWI data Click on Apply Click on Browse and load the file namic01-dwi.nhdr in the directory Dwi-dicom Check that the path to the file is correct. If needed, manually enter it

15 Surgical Planning Laboratory Brigham and Womens Hospital Loading DWI data Slicer loads the Nrrd DWI dataset

16 Surgical Planning Laboratory Brigham and Womens Hospital Loading DWI data Left-click on the button Or, and select the orientation Slices

17 Surgical Planning Laboratory Brigham and Womens Hospital Loading DWI data The anatomical slices are now aligned with the sampling grid

18 Surgical Planning Laboratory Brigham and Womens Hospital Loading DWI data Change the FOV to 2000

19 Surgical Planning Laboratory Brigham and Womens Hospital Loading DWI data The sagittal and coronal viewers display the 14 MR volumes: 2 baselines and 12 diffusion weighted volumes

20 Surgical Planning Laboratory Brigham and Womens Hospital Loading DWI data Left-Click on the V button to display the axial and sagittal slices inside the viewer. Use the axial slider to slice trough the baselines and diffusion weighted MR volumes.

21 Surgical Planning Laboratory Brigham and Womens Hospital DT-MRI Module Select Modules in the Main Menu Select Visualisation DTMRI

22 Surgical Planning Laboratory Brigham and Womens Hospital DT-MRI Module The panel Input of the DTMRI module appears Click on the tab Conv

23 Surgical Planning Laboratory Brigham and Womens Hospital DT-MRI Module The panel Conv of the DTMRI module appears

24 Surgical Planning Laboratory Brigham and Womens Hospital Converting DWI data to tensors Select the Input Volume namic01-dwi.nhdr and click on ConvertVolume

25 Surgical Planning Laboratory Brigham and Womens Hospital Converting DWI data to tensors zzzyzx yzyyyx xzxyxx DDD DDD DDD (Stejskal and Tanner 1965, Basser 1994 ) {Si} represent the signal intensities in presence of the gradients gi Slicer computes the symmetric 3x3 tensor matrix D for each voxel

26 Surgical Planning Laboratory Brigham and Womens Hospital At the end of the calculation, Slicer displays the average of all diffusion weighted images (_AvGradient) and the baseline volume (_Baseline). The tensors volume is available from the DTMRI module for additional calculations. Converting DWI data to tensors

27 Surgical Planning Laboratory Brigham and Womens Hospital Converting DWI data to tensors Slicer displays the anatomical views of the average of all 12 diffusion weighted images (average over all gradient directions)

28 Surgical Planning Laboratory Brigham and Womens Hospital Adjusting Window Level Click on the Module Volumes and select the tab Display

29 Surgical Planning Laboratory Brigham and Womens Hospital Adjusting Window Level Select the Active Volume namic01-dwi-nhdr_AvGradient Use the sliders Win and Lev to adjust the Window level

30 Surgical Planning Laboratory Brigham and Womens Hospital Adjusting Window Level Slicer displays the anatomical views of the average of all 12 diffusion weighted images (average over all gradient directions) Inspect the anatomy using the axial, sagittal and coronal sliders.

31 Surgical Planning Laboratory Brigham and Womens Hospital Left-click on Bg and select the volume namic01-dwi nhdr_Baseline Converting DWI data to tensors

32 Surgical Planning Laboratory Brigham and Womens Hospital Browse the baseline images to check if the anatomy is correct Converting DWI data to tensors Slicer displays the baseline (T2) images.

33 Surgical Planning Laboratory Brigham and Womens Hospital Converting DWI data to tensors Click on the module Data Slicer displays the list of DTI volumes

34 Surgical Planning Laboratory Brigham and Womens Hospital Converting DWI data to tensors Select File Close in the Main Menu to clear the scene

35 Surgical Planning Laboratory Brigham and Womens Hospital Loading the DWI Training Dataset 2 Click on Add Volume

36 Surgical Planning Laboratory Brigham and Womens Hospital Loading Slicer Sample DWI data Select ImageHeaders: Auto Click Apply Select the Props Panel Use the Basic Reader Click on Browse Navigate to the folder containing the tutorial data Select the first file D.001 Click Open

37 Surgical Planning Laboratory Brigham and Womens Hospital The DWI images appear in the Viewer Loading Slicer Sample DWI data

38 Surgical Planning Laboratory Brigham and Womens Hospital Observe the axial slices using the slider Loading Slicer Sample DWI data

39 Surgical Planning Laboratory Brigham and Womens Hospital A sequence of white stripes appears in the diffusion weighted images. They correspond to intersections with the baseline images in Slicer Axial/Sagittal/Coronal (AxiSagCor) slice mode. Loading Slicer Sample DWI data

40 Surgical Planning Laboratory Brigham and Womens Hospital Inferior Superior In Axial/Sagittal/Coronal mode the slices planes, which are aligned with the RAS coordinates, are cutting through the DWI volume Loading Slicer Sample DWI data

41 Surgical Planning Laboratory Brigham and Womens Hospital Left click on Or and select the orientation Slices in the Menu Loading Slicer Sample DWI data

42 Surgical Planning Laboratory Brigham and Womens Hospital The original slices appear in the Viewer Loading Slicer Sample DWI data

43 Surgical Planning Laboratory Brigham and Womens Hospital Inferior Superior In AxiSlice/SagiSlice/CorSlice mode the slices are aligned with the DWI volume Loading Slicer Sample DWI data

44 Surgical Planning Laboratory Brigham and Womens Hospital Loading Slicer Sample DWI data Notice that the viewer displays the stack of S 0 and diffusion weighted images {Si}

45 Surgical Planning Laboratory Brigham and Womens Hospital Browse the original axial slices corresponding to the baseline (S 0 ) image. Loading Slicer Sample DWI data Example: display the slice 209

46 Surgical Planning Laboratory Brigham and Womens Hospital Loading Slicer Sample DWI data Adjust the window level and observe the baseline image (S 0 )

47 Surgical Planning Laboratory Brigham and Womens Hospital Adjusting Image Window Level Select the Volumes module Adjust Window and Level Select the volume D Select the Display panel

48 Surgical Planning Laboratory Brigham and Womens Hospital Loading Slicer Sample DWI data Observe the baseline image (S 0 )

49 Surgical Planning Laboratory Brigham and Womens Hospital Notice that the image intensity for each of the six gradient orientations is much lower than the S 0 image. Loading Slicer Sample DWI data

50 Surgical Planning Laboratory Brigham and Womens Hospital DT-MRI Module Select Modules in the Main Menu Select Visualization DTMRI

51 Surgical Planning Laboratory Brigham and Womens Hospital DT-MRI Module Select the Conversion Panel: Conv Select the module DTMRI

52 Surgical Planning Laboratory Brigham and Womens Hospital Convert DWI data to tensors Select InputVolume D Select Protocol BWH_6g.1bSlice Click on Prop to display the parameters of the acquisition protocol

53 Surgical Planning Laboratory Brigham and Womens Hospital Acquisition protocol Slicer displays the parameters of the acquisition protocol used to acquire the DTI Sample Data BWH_6g.1bSlice at Brigham and Womens Hospital, corresponding to: n=6 gradients Gradient directions = { }, { }, { }, { }, { }, { } Gradient order: Slice interleaved b=1 baseline B-value = 1000

54 Surgical Planning Laboratory Brigham and Womens Hospital Convert DWI data to tensors Click on Convert Volume

55 Surgical Planning Laboratory Brigham and Womens Hospital Converting DWI data to tensors Slicer displays the anatomical views of the average of all 6 diffusion weighted images

56 Surgical Planning Laboratory Brigham and Womens Hospital Converting DWI data to tensors Left Click on the button Bg and select the volume D_Baseline

57 Surgical Planning Laboratory Brigham and Womens Hospital Converting DWI data to tensors Observe the volume D_Baseline

58 Surgical Planning Laboratory Brigham and Womens Hospital Overview Part 1: Loading and Converting DTI Data Part 2: Computing Fractional Anisotropy Part 3: Generating Fiber Tracts Part 4: Selective Seeding Part 5: Clustering

59 Surgical Planning Laboratory Brigham and Womens Hospital Computing Fractional Anisotropy In the DT-MRI module, click on More to navigate in the different panels

60 Surgical Planning Laboratory Brigham and Womens Hospital Computing Fractional Anisotropy Select the panel Scalars Browse the menu Create Volume to see the list of calculations that Slicer can perform on the D_Tensor dataset. Select Fractional Anisotropy

61 Surgical Planning Laboratory Brigham and Womens Hospital The Fractional Anisotropy (FA) is a measure of the diffusion anisotropy that can be calculated without explicitly computing any eigenvalue: where |D| and trace(D) are the norm and trace of the Diffusion Tensor. Computing Fractional Anisotropy

62 Surgical Planning Laboratory Brigham and Womens Hospital Computing Fractional Anisotropy Click on Apply Select the Region of Interest ROI:Mask The Scale Factor is set by default to 1000, because the standard range of FA values (0.0 to 1.0) is not compatible with Slicer The Fractional Anisotropy Panel appears

63 Surgical Planning Laboratory Brigham and Womens Hospital Computing Fractional Anisotropy The Viewer displays the FA volume. Move the mouse in the slices to see FA values for each voxel.

64 Surgical Planning Laboratory Brigham and Womens Hospital Computing Fractional Anisotropy Note high FA values over large tracts such as the corpus callosum Note low FA values over gray matter

65 Surgical Planning Laboratory Brigham and Womens Hospital Fractional Anisotropy Statistics Goal Measure Fractional Anisotropy Statistics in a Region of Interest (ROI)

66 Surgical Planning Laboratory Brigham and Womens Hospital ROI Drawing Select the Editor module in the main Menu. Select the Volumes panel. Select the Original Grayscale FractionalAnisotropy_D Select the Working Labelmap NEW and keep the Default Descriptive Name Working. Click on Start Editing

67 Surgical Planning Laboratory Brigham and Womens Hospital ROI Drawing Select the Effects panel Left click on Draw in the Effects Menu

68 Surgical Planning Laboratory Brigham and Womens Hospital ROI Drawing The Draw Panel of the Editor Module appears Left-click on Output, and select the color label #2 (pink)

69 Surgical Planning Laboratory Brigham and Womens Hospital ROI Drawing Draw the contour of the Corpus Callosum with the mouse in the sagittal slice

70 Surgical Planning Laboratory Brigham and Womens Hospital ROI Drawing Click on Apply in the Editor Module

71 Surgical Planning Laboratory Brigham and Womens Hospital Measure FA Statistics in ROI Select Modules Measurement VolumeMath in the Main Menu

72 Surgical Planning Laboratory Brigham and Womens Hospital MaskStat Select MaskStat The MaskStat functionality uses the labelmap as a mask over the FA volume, and calculates stats on the region contained under the labelmap.

73 Surgical Planning Laboratory Brigham and Womens Hospital MaskStat Set Volume to Mask to FractionalAnisotropy_D_Tensor Set LabelMap to Working Set Masked Output to Create New

74 Surgical Planning Laboratory Brigham and Womens Hospital MaskStat Click on Run Click on Mask, select the same color as your labelmap Click on Browse to select a directory to place the output text file and enter the file name FractionalAnisotropy_D_Tensor_hist.txt

75 Surgical Planning Laboratory Brigham and Womens Hospital MaskStat Result A window shows the statistics (multiplied by the Scale Factor): minimal, maximal, mean and standard deviation of the FA values. The results have been saved in the file FractionalAnisotropy_D_Tensor_hist.txt written on the disk.

76 Surgical Planning Laboratory Brigham and Womens Hospital Save FA volume and ROI Select the module Editor Select the panel Volumes and click on Save Enter a FilenamePrefix and select the format NRRD(.nhdr) Click on Save

77 Surgical Planning Laboratory Brigham and Womens Hospital Save FA volume and ROI Slicer generates a Nrrd header file (FA.nhdr), and a raw compressed file (FA.raw.gz). Save the Working volume containing the label map using the same process. (Slicer Training #7: Saving data.)

78 Surgical Planning Laboratory Brigham and Womens Hospital Overview Part 1: Loading and Converting DTI Data Part 2: Computing Fractional Anisotropy Part 3: Generating Fiber Tracts Part 4: Selective Seeding Part 5: Clustering

79 Surgical Planning Laboratory Brigham and Womens Hospital Tractography Panel Select the DTMRI module and click on the Panel More Select the Panel Tracts inside the DTMRI module

80 Surgical Planning Laboratory Brigham and Womens Hospital Tractography Panel Select the Tab Settings Left-click on Color

81 Surgical Planning Laboratory Brigham and Womens Hospital Tractography Panel A Color selection panel appears Select a new color for the tracts

82 Surgical Planning Laboratory Brigham and Womens Hospital Create a single tract Position the mouse on a point inside the Corpus Callosum, and hit the s key.

83 Surgical Planning Laboratory Brigham and Womens Hospital Create a single tract A tract appears in the 3D Viewer. Drag right mouse button down in the 3D Viewer to zoom in.

84 Surgical Planning Laboratory Brigham and Womens Hospital Create a single tract Click on the V buttons The 3D window shows a closer view of the tract.

85 Surgical Planning Laboratory Brigham and Womens Hospital Create a single tract Slicer displays the slices in the 3D window. Drag left mouse button in the 3D Viewer to rotate the volume, Drag right mouse button to zoom in, until you get to a convenient view.

86 Surgical Planning Laboratory Brigham and Womens Hospital Generate Multiple Tracts Position the mouse on different points in the corpus callosum and hit the s key.

87 Surgical Planning Laboratory Brigham and Womens Hospital Generate Multiple Tracts The tracts that correspond to the visited points appear in the 3D Viewer.

88 Surgical Planning Laboratory Brigham and Womens Hospital Generate Multiple Tracts Hold down the s key and move the mouse in the corpus callosum

89 Surgical Planning Laboratory Brigham and Womens Hospital Generate Multiple Tracts Multiple tracts are generated for each point visited by the mouse.

90 Surgical Planning Laboratory Brigham and Womens Hospital ROI Seeding Slicer has functionalities to generate tracts from a pre-defined Region Of Interest (ROI). Training dataset ROI: ROI1: Temporal stem, between frontal and temporal lobes ROI2: Posterior temporal lobe ROI3: Splenium of the corpus callosum

91 Surgical Planning Laboratory Brigham and Womens Hospital ROI Drawing Select the Editor module in the main Menu. Select the Volumes panel and click Setup Select the Original Grayscale FractionalAnisotropy_D_Tensor Select the Labelmap Working. Click on Start Editing

92 Surgical Planning Laboratory Brigham and Womens Hospital ROI Drawing Select the Effects panel Left click on Draw in the Effects Menu

93 Surgical Planning Laboratory Brigham and Womens Hospital ROI Drawing Select the color label #7 in the module Editor

94 Surgical Planning Laboratory Brigham and Womens Hospital ROI1: Temporal stem Draw a region of interest in the Temporal stem (slice #156) Select View 1x512 COR in the Main Menu Click on Apply in the module Editor

95 Surgical Planning Laboratory Brigham and Womens Hospital ROI Drawing Select the color label #10 in the module Editor

96 Surgical Planning Laboratory Brigham and Womens Hospital ROI2: Posterior temporal lobe Draw a region of interest in the Posterior Temporal Lobe (slice #128) Select View 1x512 COR in the Main Menu. Click on Apply in the module Editor

97 Surgical Planning Laboratory Brigham and Womens Hospital ROI Drawing Select the color label #5 in the module Editor

98 Surgical Planning Laboratory Brigham and Womens Hospital ROI3: Splenium Draw a region of interest in the Splenium of the Corpus Callosum (slice #131) Select View 1x512 SAG in the Main Menu. Click on Apply in the module Editor.

99 Surgical Planning Laboratory Brigham and Womens Hospital Come back to the DTMRI module and select the panel Tracts. Click on the tab Seed and select the SeedROI Working ROI Seeding Select the color label #7 corresponding to the ROI1

100 Surgical Planning Laboratory Brigham and Womens Hospital Click on Seed Tracts ROI Seeding A warning message appears, Click Yes if you are ready to process the data.

101 Surgical Planning Laboratory Brigham and Womens Hospital ROI1 Seeding Slicer displays the tracts from ROI1

102 Surgical Planning Laboratory Brigham and Womens Hospital ROI Seeding Select the color label #10 corresponding to the ROI2 Click on Seed Tracts A warning message appears, Click Yes if you are ready to process the data.

103 Surgical Planning Laboratory Brigham and Womens Hospital ROI2 Seeding Slicer displays the tracts from ROI2

104 Surgical Planning Laboratory Brigham and Womens Hospital ROI Seeding Select the color label #5 corresponding to the ROI3 Click on Seed Tracts A warning message appears, Click Yes if you are ready to process the data.

105 Surgical Planning Laboratory Brigham and Womens Hospital ROI3 Seeding Slicer displays the tracts from ROI3

106 Surgical Planning Laboratory Brigham and Womens Hospital Selective Seeding Slicer displays the tracts from the 3 segmented ROIs

107 Surgical Planning Laboratory Brigham and Womens Hospital Overview Part 1: Loading and Converting DTI Data Part 2: Computing Fractional Anisotropy Part 3: Generating Fiber Tracts Part 4: Selective Seeding Part 5: Clustering

108 Surgical Planning Laboratory Brigham and Womens Hospital Selective Seeding AND and NOT operators can be used to select tracts generated from different Regions Of Interest.

109 Surgical Planning Laboratory Brigham and Womens Hospital Selective Seeding Slicer displays the tracts from the 3 segmented ROIs

110 Surgical Planning Laboratory Brigham and Womens Hospital AND/NOT operators: example ROI1: Temporal stem, between frontal and temporal lobes ROI2: Posterior temporal lobe ROI3: Splenium of the corpus callosum Target: Inferior Occipito-frontal Fasciculus from the Frontal lobe to Occipital Lobe, through Temporal lobe

111 Surgical Planning Laboratory Brigham and Womens Hospital Selective Seeding Click on the tab Select in the Panel Tract Select the ROI Labelmap Working Enter the labels of the ROI1 (label #7) and ROI2 (label #10) in the list of labels called AND.

112 Surgical Planning Laboratory Brigham and Womens Hospital Selective Seeding Click on Find Tracts through ROI Enter the label of the ROI3 (label #5) in the list of labels called NOT.

113 Surgical Planning Laboratory Brigham and Womens Hospital Selective Seeding Slicer displays the resulting tracts of the Inferior Occipito- frontal Fasciculus in red.

114 Surgical Planning Laboratory Brigham and Womens Hospital Selective Seeding The tracts that were not selected appear transparent.

115 Surgical Planning Laboratory Brigham and Womens Hospital Deleting Tracts Select the tab Display and click on Delete to delete all the tracts and clear the scene.

116 Surgical Planning Laboratory Brigham and Womens Hospital Deleting Tracts Slicer removes all the tracts generated from the ROIs.

117 Surgical Planning Laboratory Brigham and Womens Hospital Overview Part 1: Loading and Converting DTI Data Part 2: Computing Fractional Anisotropy Part 3: Generating Fiber Tracts Part 4: Selective Seeding Part 5: Clustering

118 Surgical Planning Laboratory Brigham and Womens Hospital ROI Seeding Select Seed in the Tracts Panel

119 Surgical Planning Laboratory Brigham and Womens Hospital Select the ROI Working Click on Seed Tracts ROI Seeding Select the color label of the ROI (#2) A warning message appears, Click Yes if you are ready to process the data.

120 Surgical Planning Laboratory Brigham and Womens Hospital The resulting tracts appear in the 3D Viewer. ROI Seeding

121 Surgical Planning Laboratory Brigham and Womens Hospital Corpus Callosum Tracts

122 Surgical Planning Laboratory Brigham and Womens Hospital Clustering Method Estimation of a similarity measurement for all pairs of tracts

123 Surgical Planning Laboratory Brigham and Womens Hospital Similarity Measurement The similarity measurement is based on the mean closest point distance between the tracts.

124 Surgical Planning Laboratory Brigham and Womens Hospital Clustering Method* High dimensional clustering space

125 Surgical Planning Laboratory Brigham and Womens Hospital Clustering Method* Cluster-colored tracts (*) White Matter Tract Clustering and Correspondence in Populations ODonnel L, Westin C-F Medical Image Computing and Computer-Assisted Interventions (MICCAI2005)

126 Surgical Planning Laboratory Brigham and Womens Hospital Tract Clustering Algorithm Click on More and select the panel TC In this tutorial example, we cluster the fiber tracts generated from the ROI in the Corpus Callosum

127 Surgical Planning Laboratory Brigham and Womens Hospital Tract Clustering Algorithm The Number of Clusters is the number of bundles expected.

128 Surgical Planning Laboratory Brigham and Womens Hospital Tract Clustering Algorithm N is the Sampling resolution along the fibers In this example, N=8 The default settings of the algorithm is N=15

129 Surgical Planning Laboratory Brigham and Womens Hospital Tract Clustering Algorithm The ShapeFeature corresponds to the Similarity Measurement

130 Surgical Planning Laboratory Brigham and Womens Hospital Tract Clustering Algorithm The ShapeFeature corresponds to the Similarity Measurement The default setting of the algorithm is MeanClosestPoint

131 Surgical Planning Laboratory Brigham and Womens Hospital Tract Clustering Algorithm Click on Cluster to start the algorithm

132 Surgical Planning Laboratory Brigham and Womens Hospital Tract Clustering Result Slicer displays the result of the tract clustering in the Corpus Callosum.

133 Surgical Planning Laboratory Brigham and Womens Hospital Tract Clustering Result Slicer displays the result of the tract clustering in the Corpus Callosum.

134 Surgical Planning Laboratory Brigham and Womens Hospital Conclusion Intuitive interface for manual and automatic tracts generation Enhanced visualization of the anatomy by fusion of tracts and DWI images Open-source environment


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