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Diffusion Tensor Imaging Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D. National Alliance for Medical Image Computing
Acknowledgments <ul><li>National Alliance for Medical Image   Computing </li></ul><ul><li>NIH U54EB005149  </li></ul><ul><...
Material <ul><li>Slicer 2.6 </li></ul><ul><li>http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started </li><...
Goal of this tutorial Guiding you step-by-step through the DWI data analysis capabilities of Slicer, including generation ...
Slicer DT-MRI Module
Overview <ul><li>Part 1: Loading and Converting DTI Data  </li></ul><ul><li>Part 2: Computing Fractional Anisotropy </li><...
Diffusion Weighted Imaging (DWI) Diffusion Sensitizing Gradients  Diffusion Weighted  Images
Diffusion Weighted Imaging (DWI) Example: Correlation between the orientation of the 11 th  gradient and the signal intens...
Loading DTI Data <ul><li>Slicer can load </li></ul><ul><li>DWI Volumes ……………………. </li></ul><ul><li>Tensors…………………………… </li...
DWI Training Dataset 1 <ul><li>2 Baselines and 12 Gradients   </li></ul>
DWI Training Dataset 2 <ul><li>1 Baseline and 6 Gradients   </li></ul>
Loading the DWI Training Dataset 1 Click on  Add Volume  to load the  Dicom-DWI  training dataset
Loading DWI data Select  Nrrd Reader  in the  Properties  field The  Props Panel  of the module  Volumes  appears.
Loading DWI data  Click on  Apply Click on Browse and load the file  namic01-dwi.nhdr  in the directory Dwi-dicom Check th...
Loading DWI data Slicer loads the Nrrd DWI  dataset
Loading DWI data  Left-click on the button  Or , and select the orientation  Slices
Loading DWI data The anatomical slices are now aligned with the sampling grid
Loading DWI data Change the  FOV  to 2000
Loading DWI data The sagittal and coronal viewers display the 14 MR volumes: 2 baselines and 12 diffusion weighted volumes
Loading DWI data Left-Click on the  V  button to display the axial and sagittal slices inside the viewer. Use the axial sl...
DT-MRI Module  Select  Modules  in the Main Menu Select  Visualisation  DTMRI
DT-MRI Module  The panel  Input  of the DTMRI module appears Click on the tab  Conv
DT-MRI Module  The panel  Conv  of the DTMRI module appears
Converting DWI data to tensors Select the Input Volume  namic01-dwi.nhdr  and click on  ConvertVolume
Converting DWI data to tensors (Stejskal and Tanner 1965, Basser 1994 ) {Si} represent the signal intensities in presence ...
<ul><li>At the end of the calculation, Slicer displays the average of all diffusion weighted images  (_AvGradient)  and th...
Converting DWI data to tensors Slicer displays the anatomical views of the average of all 12 diffusion weighted images (av...
Adjusting Window Level Click on the Module  Volumes  and select the tab  Display
Adjusting Window Level Select the  Active Volume namic01-dwi-nhdr_AvGradient Use the sliders  Win  and  Lev  to adjust the...
Adjusting Window Level Slicer displays the anatomical views of the average of all 12 diffusion weighted images (average ov...
Converting DWI data to tensors Left-click on  Bg  and select the volume  namic01-dwi nhdr _Baseline
Converting DWI data to tensors Browse the baseline images to check if the anatomy is correct Slicer displays the baseline ...
Converting DWI data to tensors Click on the module  Data Slicer displays the list of DTI volumes
Converting DWI data to tensors Select  File   Close  in the Main Menu to clear the scene
Loading the DWI Training Dataset 2 Click on  Add Volume
Loading Slicer Sample DWI data Select  ImageHeaders: Auto Click  Apply Select the  Props  Panel Use the  Basic  Reader Cli...
Loading Slicer Sample DWI data The DWI images appear in the Viewer
Loading Slicer Sample DWI data Observe the axial  slices using the slider
Loading Slicer Sample DWI data A sequence of white stripes appears in the diffusion weighted images. They correspond to in...
Loading Slicer Sample DWI data Inferior Superior In Axial/Sagittal/Coronal mode the slices planes, which are aligned with ...
Loading Slicer Sample DWI data Left click on   Or  and select  the orientation  Slices  in the Menu
Loading Slicer Sample DWI data The original slices appear in the Viewer
Loading Slicer Sample DWI data Inferior Superior In AxiSlice/SagiSlice/CorSlice mode the slices are aligned with the DWI v...
Loading Slicer Sample DWI data Notice that the viewer displays the stack of S 0  and diffusion weighted images {Si}
Loading Slicer Sample DWI data Browse the original axial slices corresponding to the baseline (S 0 ) image. Example: displ...
Loading Slicer Sample DWI data Adjust the window level and observe the baseline image (S 0 )
Adjusting Image Window Level Select the  Volumes  module Adjust  Window  and  Level Select the volume  D Select the  Displ...
Loading Slicer Sample DWI data Observe the baseline image (S 0 )
Loading Slicer Sample DWI data Notice that the image intensity for each of the six gradient orientations is much lower tha...
DT-MRI Module  Select  Modules  in the Main Menu Select  Visualization  DTMRI
DT-MRI Module  Select the Conversion Panel:  Conv Select the module DTMRI
Convert DWI data to tensors Select  InputVolume D  Select Protocol  BWH_6g.1bSlice Click on  Prop  to display the paramete...
Acquisition protocol <ul><li>Slicer displays the parameters of the acquisition protocol used </li></ul><ul><li>to acquire ...
Convert DWI data to tensors Click on  Convert Volume
Converting DWI data to tensors Slicer displays the anatomical views of the average of all 6 diffusion weighted images
Converting DWI data to tensors Left Click on the button Bg and select the volume D_Baseline
Converting DWI data to tensors Observe the volume D_Baseline
Overview <ul><li>Part 1: Loading and Converting DTI Data  </li></ul><ul><li>Part 2: Computing Fractional Anisotropy </li><...
Computing Fractional Anisotropy In the DT-MRI module,  click on  More  to navigate  in the different panels
Computing Fractional Anisotropy Select the panel  Scalars Browse the menu  Create Volume  to see the list of calculations ...
<ul><li>The  Fractional Anisotropy   (FA)  is a measure of the diffusion anisotropy that can be calculated without explici...
Computing Fractional Anisotropy Click on  Apply Select the Region of Interest  ROI:Mask The  Scale Factor  is set by defau...
Computing Fractional Anisotropy The Viewer displays the FA volume. Move the mouse in the slices to see FA values for each ...
Computing Fractional Anisotropy <ul><li>Note  high FA values  over large tracts such as the  corpus callosum   </li></ul><...
Fractional Anisotropy Statistics <ul><li>Goal  </li></ul><ul><li>Measure Fractional </li></ul><ul><li>Anisotropy Statistic...
ROI Drawing Select the  Editor  module in the main Menu. Select the  Volumes  panel. Select the Original Grayscale  Fracti...
ROI Drawing Select the  Effects  panel Left click on  Draw  in the Effects Menu
ROI Drawing The Draw Panel of the Editor Module appears Left-click on  Output,  and select the color label #2 (pink)
ROI Drawing Draw the contour of the Corpus Callosum with the mouse in the sagittal slice
ROI Drawing Click on  Apply  in the Editor Module
Measure FA Statistics in ROI Select  Modules   Measurement  VolumeMath   in the Main Menu
MaskStat Select  MaskStat The  MaskStat  functionality uses the labelmap as a  mask  over the FA volume, and calculates “ ...
MaskStat Set  Volume to Mask  to  FractionalAnisotropy_D_Tensor Set  LabelMap  to  Working Set  Masked Output  to  Create ...
MaskStat Click on  Run Click on  Mask , select the same color as your labelmap Click on  Browse  to select a directory to ...
MaskStat Result A window shows the statistics (multiplied by the Scale Factor): minimal, maximal, mean and standard deviat...
Save FA volume and ROI Select the module  Editor Select the panel  Volumes and click on  Save Enter a FilenamePrefix and s...
Save FA volume and ROI Slicer generates a Nrrd header file (FA.nhdr), and a raw compressed file (FA.raw.gz). Save the  Wor...
Overview <ul><li>Part 1: Loading and Converting DTI Data  </li></ul><ul><li>Part 2: Computing Fractional Anisotropy </li><...
Tractography Panel Select the  DTMRI module  and click on the Panel  More Select the Panel  Tracts  inside the  DTMRI  mod...
Tractography Panel Select the Tab  Settings  Left-click on  Color
Tractography Panel A Color selection  panel appears Select a new color  for the tracts
Create a single tract Position the mouse on a point inside the Corpus Callosum, and hit the  s  key.
Create a single tract A tract appears in the 3D Viewer. Drag right mouse button down in the 3D Viewer to zoom in.
Create a single tract Click on the  V  buttons The 3D window shows a closer view of the tract.
Create a single tract Slicer displays the slices in the 3D window. Drag left mouse button in the 3D Viewer to rotate the v...
Generate Multiple Tracts Position the mouse on different points in the corpus callosum and hit the  s  key.
Generate Multiple Tracts The tracts that correspond to the visited points appear in the 3D Viewer.
Generate Multiple Tracts Hold down the  s  key and  move the mouse in the corpus callosum
Generate Multiple Tracts Multiple tracts are generated for each point visited by the mouse.
ROI Seeding <ul><li>Slicer has functionalities to generate tracts </li></ul><ul><li>from a pre-defined  Region Of Interest...
ROI Drawing Select the  Editor  module in the main Menu. Select the  Volumes  panel and click  Setup Select the Original G...
ROI Drawing Select the  Effects  panel Left click on  Draw  in the Effects Menu
ROI Drawing Select the color label #7 in the module  Editor
ROI1: Temporal stem Draw a region of interest in the  Temporal stem (slice #156) Select  View  1x512   COR  in the Main M...
ROI Drawing Select the color label #10 in the module  Editor
ROI2: Posterior temporal lobe  Draw a region of interest in the  Posterior Temporal Lobe  (slice #128) Select  View  1x51...
ROI Drawing Select the color label #5 in the module  Editor
ROI3: Splenium Draw a region of interest in the  Splenium  of the  Corpus Callosum  (slice #131) Select  View  1x512   SA...
ROI Seeding Come back to the  DTMRI  module and select the panel  Tracts . Click on the tab  Seed  and select the SeedROI ...
ROI Seeding Click on  Seed Tracts A warning message appears, Click  Yes  if you are ready to process the data.
ROI1 Seeding Slicer displays the tracts from ROI1
ROI Seeding Select the  color label #10  corresponding to the  ROI2 Click on  Seed Tracts A warning message appears, Click...
ROI2 Seeding Slicer displays the tracts from ROI2
ROI Seeding Select the  color label #5  corresponding to the  ROI3 Click on  Seed Tracts A warning message appears, Click ...
ROI3 Seeding Slicer displays the tracts from ROI3
Selective Seeding Slicer displays the tracts from the 3 segmented ROIs
Overview <ul><li>Part 1: Loading and Converting DTI Data  </li></ul><ul><li>Part 2: Computing Fractional Anisotropy </li><...
Selective Seeding <ul><li>AND  and  NOT  operators can be used to </li></ul><ul><li>select tracts generated from different...
Selective Seeding Slicer displays the tracts from the 3 segmented ROIs
AND/NOT operators: example <ul><li>ROI1:  Temporal stem, between frontal and temporal lobes </li></ul><ul><li>ROI2:   Post...
Selective Seeding Click on the tab  Select  in the Panel  Tract Select the  ROI Labelmap  Working Enter the labels of the ...
Selective Seeding Click on  Find Tracts through ‘ROI’ Enter the label of the  ROI3  (label #5) in the list of labels calle...
Selective Seeding Slicer displays the resulting tracts of the  Inferior Occipito-frontal Fasciculus  in red.
Selective Seeding The tracts that were not selected appear transparent.
Deleting Tracts Select the tab  Display  and click on  Delete  to delete all the tracts and clear the scene.
Deleting Tracts Slicer removes all the tracts generated from the ROIs.
Overview <ul><li>Part 1: Loading and Converting DTI Data  </li></ul><ul><li>Part 2: Computing Fractional Anisotropy </li><...
ROI Seeding Select  Seed  in the  Tracts  Panel
ROI Seeding Select the ROI  Working Click on  Seed Tracts Select the color label of the ROI (#2) A warning message appears...
ROI Seeding The resulting  tracts appear in the 3D Viewer.
Corpus Callosum Tracts
Clustering Method Estimation of a similarity measurement for all pairs of tracts
Similarity Measurement The similarity measurement is based on the  mean closest point distance  between the tracts.
Clustering Method* High dimensional clustering space
Clustering Method* Cluster-colored  tracts (*) White Matter Tract Clustering and Correspondence in Populations O’Donnel L,...
Tract Clustering Algorithm Click on  More  and select the panel  TC In this tutorial example, we cluster the fiber tracts ...
Tract Clustering Algorithm The  Number of Clusters  is the number of bundles expected.
Tract Clustering Algorithm N is the  Sampling resolution  along the fibers In this example, N=8 The default settings of th...
Tract Clustering Algorithm The  ShapeFeature  corresponds to the Similarity Measurement
Tract Clustering Algorithm The  ShapeFeature  corresponds to the Similarity Measurement The default setting of the algorit...
Tract Clustering Algorithm Click on  Cluster  to start the algorithm
Tract Clustering Result Slicer displays the result of the tract clustering in  the Corpus Callosum.
Tract Clustering Result Slicer displays the result of the tract clustering in  the Corpus Callosum.
Conclusion <ul><li>Intuitive interface for manual and automatic tracts generation  </li></ul><ul><li>Enhanced visualizatio...
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Diffusion Tensor Imaging Analysis-3749

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  • Transcript of "Diffusion Tensor Imaging Analysis-3749"

    1. 1. Diffusion Tensor Imaging Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D. National Alliance for Medical Image Computing
    2. 2. Acknowledgments <ul><li>National Alliance for Medical Image Computing </li></ul><ul><li>NIH U54EB005149 </li></ul><ul><li>Neuroimage Analysis Center </li></ul><ul><li>NIH P41RR013218 </li></ul><ul><li>Laboratory of Mathematics in Imaging, </li></ul><ul><li>Brigham and Women’s Hospital </li></ul><ul><li>Thanks to Carl-Fredrik Westin, Lauren O’Donnell, Raul San </li></ul><ul><li>Jose Estepar, Carlos Isorna, Maxime Boucher, Matthan Caan </li></ul>
    3. 3. Material <ul><li>Slicer 2.6 </li></ul><ul><li>http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started </li></ul><ul><li>DTI Sample Data Set </li></ul><ul><li>Dwi-dicom.zip </li></ul><ul><li>SlicerSampleDTI.zip </li></ul><ul><li>http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 </li></ul>
    4. 4. 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. 5. Slicer DT-MRI Module
    6. 6. Overview <ul><li>Part 1: Loading and Converting DTI Data </li></ul><ul><li>Part 2: Computing Fractional Anisotropy </li></ul><ul><li>Part 3: Generating Fiber Tracts </li></ul><ul><li>Part 4: Selective Seeding </li></ul><ul><li>Part 5: Clustering </li></ul>
    7. 7. Diffusion Weighted Imaging (DWI) Diffusion Sensitizing Gradients Diffusion Weighted Images
    8. 8. 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. 9. Loading DTI Data <ul><li>Slicer can load </li></ul><ul><li>DWI Volumes ……………………. </li></ul><ul><li>Tensors…………………………… </li></ul><ul><li>Tracts……………………………… </li></ul><ul><li>DTI Scenes ………………………. </li></ul>
    10. 10. DWI Training Dataset 1 <ul><li>2 Baselines and 12 Gradients </li></ul>
    11. 11. DWI Training Dataset 2 <ul><li>1 Baseline and 6 Gradients </li></ul>
    12. 12. Loading the DWI Training Dataset 1 Click on Add Volume to load the Dicom-DWI training dataset
    13. 13. Loading DWI data Select Nrrd Reader in the Properties field The Props Panel of the module Volumes appears.
    14. 14. 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. 15. Loading DWI data Slicer loads the Nrrd DWI dataset
    16. 16. Loading DWI data Left-click on the button Or , and select the orientation Slices
    17. 17. Loading DWI data The anatomical slices are now aligned with the sampling grid
    18. 18. Loading DWI data Change the FOV to 2000
    19. 19. Loading DWI data The sagittal and coronal viewers display the 14 MR volumes: 2 baselines and 12 diffusion weighted volumes
    20. 20. 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. 21. DT-MRI Module Select Modules in the Main Menu Select Visualisation  DTMRI
    22. 22. DT-MRI Module The panel Input of the DTMRI module appears Click on the tab Conv
    23. 23. DT-MRI Module The panel Conv of the DTMRI module appears
    24. 24. Converting DWI data to tensors Select the Input Volume namic01-dwi.nhdr and click on ConvertVolume
    25. 25. Converting DWI data to tensors (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 zz zy zx yz yy yx xz xy xx D D D D D D D D D
    26. 26. <ul><li>At the end of the calculation, Slicer displays the average of all diffusion weighted images (_AvGradient) and the baseline volume (_Baseline) . </li></ul><ul><li>The tensors volume is available from the DTMRI module for additional calculations. </li></ul>Converting DWI data to tensors
    27. 27. 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. 28. Adjusting Window Level Click on the Module Volumes and select the tab Display
    29. 29. Adjusting Window Level Select the Active Volume namic01-dwi-nhdr_AvGradient Use the sliders Win and Lev to adjust the Window level
    30. 30. 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. 31. Converting DWI data to tensors Left-click on Bg and select the volume namic01-dwi nhdr _Baseline
    32. 32. Converting DWI data to tensors Browse the baseline images to check if the anatomy is correct Slicer displays the baseline (T2) images.
    33. 33. Converting DWI data to tensors Click on the module Data Slicer displays the list of DTI volumes
    34. 34. Converting DWI data to tensors Select File  Close in the Main Menu to clear the scene
    35. 35. Loading the DWI Training Dataset 2 Click on Add Volume
    36. 36. 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. 37. Loading Slicer Sample DWI data The DWI images appear in the Viewer
    38. 38. Loading Slicer Sample DWI data Observe the axial slices using the slider
    39. 39. Loading Slicer Sample DWI data 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.
    40. 40. Loading Slicer Sample DWI data Inferior Superior In Axial/Sagittal/Coronal mode the slices planes, which are aligned with the RAS coordinates, are cutting through the DWI volume
    41. 41. Loading Slicer Sample DWI data Left click on Or and select the orientation Slices in the Menu
    42. 42. Loading Slicer Sample DWI data The original slices appear in the Viewer
    43. 43. Loading Slicer Sample DWI data Inferior Superior In AxiSlice/SagiSlice/CorSlice mode the slices are aligned with the DWI volume
    44. 44. Loading Slicer Sample DWI data Notice that the viewer displays the stack of S 0 and diffusion weighted images {Si}
    45. 45. Loading Slicer Sample DWI data Browse the original axial slices corresponding to the baseline (S 0 ) image. Example: display the slice 209
    46. 46. Loading Slicer Sample DWI data Adjust the window level and observe the baseline image (S 0 )
    47. 47. Adjusting Image Window Level Select the Volumes module Adjust Window and Level Select the volume D Select the Display panel
    48. 48. Loading Slicer Sample DWI data Observe the baseline image (S 0 )
    49. 49. Loading Slicer Sample DWI data Notice that the image intensity for each of the six gradient orientations is much lower than the S 0 image.
    50. 50. DT-MRI Module Select Modules in the Main Menu Select Visualization  DTMRI
    51. 51. DT-MRI Module Select the Conversion Panel: Conv Select the module DTMRI
    52. 52. 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. 53. Acquisition protocol <ul><li>Slicer displays the parameters of the acquisition protocol used </li></ul><ul><li>to acquire the DTI Sample Data BWH_6g.1bSlice at </li></ul><ul><li>Brigham and Women’s Hospital, corresponding to: </li></ul><ul><li>n=6 gradients </li></ul><ul><li>Gradient directions = {0.707107 0.707107 0} , </li></ul><ul><li>{0 0.707107 0.707107 }, {0.707107 0 0.707107 }, </li></ul><ul><li>{0 0.707107 -0.707107 }, {0.707107 -0.707107 0}, </li></ul><ul><li>{-0.707107 0 0.707107} </li></ul><ul><li>Gradient order: Slice interleaved </li></ul><ul><li>b=1 baseline </li></ul><ul><li>B-value = 1000 </li></ul>
    54. 54. Convert DWI data to tensors Click on Convert Volume
    55. 55. Converting DWI data to tensors Slicer displays the anatomical views of the average of all 6 diffusion weighted images
    56. 56. Converting DWI data to tensors Left Click on the button Bg and select the volume D_Baseline
    57. 57. Converting DWI data to tensors Observe the volume D_Baseline
    58. 58. Overview <ul><li>Part 1: Loading and Converting DTI Data </li></ul><ul><li>Part 2: Computing Fractional Anisotropy </li></ul><ul><li>Part 3: Generating Fiber Tracts </li></ul><ul><li>Part 4: Selective Seeding </li></ul><ul><li>Part 5: Clustering </li></ul>
    59. 59. Computing Fractional Anisotropy In the DT-MRI module, click on More to navigate in the different panels
    60. 60. 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. 61. <ul><li>The Fractional Anisotropy (FA) is a measure of the diffusion anisotropy that can be calculated without explicitly computing any eigenvalue: </li></ul><ul><li>where |D| and trace(D) are the norm and trace of the Diffusion Tensor. </li></ul>Computing Fractional Anisotropy
    62. 62. 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. 63. Computing Fractional Anisotropy The Viewer displays the FA volume. Move the mouse in the slices to see FA values for each voxel.
    64. 64. Computing Fractional Anisotropy <ul><li>Note high FA values over large tracts such as the corpus callosum </li></ul><ul><li>Note low FA values over gray matter </li></ul>
    65. 65. Fractional Anisotropy Statistics <ul><li>Goal </li></ul><ul><li>Measure Fractional </li></ul><ul><li>Anisotropy Statistics in a </li></ul><ul><li>Region of Interest (ROI) </li></ul>
    66. 66. 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. 67. ROI Drawing Select the Effects panel Left click on Draw in the Effects Menu
    68. 68. ROI Drawing The Draw Panel of the Editor Module appears Left-click on Output, and select the color label #2 (pink)
    69. 69. ROI Drawing Draw the contour of the Corpus Callosum with the mouse in the sagittal slice
    70. 70. ROI Drawing Click on Apply in the Editor Module
    71. 71. Measure FA Statistics in ROI Select Modules  Measurement  VolumeMath in the Main Menu
    72. 72. 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. 73. MaskStat Set Volume to Mask to FractionalAnisotropy_D_Tensor Set LabelMap to Working Set Masked Output to Create New
    74. 74. 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. 75. 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. 76. 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. 77. 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. 78. Overview <ul><li>Part 1: Loading and Converting DTI Data </li></ul><ul><li>Part 2: Computing Fractional Anisotropy </li></ul><ul><li>Part 3: Generating Fiber Tracts </li></ul><ul><li>Part 4: Selective Seeding </li></ul><ul><li>Part 5: Clustering </li></ul>
    79. 79. Tractography Panel Select the DTMRI module and click on the Panel More Select the Panel Tracts inside the DTMRI module
    80. 80. Tractography Panel Select the Tab Settings Left-click on Color
    81. 81. Tractography Panel A Color selection panel appears Select a new color for the tracts
    82. 82. Create a single tract Position the mouse on a point inside the Corpus Callosum, and hit the s key.
    83. 83. Create a single tract A tract appears in the 3D Viewer. Drag right mouse button down in the 3D Viewer to zoom in.
    84. 84. Create a single tract Click on the V buttons The 3D window shows a closer view of the tract.
    85. 85. 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. 86. Generate Multiple Tracts Position the mouse on different points in the corpus callosum and hit the s key.
    87. 87. Generate Multiple Tracts The tracts that correspond to the visited points appear in the 3D Viewer.
    88. 88. Generate Multiple Tracts Hold down the s key and move the mouse in the corpus callosum
    89. 89. Generate Multiple Tracts Multiple tracts are generated for each point visited by the mouse.
    90. 90. ROI Seeding <ul><li>Slicer has functionalities to generate tracts </li></ul><ul><li>from a pre-defined Region Of Interest (ROI). </li></ul><ul><li>Training dataset ROI: </li></ul><ul><li>ROI1: Temporal stem, between frontal and temporal lobes </li></ul><ul><li>ROI2: Posterior temporal lobe </li></ul><ul><li>ROI3: Splenium of the corpus callosum </li></ul>
    91. 91. 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. 92. ROI Drawing Select the Effects panel Left click on Draw in the Effects Menu
    93. 93. ROI Drawing Select the color label #7 in the module Editor
    94. 94. 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. 95. ROI Drawing Select the color label #10 in the module Editor
    96. 96. 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. 97. ROI Drawing Select the color label #5 in the module Editor
    98. 98. 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. 99. ROI Seeding Come back to the DTMRI module and select the panel Tracts . Click on the tab Seed and select the SeedROI Working Select the color label #7 corresponding to the ROI1
    100. 100. ROI Seeding Click on Seed Tracts A warning message appears, Click Yes if you are ready to process the data.
    101. 101. ROI1 Seeding Slicer displays the tracts from ROI1
    102. 102. 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. 103. ROI2 Seeding Slicer displays the tracts from ROI2
    104. 104. 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. 105. ROI3 Seeding Slicer displays the tracts from ROI3
    106. 106. Selective Seeding Slicer displays the tracts from the 3 segmented ROIs
    107. 107. Overview <ul><li>Part 1: Loading and Converting DTI Data </li></ul><ul><li>Part 2: Computing Fractional Anisotropy </li></ul><ul><li>Part 3: Generating Fiber Tracts </li></ul><ul><li>Part 4: Selective Seeding </li></ul><ul><li>Part 5: Clustering </li></ul>
    108. 108. Selective Seeding <ul><li>AND and NOT operators can be used to </li></ul><ul><li>select tracts generated from different </li></ul><ul><li>Regions Of Interest. </li></ul>
    109. 109. Selective Seeding Slicer displays the tracts from the 3 segmented ROIs
    110. 110. AND/NOT operators: example <ul><li>ROI1: Temporal stem, between frontal and temporal lobes </li></ul><ul><li>ROI2: Posterior temporal lobe </li></ul><ul><li>ROI3: Splenium of the corpus callosum </li></ul><ul><li>Target: Inferior Occipito-frontal Fasciculus from the Frontal lobe to Occipital Lobe, through Temporal lobe </li></ul>
    111. 111. 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. 112. Selective Seeding Click on Find Tracts through ‘ROI’ Enter the label of the ROI3 (label #5) in the list of labels called NOT.
    113. 113. Selective Seeding Slicer displays the resulting tracts of the Inferior Occipito-frontal Fasciculus in red.
    114. 114. Selective Seeding The tracts that were not selected appear transparent.
    115. 115. Deleting Tracts Select the tab Display and click on Delete to delete all the tracts and clear the scene.
    116. 116. Deleting Tracts Slicer removes all the tracts generated from the ROIs.
    117. 117. Overview <ul><li>Part 1: Loading and Converting DTI Data </li></ul><ul><li>Part 2: Computing Fractional Anisotropy </li></ul><ul><li>Part 3: Generating Fiber Tracts </li></ul><ul><li>Part 4: Selective Seeding </li></ul><ul><li>Part 5: Clustering </li></ul>
    118. 118. ROI Seeding Select Seed in the Tracts Panel
    119. 119. ROI Seeding Select the ROI Working Click on Seed Tracts Select the color label of the ROI (#2) A warning message appears, Click Yes if you are ready to process the data.
    120. 120. ROI Seeding The resulting tracts appear in the 3D Viewer.
    121. 121. Corpus Callosum Tracts
    122. 122. Clustering Method Estimation of a similarity measurement for all pairs of tracts
    123. 123. Similarity Measurement The similarity measurement is based on the mean closest point distance between the tracts.
    124. 124. Clustering Method* High dimensional clustering space
    125. 125. Clustering Method* Cluster-colored tracts (*) White Matter Tract Clustering and Correspondence in Populations O’Donnel L, Westin C-F Medical Image Computing and Computer-Assisted Interventions (MICCAI2005)
    126. 126. 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. 127. Tract Clustering Algorithm The Number of Clusters is the number of bundles expected.
    128. 128. 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. 129. Tract Clustering Algorithm The ShapeFeature corresponds to the Similarity Measurement
    130. 130. Tract Clustering Algorithm The ShapeFeature corresponds to the Similarity Measurement The default setting of the algorithm is MeanClosestPoint
    131. 131. Tract Clustering Algorithm Click on Cluster to start the algorithm
    132. 132. Tract Clustering Result Slicer displays the result of the tract clustering in the Corpus Callosum.
    133. 133. Tract Clustering Result Slicer displays the result of the tract clustering in the Corpus Callosum.
    134. 134. Conclusion <ul><li>Intuitive interface for manual and automatic tracts generation </li></ul><ul><li>Enhanced visualization of the anatomy by fusion of tracts and DWI images </li></ul><ul><li>Open-source environment </li></ul>
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