FreeSurfer Reader-3766

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  • 1. Slicer Tutorial 6 Module: vtkFreeSurferReaders Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D.
  • 2. Acknowledgments
    • National Alliance for Medical Image Computing
    • NIH U54EB005149
    • Neuroimage Analysis Center
    • NIH P41RR013218
    • Center for Functional Neuroimaging Technologies
    • NIH P41RR14075
    • Morphometry Biomedical Informatics Research Network
    • NIH U24 RRO21382
    • Surgical Planning Laboratory
    • Thanks to Nicole Aucoin
  • 3. Disclaimer
    • It is the responsibility of the user of 3DSlicer
    • and FreeSurfer to comply with both the terms
    • of the licenses and with the applicable laws,
    • regulations and rules.
  • 4. Materials Needed
    • Slicer 2.5MGH
    • http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.5MGH_Getting_Started
    • Free Surfer Sample Data: FreesurferSubjects.zip
    • http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101
  • 5. Goal of this tutorial Guide you step-by-step through the process of loading and viewing FreeSurfer segmentation, surface reconstruction and parcellation results within Slicer.
  • 6. Prerequisites
    • This tutorial assumes a working
    • knowledge of how to use
    • FreeSurfer to generate the
    • segmentation and surface files.
    • Tutorial materials for FreeSurfer
    • are available at
    https://surfer.nmr.mgh.harvard.edu/fswiki https://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsTutorial/
  • 7. Prerequisites
    • This tutorial assumes a basic
    • knowledge of how to use
    • 3DSlicer.
    • Slicer Training 1: Loading
    • and Viewing Data
    • Slicer Training 7: Saving Data
    http://www.namic.org/Wiki/index.php/ Slicer:Workshops:User_Training_101
  • 8. vtkFreeSurferReaders Module
  • 9. Loading FreeSurfer Data
    • Slicer can load
    • Brain Volumes …………………….
    • ASEG Volumes ………………………
    • Surfaces…………………………………
    • Overlays ………………………………….
  • 10.
    • Part 1: Loading FreeSurfer Volumes
    • Part 2: Overlay Brain and Segmentation
    • Part 3: Building 3D Models
    • Part 4: Loading Surfaces
    • Part 5: Group Statistics
    Overview of Training 6
  • 11. vtkFreeSurferReaders Module Select the Menu Modules in the Main Panel Select the category IO and the module vtkFreeSurferReaders
  • 12. vtkFreeSurferReaders Module The vtkFreeSurferReaders module appears in the Main Panel of Slicer. The Volumes tab comes up by default.
  • 13. Loading a Brain file Brain.mgz Skull Stripping and Noise Filtering Watershed algorithm Intensity corrected T1 volume FreeSurfer Pipeline
  • 14. Loading a Brain file Select the Tab Volumes in the FreeSurfer Module Click on Browse and select the subject bert Click on the mri folder to access the brain volume.
  • 15. Loading a Brain file Select the file brain.mgz Select the data type GrayScale Click Apply
  • 16. Loading a Brain file The volume Brain.mgz appears in the Viewer .
  • 17. Loading a Brain file Click on the V buttons in the Axial, Sagittal and Coronal views.
  • 18. Loading a Brain file The three anatomical slices appear in the 3D Viewer .
  • 19. Loading an ASEG file Aseg.mgz Segmentation Subcortical processing Intensity corrected T1 volume FreeSurfer Pipeline
  • 20. Loading an ASEG file Select the Tab Volumes in the FreeSurfer Module. Click on Browse and select the subject bert Click on the mri folder to access the aseg volume.
  • 21. Loading an ASEG file Select the file aseg.mgz Select the data type Label Map Click on Apply
  • 22. Loading an ASEG file The labels are superimposed on the gray level brain images. The volume aseg.mgz appears in the Viewer .
  • 23. Determining label numbers in an ASEG file # ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range 1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 2 2 245171 245171.0 Left-Cerebral-White-Matter 121.7886 8.0072 40.0000 186.0000 146.0000 3 3 287069 287069.0 Left-Cerebral-Cortex 91.3494 13.8505 31.0000 220.0000 189.0000 4 4 6876 6876.0 Left-Lateral-Ventricle 48.2126 14.3628 25.0000 106.0000 81.0000 5 5 200 200.0 Left-Inf-Lat-Vent 67.3513 10.8024 35.0000 102.0000 67.0000 6 6 0 0.0 Left-Cerebellum-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 7 7 10514 10514.0 Left-Cerebellum-White-Matter 120.4405 8.5863 43.0000 134.0000 91.0000 8 8 66561 66561.0 Left-Cerebellum-Cortex 98.8117 14.1726 32.0000 211.0000 179.0000 9 9 0 0.0 Left-Thalamus 0.0000 0.0000 0.0000 0.0000 0.0000 10 10 9887 9887.0 Left-Thalamus-Proper 113.5839 10.3047 45.0000 133.0000 88.0000 11 11 3819 3819.0 Left-Caudate 102.9627 12.1416 62.0000 132.0000 70.0000 12 12 6755 6755.0 Left-Putamen 110.0479 7.4787 76.0000 132.0000 56.0000 13 13 2229 2229.0 Left-Pallidum 122.5797 4.2841 105.0000 134.0000 29.0000 14 14 793 793.0 3rd-Ventricle 54.2582 15.3296 28.0000 93.0000 65.0000 15 15 1819 1819.0 4th-Ventricle 51.8305 15.5400 27.0000 108.0000 81.0000 16 16 26616 26616.0 Brain-Stem 113.1949 12.7048 39.0000 136.0000 97.0000 17 17 4489 4489.0 Left-Hippocampus 96.0929 8.6315 56.0000 122.0000 66.0000 18 18 1869 1869.0 Left-Amygdala 94.8671 8.2028 61.0000 118.0000 57.0000 19 19 0 0.0 Left-Insula 0.0000 0.0000 0.0000 0.0000 0.0000 20 20 0 0.0 Left-Operculum 0.0000 0.0000 0.0000 0.0000 0.0000 21 21 0 0.0 Line-1 0.0000 0.0000 0.0000 0.0000 0.0000 22 22 0 0.0 Line-2 0.0000 0.0000 0.0000 0.0000 0.0000 23 23 0 0.0 Line-3 0.0000 0.0000 0.0000 0.0000 0.0000 24 24 1611 1611.0 CSF 59.9684 15.4368 30.0000 107.0000 77.0000 25 25 0 0.0 Left-Lesion 0.0000 0.0000 0.0000 0.0000 0.0000 26 26 733 733.0 Left-Accumbens-area 97.8124 6.7471 67.0000 121.0000 54.0000 27 27 0 0.0 Left-Substancia-Nigra 0.0000 0.0000 0.0000 0.0000 0.0000 28 28 3957 3957.0 Left-VentralDC 117.4001 10.5813 47.0000 135.0000 88.0000 29 29 0 0.0 Left-undetermined 0.0000 0.0000 0.0000 0.0000 0.0000 30 30 56 56.0 Left-vessel 81.5250 7.9485 62.0000 97.0000 35.0000 The file aseg.stats gives the list of the available segmented structures in the dataset. Example of the first 30 structures .
  • 24. Determining label numbers in an ASEG file # ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range 1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 2 2 245171 245171.0 Left-Cerebral-White-Matter 121.7886 8.0072 40.0000 186.0000 146.0000 3 3 287069 287069.0 Left-Cerebral-Cortex 91.3494 13.8505 31.0000 220.0000 189.0000 4 4 6876 6876.0 Left-Lateral-Ventricle 48.2126 14.3628 25.0000 106.0000 81.0000 5 5 200 200.0 Left-Inf-Lat-Vent 67.3513 10.8024 35.0000 102.0000 67.0000 6 6 0 0.0 Left-Cerebellum-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 7 7 10514 10514.0 Left-Cerebellum-White-Matter 120.4405 8.5863 43.0000 134.0000 91.0000 8 8 66561 66561.0 Left-Cerebellum-Cortex 98.8117 14.1726 32.0000 211.0000 179.0000 9 9 0 0.0 Left-Thalamus 0.0000 0.0000 0.0000 0.0000 0.0000 10 10 9887 9887.0 Left-Thalamus-Proper 113.5839 10.3047 45.0000 133.0000 88.0000 11 11 3819 3819.0 Left-Caudate 102.9627 12.1416 62.0000 132.0000 70.0000 12 12 6755 6755.0 Left-Putamen 110.0479 7.4787 76.0000 132.0000 56.0000 13 13 2229 2229.0 Left-Pallidum 122.5797 4.2841 105.0000 134.0000 29.0000 14 14 793 793.0 3rd-Ventricle 54.2582 15.3296 28.0000 93.0000 65.0000 15 15 1819 1819.0 4th-Ventricle 51.8305 15.5400 27.0000 108.0000 81.0000 16 16 26616 26616.0 Brain-Stem 113.1949 12.7048 39.0000 136.0000 97.0000 17 17 4489 4489.0 Left-Hippocampus 96.0929 8.6315 56.0000 122.0000 66.0000 18 18 1869 1869.0 Left-Amygdala 94.8671 8.2028 61.0000 118.0000 57.0000 19 19 0 0.0 Left-Insula 0.0000 0.0000 0.0000 0.0000 0.0000 20 20 0 0.0 Left-Operculum 0.0000 0.0000 0.0000 0.0000 0.0000 21 21 0 0.0 Line-1 0.0000 0.0000 0.0000 0.0000 0.0000 22 22 0 0.0 Line-2 0.0000 0.0000 0.0000 0.0000 0.0000 23 23 0 0.0 Line-3 0.0000 0.0000 0.0000 0.0000 0.0000 24 24 1611 1611.0 CSF 59.9684 15.4368 30.0000 107.0000 77.0000 25 25 0 0.0 Left-Lesion 0.0000 0.0000 0.0000 0.0000 0.0000 26 26 733 733.0 Left-Accumbens-area 97.8124 6.7471 67.0000 121.0000 54.0000 27 27 0 0.0 Left-Substancia-Nigra 0.0000 0.0000 0.0000 0.0000 0.0000 28 28 3957 3957.0 Left-VentralDC 117.4001 10.5813 47.0000 135.0000 88.0000 29 29 0 0.0 Left-undetermined 0.0000 0.0000 0.0000 0.0000 0.0000 30 30 56 56.0 Left-vessel 81.5250 7.9485 62.0000 97.0000 35.0000 The label #10 represents the Left-Thalamus Proper. The corresponding segmented volume is available in the current dataset.
  • 25. Determining label numbers in an ASEG file # ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range 1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 2 2 245171 245171.0 Left-Cerebral-White-Matter 121.7886 8.0072 40.0000 186.0000 146.0000 3 3 287069 287069.0 Left-Cerebral-Cortex 91.3494 13.8505 31.0000 220.0000 189.0000 4 4 6876 6876.0 Left-Lateral-Ventricle 48.2126 14.3628 25.0000 106.0000 81.0000 5 5 200 200.0 Left-Inf-Lat-Vent 67.3513 10.8024 35.0000 102.0000 67.0000 6 6 0 0.0 Left-Cerebellum-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 7 7 10514 10514.0 Left-Cerebellum-White-Matter 120.4405 8.5863 43.0000 134.0000 91.0000 8 8 66561 66561.0 Left-Cerebellum-Cortex 98.8117 14.1726 32.0000 211.0000 179.0000 9 9 0 0.0 Left-Thalamus 0.0000 0.0000 0.0000 0.0000 0.0000 10 10 9887 9887.0 Left-Thalamus-Proper 113.5839 10.3047 45.0000 133.0000 88.0000 11 11 3819 3819.0 Left-Caudate 102.9627 12.1416 62.0000 132.0000 70.0000 12 12 6755 6755.0 Left-Putamen 110.0479 7.4787 76.0000 132.0000 56.0000 13 13 2229 2229.0 Left-Pallidum 122.5797 4.2841 105.0000 134.0000 29.0000 14 14 793 793.0 3rd-Ventricle 54.2582 15.3296 28.0000 93.0000 65.0000 15 15 1819 1819.0 4th-Ventricle 51.8305 15.5400 27.0000 108.0000 81.0000 16 16 26616 26616.0 Brain-Stem 113.1949 12.7048 39.0000 136.0000 97.0000 17 17 4489 4489.0 Left-Hippocampus 96.0929 8.6315 56.0000 122.0000 66.0000 18 18 1869 1869.0 Left-Amygdala 94.8671 8.2028 61.0000 118.0000 57.0000 19 19 0 0.0 Left-Insula 0.0000 0.0000 0.0000 0.0000 0.0000 20 20 0 0.0 Left-Operculum 0.0000 0.0000 0.0000 0.0000 0.0000 21 21 0 0.0 Line-1 0.0000 0.0000 0.0000 0.0000 0.0000 22 22 0 0.0 Line-2 0.0000 0.0000 0.0000 0.0000 0.0000 23 23 0 0.0 Line-3 0.0000 0.0000 0.0000 0.0000 0.0000 24 24 1611 1611.0 CSF 59.9684 15.4368 30.0000 107.0000 77.0000 25 25 0 0.0 Left-Lesion 0.0000 0.0000 0.0000 0.0000 0.0000 26 26 733 733.0 Left-Accumbens-area 97.8124 6.7471 67.0000 121.0000 54.0000 27 27 0 0.0 Left-Substancia-Nigra 0.0000 0.0000 0.0000 0.0000 0.0000 28 28 3957 3957.0 Left-VentralDC 117.4001 10.5813 47.0000 135.0000 88.0000 29 29 0 0.0 Left-undetermined 0.0000 0.0000 0.0000 0.0000 0.0000 30 30 56 56.0 Left-vessel 81.5250 7.9485 62.0000 97.0000 35.0000 The label #19 representing the Left-Insula. The corresponding segmented volume is not available in the current dataset.
  • 26.
    • Part 1: Loading FreeSurfer Volumes
    • Part 2: Overlay Brain and Segmentation
    • Part 3: Building 3D Models
    • Part 4: Loading Surfaces
    • Part 5: Group Statistics
    Overview of Training 6
  • 27. Overlay Brain and Segmentation Click on the button Bg (Background) and select the volume aseg in the Axial view.
  • 28. Overlay Brain and Segmentation Move the mouse over the labels in the Axial view.
  • 29. Overlay Brain and Segmentation The names of the labels appear in the window.
  • 30. Overlay Brain and Segmentation Find the labels corresponding to the Left Thalamus Proper , Left Caudate and Left Putamen in the three anatomical views.
  • 31. Overlay Brain and Segmentation Left Thalamus Proper = 10
  • 32. Overlay Brain and Segmentation Left Putamen = 12
  • 33. Overlay Brain and Segmentation Left Caudate = 11
  • 34. Overlay Brain and Segmentation Select View  3D in the MainMenu
  • 35. Overlay Brain and Segmentation Drag right mouse button down in the 3D Viewer to zoom in .
  • 36. Overlay Brain and Segmentation The Viewer displays a zoom view of the brain and aseg slices superimposed. Drag right mouse button up in the Viewer to zoom out .
  • 37.
    • Part 1: Loading FreeSurfer Volumes
    • Part 2: Overlay Brain and Segmentation
    • Part 3: Building 3D Models
    • Part 4: Loading Surfaces
    • Part 5: Group Statistics
    Overview of Training 6
  • 38. Building a single Model Select the module ModelMaker in the MainMenu Select the panel Create Select the Volume aseg and click on the button Label
  • 39. Building a single Model Slicer displays the Color Map corresponding to the structures that FreeSurfer can segment.
  • 40. Building a single Model Move the mouse over the table and select the label of the right hippocampus (label 53).
  • 41. Building a single Model The label of the right hippocampus appears in the Create panel. Click on Create to build the 3D model.
  • 42. Building a single Model The 3D model of the right hippocampus appears in the Viewer. Switch to the view 3D , and drag right mouse button down in the Viewer to zoom in.
  • 43. Building a single Model Slicer displays a zoom view of the right hippocampus .
  • 44. Building 3D Models Select the module ModelMaker in the MainMenu Select the panel Create Multiple
  • 45. Building 3D Models Select the Volume aseg and click on the button Starting Label The Panel Create Multiple provides the interface to build a set of continuous models from the values in the interval [Starting Label, Ending Label]
  • 46. Building 3D Models Click on the label corresponding to the Left Thalamus Proper (Label 10).
  • 47. Building 3D Models Click on the button Ending Label The value and the color of the selected label appear in the panel.
  • 48. Building 3D Models Click on the label corresponding to the Left Pallidum (Label 13).
  • 49. Building 3D Models Click on Create all to build the 3D models of the selected labels. Slicer reconstructs the 3D models from the labels 10,11,12 and 13.
  • 50. Building 3D Models The 3D models of the selected structures appear inside the Viewer.
  • 51. Building 3D Models Left click and move the mouse to orient the models in the Viewer
  • 52. Building 3D Models Click in the module Models in the Main Menu and select the panel Display. The list of models appears in the panel. Deselect the models of the Left Putamen and Left Caudate.
  • 53. Building 3D Models Slicer displays the left Thalamus Proper , left Pallidum and right Hippocampus in the Viewer.
  • 54. Building 3D Models Click on Show None to make all the models disappear from the Scene.
  • 55.
    • Part 1: Loading FreeSurfer Volumes
    • Part 2: Overlay Brain and Segmentation
    • Part 3: Building 3D Models
    • Part 4: Loading Surfaces
    • Part 5: Group Statistics
    Overview of Training 6
  • 56. Loading Surfaces Select the panel Models in the vtkFreeSurferReaders module. Click on Browse and select the surface lh.white in the directory subjects/bert/surf
  • 57. Loading Surfaces Click Apply to load the surface in Slicer. The name of the surface selected appears in the Models panel.
  • 58. Loading Surface The surface of the white matter of the left hemisphere appears in the Viewer.
  • 59. Parcellation Visualization In the panel Models click on aparc to select the parcellation map of the model lh.white Click on Apply to load the overlay.
  • 60. Parcellation Visualization Slicer displays the parcellation results overlaid on the white matter surface in the Viewer. Switch to 3D view in the main menu and zoom in the model.
  • 61. Parcellation Visualization Cortical parcellation of the white matter surface in the left hemisphere.
  • 62.
    • Part 1: Loading FreeSurfer Volumes
    • Part 2: Overlay Brain and Segmentation
    • Part 3: Building 3D Models
    • Part 4: Loading Surfaces
    • Part 5: Group Statistics
    Overview of Training 6
  • 63. Group Statistics
    • After completion of surface reconstruction for all subjects in a study, FreeSurfer can perform group averaging and statistical inference of the cortical surface measurements such as thickness.
    • The observed data is a set of cortical surface measurements at each vertex for each subject in the group.
    • The process fits a General Linear Model at each vertex to summarize the data from all the subjects.
    • The group analysis results in a statistical parametric map that can be loaded into Slicer for visualisation as an overlay on the average surface.
  • 64. Group Statistics Statistical Parametric Map Average Subject creation General Linear Modeling
  • 65. Group Statistics - example Statistical Parametric Map sigt_Age_dossthickness-100lh.w Average Subject creation lh.pial_avg For my cohort of x sujects, does cortical thickness vary with age? General Linear Modeling y_doss_thickness-100lh.fsgd
  • 66. Group Statistics Select the Tab Models in the vtkFreeSurferReaders module. Click on Browse and select the surface lh.pial_avg in the directory subjects/average/surf
  • 67. Group Statistics Select the Tab Display in the vtkFreeSurferReaders module. Click on Browse and select the overlay subjects/stats/sigt_Age_doss-thickness-100lh.w Click on Load Scalar File.
  • 68. Group Statistics Slicer displays the statistical map as an overlay superimposed on the average surface. Move the model with the mouse to update the Viewer display.
  • 69. Group Statistics Select the Panel Plot in the vtkFreeSurferReaders module. Click on Browse and select the file y_doss-thickness-100lh.fsgd in the directory subjects/stats.
  • 70. Group Statistics Select the Active Model lh.pial_avg in the list of models. Click on Apply to load the Group Statistics results.
  • 71. Group Statistics Slicer displays statistical distribution of the cortical thickness of the left hemisphere parameterized by the age of the population.
  • 72. Group Statistics Select the Mode subject in the Group Statistics Window.
  • 73. Group Statistics Slicer displays the subjects included in the Statistical Analysis. Move the mouse over the subjects table and select the subject #108.
  • 74. Group Statistics A red circle shows the position of the subject #108 in the analysis.
  • 75. Group Statistics The Configure Classes menu displays the visualization options of the population.
  • 76. Group Statistics Select the pattern diamond and the color black for the male subjects. Select the pattern circle and the color purple for the female subjects.
  • 77. Group Statistics Slicer updates the interface with the new configuration parameters.
  • 78. Group Statistics To generate a plot for a particular vertex, select a point by clicking on the parametric map at that vertex on the 3D model in the Viewer
  • 79. Group Statistics Slicer updates the thickness results with the values corresponding to the selected vertex.
  • 80. Conclusion
    • 3D visualization of brain segmented
    • surfaces, parcellation maps and
    • statistical results from FreeSurfer
    • Intuitive graphical user interface to interact with the data
    • Open-Source environment