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Slicer Tutorial 6 Module: vtkFreeSurferReaders

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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
Free Surfer Sample Data: FreesurferSubjects.zip

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

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 Slicer:Workshops:User_Training_101

8 vtkFreeSurferReaders Module

9 Loading FreeSurfer Data
Slicer can load Brain Volumes ……………………. ASEG Volumes ……………………… Surfaces………………………………… Overlays ………………………………….

10 Overview of Training 6 Part 1: Loading FreeSurfer Volumes
Part 2: Overlay Brain and Segmentation Part 3: Building 3D Models Part 4: Loading Surfaces Part 5: Group Statistics

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 Skull Stripping and Noise Filtering
Loading a Brain file Intensity corrected T1 volume FreeSurfer Pipeline Skull Stripping and Noise Filtering Watershed algorithm Brain.mgz

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 Subcortical processing
Loading an ASEG file Intensity corrected T1 volume FreeSurfer Pipeline Subcortical processing Segmentation Aseg.mgz

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 volume aseg.mgz appears in the Viewer.
The labels are superimposed on the gray level brain images.

23 Determining label numbers in an ASEG file
# ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range Left-Cerebral-Exterior Left-Cerebral-White-Matter Left-Cerebral-Cortex Left-Lateral-Ventricle Left-Inf-Lat-Vent Left-Cerebellum-Exterior Left-Cerebellum-White-Matter Left-Cerebellum-Cortex Left-Thalamus Left-Thalamus-Proper Left-Caudate Left-Putamen Left-Pallidum rd-Ventricle th-Ventricle Brain-Stem Left-Hippocampus Left-Amygdala Left-Insula Left-Operculum Line Line Line CSF Left-Lesion Left-Accumbens-area Left-Substancia-Nigra Left-VentralDC Left-undetermined Left-vessel 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 Left-Cerebral-Exterior Left-Cerebral-White-Matter Left-Cerebral-Cortex Left-Lateral-Ventricle Left-Inf-Lat-Vent Left-Cerebellum-Exterior Left-Cerebellum-White-Matter Left-Cerebellum-Cortex Left-Thalamus Left-Thalamus-Proper Left-Caudate Left-Putamen Left-Pallidum rd-Ventricle th-Ventricle Brain-Stem Left-Hippocampus Left-Amygdala Left-Insula Left-Operculum Line Line Line CSF Left-Lesion Left-Accumbens-area Left-Substancia-Nigra Left-VentralDC Left-undetermined Left-vessel 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 Left-Cerebral-Exterior Left-Cerebral-White-Matter Left-Cerebral-Cortex Left-Lateral-Ventricle Left-Inf-Lat-Vent Left-Cerebellum-Exterior Left-Cerebellum-White-Matter Left-Cerebellum-Cortex Left-Thalamus Left-Thalamus-Proper Left-Caudate Left-Putamen Left-Pallidum rd-Ventricle th-Ventricle Brain-Stem Left-Hippocampus Left-Amygdala Left-Insula Left-Operculum Line Line Line CSF Left-Lesion Left-Accumbens-area Left-Substancia-Nigra Left-VentralDC Left-undetermined Left-vessel The label #19 representing the Left-Insula. The corresponding segmented volume is not available in the current dataset.

26 Overview of Training 6 Part 1: Loading FreeSurfer Volumes
Part 2: Overlay Brain and Segmentation Part 3: Building 3D Models Part 4: Loading Surfaces Part 5: Group Statistics

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 Overview of Training 6 Part 1: Loading FreeSurfer Volumes
Part 2: Overlay Brain and Segmentation Part 3: Building 3D Models Part 4: Loading Surfaces Part 5: Group Statistics

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 The Panel Create Multiple provides the interface to build a set of continuous models from the values in the interval [Starting Label, Ending Label] Select the Volume aseg and click on the button Starting Label

46 Building 3D Models Click on the label corresponding to the Left Thalamus Proper (Label 10).

47 Building 3D Models The value and the color of the selected label appear in the panel. Click on the button Ending Label

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 Overview of Training 6 Part 1: Loading FreeSurfer Volumes
Part 2: Overlay Brain and Segmentation Part 3: Building 3D Models Part 4: Loading Surfaces Part 5: Group Statistics

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 The name of the surface selected appears in the Models panel. Click Apply to load the surface in Slicer.

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 Overview of Training 6 Part 1: Loading FreeSurfer Volumes
Part 2: Overlay Brain and Segmentation Part 3: Building 3D Models Part 4: Loading Surfaces Part 5: Group Statistics

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 Average Subject creation General Linear Modeling
Statistical Parametric Map

65 Group Statistics - example
For my cohort of x sujects, does cortical thickness vary with age? Average Subject creation lh.pial_avg General Linear Modeling y_doss_thickness-100lh.fsgd Statistical Parametric Map sigt_Age_dossthickness-100lh.w

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 Click on Load Scalar File.
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 Move the model with the mouse to update the Viewer display. Slicer displays the statistical map as an overlay superimposed on the average surface.

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


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