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Surgical Planning Laboratory -1- Brigham and Womens Hospital Slicer Tutorial 6 Module: vtkFreeSurferReaders Sonia Pujol, Ph.D. Randy.

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Presentation on theme: "Surgical Planning Laboratory -1- Brigham and Womens Hospital Slicer Tutorial 6 Module: vtkFreeSurferReaders Sonia Pujol, Ph.D. Randy."— Presentation transcript:

1 Surgical Planning Laboratory -1- Brigham and Womens Hospital Slicer Tutorial 6 Module: vtkFreeSurferReaders Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D.

2 Surgical Planning Laboratory -2- Brigham and Womens Hospital Acknowledgments National Alliance for Medical Image Computing NIH U54EB Neuroimage Analysis Center NIH P41RR Center for Functional Neuroimaging Technologies NIH P41RR14075 Morphometry Biomedical Informatics Research Network NIH U24 RRO21382 Surgical Planning Laboratory Thanks to Nicole Aucoin

3 Surgical Planning Laboratory -3- Brigham and Womens Hospital 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 Surgical Planning Laboratory -4- Brigham and Womens Hospital Materials Needed Slicer 2.5MGH Free Surfer Sample Data: FreesurferSubjects.zip

5 Surgical Planning Laboratory -5- Brigham and Womens Hospital 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 Surgical Planning Laboratory -6- Brigham and Womens Hospital 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/ft p/pub/docs/fsTutorial/

7 Surgical Planning Laboratory -7- Brigham and Womens Hospital 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 Surgical Planning Laboratory -8- Brigham and Womens Hospital vtkFreeSurferReaders Module

9 Surgical Planning Laboratory -9- Brigham and Womens Hospital Loading FreeSurfer Data Slicer can load Brain Volumes ……………………. ASEG Volumes ……………………… Surfaces………………………………… Overlays ………………………………….

10 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital vtkFreeSurferReaders Module Select the Menu Modules in the Main Panel Select the category IO and the module vtkFreeSurferReaders

12 Surgical Planning Laboratory Brigham and Womens Hospital vtkFreeSurferReaders Module The vtkFreeSurferReaders module appears in the Main Panel of Slicer. The Volumes tab comes up by default.

13 Surgical Planning Laboratory Brigham and Womens Hospital Loading a Brain file Brain.mgz Skull Stripping and Noise Filtering Watershed algorithm Intensity corrected T1 volume FreeSurfer Pipeline

14 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital Loading a Brain file Select the file brain.mgz Select the data type GrayScale Click Apply

16 Surgical Planning Laboratory Brigham and Womens Hospital Loading a Brain file The volume Brain.mgz appears in the Viewer.

17 Surgical Planning Laboratory Brigham and Womens Hospital Loading a Brain file Click on the V buttons in the Axial, Sagittal and Coronal views.

18 Surgical Planning Laboratory Brigham and Womens Hospital Loading a Brain file The three anatomical slices appear in the 3D Viewer.

19 Surgical Planning Laboratory Brigham and Womens Hospital Loading an ASEG file Aseg.mgz Segmentation Subcortical processing Intensity corrected T1 volume FreeSurfer Pipeline

20 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital Loading an ASEG file Select the file aseg.mgz Select the data type Label Map Click on Apply

22 Surgical Planning Laboratory Brigham and Womens Hospital Loading an ASEG file The labels are superimposed on the gray level brain images. The volume aseg.mgz appears in the Viewer.

23 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital # 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. Determining label numbers in an ASEG file

25 Surgical Planning Laboratory Brigham and Womens Hospital # 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. Determining label numbers in an ASEG file

26 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital Click on the button Bg (Background) and select the volume aseg in the Axial view. Overlay Brain and Segmentation

28 Surgical Planning Laboratory Brigham and Womens Hospital Overlay Brain and Segmentation Move the mouse over the labels in the Axial view.

29 Surgical Planning Laboratory Brigham and Womens Hospital Overlay Brain and Segmentation The names of the labels appear in the window.

30 Surgical Planning Laboratory Brigham and Womens Hospital Overlay Brain and Segmentation Find the labels corresponding to the Left Thalamus Proper, Left Caudate and Left Putamen in the three anatomical views.

31 Surgical Planning Laboratory Brigham and Womens Hospital Overlay Brain and Segmentation Left Thalamus Proper = 10

32 Surgical Planning Laboratory Brigham and Womens Hospital Overlay Brain and Segmentation Left Putamen = 12

33 Surgical Planning Laboratory Brigham and Womens Hospital Overlay Brain and Segmentation Left Caudate = 11

34 Surgical Planning Laboratory Brigham and Womens Hospital Overlay Brain and Segmentation Select View 3D in the MainMenu

35 Surgical Planning Laboratory Brigham and Womens Hospital Overlay Brain and Segmentation Drag right mouse button down in the 3D Viewer to zoom in.

36 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital Building a single Model Slicer displays the Color Map corresponding to the structures that FreeSurfer can segment.

40 Surgical Planning Laboratory Brigham and Womens Hospital Building a single Model Move the mouse over the table and select the label of the right hippocampus (label 53).

41 Surgical Planning Laboratory Brigham and Womens Hospital Building a single Model The label of the right hippocampus appears in the Create panel. Click on Create to build the 3D model.

42 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital Building a single Model Slicer displays a zoom view of the right hippocampus.

44 Surgical Planning Laboratory Brigham and Womens Hospital Building 3D Models Select the module ModelMaker in the MainMenu Select the panel Create Multiple

45 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital Building 3D Models Click on the label corresponding to the Left Thalamus Proper (Label 10).

47 Surgical Planning Laboratory Brigham and Womens Hospital Building 3D Models Click on the button Ending Label The value and the color of the selected label appear in the panel.

48 Surgical Planning Laboratory Brigham and Womens Hospital Building 3D Models Click on the label corresponding to the Left Pallidum (Label 13).

49 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital Building 3D Models The 3D models of the selected structures appear inside the Viewer.

51 Surgical Planning Laboratory Brigham and Womens Hospital Building 3D Models Left click and move the mouse to orient the models in the Viewer

52 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital Building 3D Models Slicer displays the left Thalamus Proper, left Pallidum and right Hippocampus in the Viewer.

54 Surgical Planning Laboratory Brigham and Womens Hospital Building 3D Models Click on Show None to make all the models disappear from the Scene.

55 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital Loading Surfaces Click Apply to load the surface in Slicer. The name of the surface selected appears in the Models panel.

58 Surgical Planning Laboratory Brigham and Womens Hospital Loading Surface The surface of the white matter of the left hemisphere appears in the Viewer.

59 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital Parcellation Visualization Cortical parcellation of the white matter surface in the left hemisphere.

62 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital Group Statistics Statistical Parametric Map Average Subject creation General Linear Modeling

65 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital Group Statistics Select the Active Model lh.pial_avg in the list of models. Click on Apply to load the Group Statistics results.

71 Surgical Planning Laboratory Brigham and Womens Hospital Group Statistics Slicer displays statistical distribution of the cortical thickness of the left hemisphere parameterized by the age of the population.

72 Surgical Planning Laboratory Brigham and Womens Hospital Group Statistics Select the Mode subject in the Group Statistics Window.

73 Surgical Planning Laboratory Brigham and Womens Hospital Group Statistics Slicer displays the subjects included in the Statistical Analysis. Move the mouse over the subjects table and select the subject #108.

74 Surgical Planning Laboratory Brigham and Womens Hospital Group Statistics A red circle shows the position of the subject #108 in the analysis.

75 Surgical Planning Laboratory Brigham and Womens Hospital Group Statistics The Configure Classes menu displays the visualization options of the population.

76 Surgical Planning Laboratory Brigham and Womens Hospital 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 Surgical Planning Laboratory Brigham and Womens Hospital Group Statistics Slicer updates the interface with the new configuration parameters.

78 Surgical Planning Laboratory Brigham and Womens Hospital 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 Group Statistics

79 Surgical Planning Laboratory Brigham and Womens Hospital Slicer updates the thickness results with the values corresponding to the selected vertex. Group Statistics

80 Surgical Planning Laboratory Brigham and Womens Hospital 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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