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.
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 .
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 .
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.
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.
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.
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.
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.
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.
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.