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
Building a single Model Slicer displays the Color Map corresponding to the structures that FreeSurfer can segment.
Building a single Model Move the mouse over the table and select the label of the right hippocampus (label 53).
Building a single Model The label of the right hippocampus appears in the Create panel. Click on Create to build the 3D model.
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.
Building a single Model Slicer displays a zoom view of the right hippocampus .
Building 3D Models Select the module ModelMaker in the MainMenu Select the panel Create Multiple
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]
Building 3D Models Click on the label corresponding to the Left Thalamus Proper (Label 10).
Building 3D Models Click on the button Ending Label The value and the color of the selected label appear in the panel.
Building 3D Models Click on the label corresponding to the Left Pallidum (Label 13).
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.
Building 3D Models The 3D models of the selected structures appear inside the Viewer.
Building 3D Models Left click and move the mouse to orient the models in the Viewer
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.
Building 3D Models Slicer displays the left Thalamus Proper , left Pallidum and right Hippocampus in the Viewer.
Building 3D Models Click on Show None to make all the models disappear from the Scene.
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.
Group Statistics Statistical Parametric Map Average Subject creation General Linear Modeling
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
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
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.
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.
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.
Group Statistics Select the Active Model lh.pial_avg in the list of models. Click on Apply to load the Group Statistics results.
Group Statistics Slicer displays statistical distribution of the cortical thickness of the left hemisphere parameterized by the age of the population.
Group Statistics Select the Mode subject in the Group Statistics Window.
Group Statistics Slicer displays the subjects included in the Statistical Analysis. Move the mouse over the subjects table and select the subject #108.
Group Statistics A red circle shows the position of the subject #108 in the analysis.
Group Statistics The Configure Classes menu displays the visualization options of the population.
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.
Group Statistics Slicer updates the interface with the new configuration parameters.
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
Group Statistics Slicer updates the thickness results with the values corresponding to the selected vertex.