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FreeSurfer Tutorial: Visualization and Inspection of Group Analysis Results (30 minutes of exercises)
The statistical parametric map created from the group analysis can be loaded into [wiki:FsTutorial/TksurferInterface tksurfer] for visualizing as an overlay on the average surface, and inspecting either vertex-by-vertex, or within a defined region of interest (ROI). In particular, tksurfer is able to configure the colormap, to threshold the statistical parametric map and to plot correlation between classes or variables for both a single vertex and ROI. In these exercises, tksurfer will be used to visualize and inspect results in a number of ways.
1.0 Visualizing and plotting
Using the precomputed average surface, the following exercise shows how to load the statistical parametric map as an overlay in tksurfer, how to configure the colormap and threshold the parametric map, and how to plot correlation dynamically while interactively clicking surface vertices.
[wiki:FsTutorial/VisualizingAndPlotting Exercise A. Visualizing and plotting]
2.0 Defining a region of interest (ROI)
Tksurfer has the ability to compute and display statistics averaged over a defined region of interest (ROI), which is another popular way to test statistical hypotheses. The following exercise shows how to define, fill, select and plot statistics for an ROI.
[wiki:FsTutorial/ComputingRoiStatistics Exercise B. Computing statistics inside an ROI]
3.0 Mapping an ROI from one subject to another
After defining an ROI(<labelname>) on a subject(<source>), that ROI can then be mapped to another subject(<target>) with the command:
cd $SUBJECTS_DIR mri_label2label --srcsubject <source> --srclabel <source>/label/<labelname> --trgsubject <target> --trglabel <target>/label/<labelname> --regmethod surface --hemi <hemi>