Hello, I want to run group statistics on the cortical thickness for a study with 3 groups, each with about 30 subjects. To do this, I need to create an average cort thickness map for each group. We are interested in basic statistics, so nothing too advanced. I am wondering what would be the most efficient way to go about this. From what I can tell, FsFast is the program used to do group analysis. Would it be fastest to learn FsFast to process all my group data, or I am thinking since we only need basic stats, it may be faster and easier to register each subject's ?h.thickness file to an average sphere and then load the registered thickness file into matlab to do the stats? I think I would need to modify the commands from auto-recon stage 3 to use the thickness file, for example:
mris_sphere ?h.thickness ?h.thickness.sphere mris_register -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.thickness.sphere.reg mris_jacobian ?h.white ?h.thickness.sphere.reg ?h.jacobian_white
mrisp_paint -a 5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6 ?h.thickness.sphere.reg ?h.thickness.avg_curvWe have a cluster, so the processing could be done fairly quickly. Thank you in advance for your advice!
Jeff Sadino
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