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We are trying to calculate the volume of grey matter of the significant clusters within each region identified by our initial analyses. Is there a procedure already written in matlab to accomplish this calculation?
Right now we've calculated the mean thickness across all subjects for each vertex, and then averaged those thickness across each region (or across each significant portion of a region). Then took the areas from the regions (calculated through Freesurfer’s mri_surfcluster program, which for the whole regions will obviously only get a single cluster, and total area of that cluster) and multiplied them by the mean thicknesses to get total area. It should be possible to do the same thing to get the significant volumes.
Does the above procedure seem like the most straightforward? Or does freesurfer have a program to do this more efficiently?