Dear Dana,
I'm not exactly sure what you are asking, but from a VBM analysis you would have PVE images (from the segmentation stage) that you could calculate volumes from. These are already separated into tissue types. If you want to break this down into smaller regions (e.g. using the Harvard Oxford atlas) then you would need to calculate the intersection of your tissue segmentation and the atlas regions using fslmaths and then run fslstats to get the volume.
All the best,
Mark
On 29 May 2014, at 20:02, Dana Wagshal <[log in to unmask]> wrote:
> Hi FSL group,
>
> I'm interested in getting average cortical volumes from subjects in a VBM analysis. In the Harvard Oxford Cortical atlas, there are values associated with each structure. Is there a way that I can use fslstats and specify values or do I have to extract each region first (by using fslmaths) and then use fslstats?
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