Hi all, A few questions.
1. Is there a way to run scans of post-surgical brains that takes resections into account and gives more accurate results than "recon-all -all"?
2. Is it possible to obtain resection volumes with FreeSurfer? I tried to do this indirectly by finding the difference between total intracranial volume that FreeSurfer gave for scans pre- and post- surgery. However, I rarely obtained reasonable numbers with this method.
3. After running -hippo-subfields, I converted the voxel output of -hippo-subfields to mm^3 based on the instructions given here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-June/031188.html. Then I summed the volumes for all of the subfields (assuming that this would give me the total hippocampal volume), and compared the sum to the hippocampal volume that FreeSurfer gave after running recon-all -all. They weren't the same! Why would these differ?
Thanks very much for any advice you can give!