1. sorry, not easily that I can think of 2. I guess you could try mri_robust_register on the brain.mgz, output the halfway volumes, then count ones that are 0 in the post and not 0 in the pre (and probably are brain in the aseg of the pre)

cheers Bruce

On Mon, 30 Sep 2013, Germeyan, Sierra (NIH/NINDS) [F] wrote:

Hi all, A couple questions regarding post-surgery scans.

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.

Thanks very much for any advice you can give!

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