Re: [Freesurfer] Skullstriping problems

Hi Mateus,

Please attach the recon-all.log file for your subject and I will take a look.

Best,

Emma

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of MATEUS ROZALEM ARANHA mateus.aranha@hc.fm.usp.br Sent: Friday, August 11, 2017 9:56 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Skullstriping problems

Hi,

I had problems with skullstriping. I ran recon-all and part of the skull is being considered as cortex in the segmentation. I tried to fix this using:

recon-all -skullstrip -wsthresh 50 -clean-bm -subjid <subject name>

and than

recon-all -autorecon-pial -subjid <subject name>

But nothing changed.

Do I need to run recon-all all over?

Thanks, Mateus