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