Hi Emma,
Thanks for your quick reply. I was no longer at the office when I saw your email. Please find attached the recon.all log file.
Best Mateus
2017-08-11 11:18 GMT-03:00 Boyd, Emma EBOYD2@mgh.harvard.edu:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.