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.