Hi Mateus,

Could you clarify your original post for me:

By "nothing changed," do you mean that the brainmask.mgz is the same as before even though you used the new watershed threshold? Or that this changed but nothing downstream (like the aseg.mgz) changed?

Thanks,
Emma

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

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