try running:

recon-all -s <subjid> -skullstrip -no-wsgcaatlas

if that works, continue the rest with:

recon-all -s <subjid> -autorecon2 -autorecon3

n.

On Wed, 2012-08-29 at 17:01 +0000, Darren R Gitelman wrote:

Hi

I am having a problem getting recon-all to finish on 1 subject.

The first time I ran recon-all -all I got an mri_watershed error. (see attached log).

Based on one of the posts to the list I then ran: recon-all -skullstrip -no-wsgcaatlas -s <subj id>

This completed successfully. Then I ran: recon-all -autorecon2 -autorecon3 -s <subj id>

This did not complete successfully with the error that it can't find the brain.mgz file. I did look at the orig.mgz and T1.mgz files and they look fine. The talairach transform I think is also fine.

What do I do about this?

Thanks, Darren

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