Thanks for your response, Bruce. Since we would rather not re-run all 200+ subjects through version 5.3, would it be possible, for the sake of keeping things consistent, to add any flags to recon-all using version 5.1, to be able to include the remaining 35 subjects into our analysis?

On Fri, Apr 25, 2014 at 12:49 PM, Maia Pujara <maiapujara@gmail.com> wrote:

Hi all,

After running 200+ subjects through recon-all using version 5.1, all but 30 came back with complete surfaces. The 30 that failed seem to have the same problem with normalization.

After re-running these 30 subjects with v5.3, we were able to get a good quality brainmask.mgz output, which was not the case when we ran these subjects through v5.1. See attached for comparisons of v5.1 and v5.3 outputs.

Would we need to be adding additional flags to get 5.1 to produce usable results for these subjects? Or might there be some other workaround for this?

Thanks in advance!

Maia