Hi Marja

what ROI do you mean? We generate lots of them, and tabulate the thickness within each one. Look for example in <subject id>/stats/aparc.stats

cheers
Bruce

On Fri, 27 May 2016, Marja Caverlé wrote:

Hi all,

So I ran a recon-all -all on one of my subjects, and it completed without
errors (according to the log). Now I would like to get cortical thickness
numbers from this subject, but when I open the tutorial regarding this, it
says it assumes that you already have a roi mask and a T1 in the same
coordinate space as the roi mask. 

Did the recon -all -all by any chance create these files? And if not, how
can I?

So basically the question is; what do I have to do after recon -all -all in
order to get cortical thickness numbers in roi's of my subjects?

Thanks in advance.

Marja

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