Did you explicitly check the quality of talairach_with_skull.lta? Also, what version of FS are you using?
We previously had encountered that error in 5 brains processed under FS 4.0.2, and all five of those had errant talairach_with_skull.lta transforms. Generation of talairach_with_skull.lta was made more robust in FS 4.0.3, and indeed, using v4.0.5, we were able to process all 5 of our problem brains successfully.
cheers, Mike H.
On Fri, 2008-08-08 at 21:57 -0400, Bruce Fischl wrote:
hmmm, that's interesting. If you send us the data we'll take a look. In any case, you can run, if you create an orig_stripped.mgz you can run:
mri_mask T1.mgz orig_stripped.mgz brain.mgz
then you should be able to run from after the skull stripping forward (check the recon-all help. You'll need to run a couple of steps before autorecon2-wm and autorecon3).
cheers Bruce
On Fri, 8 Aug 2008, Vina Goghari wrote:
Hi all, I get this error for one subject: mri_watershed Error: GLOBAL region of the brain empty !
I check the talairach transformation and it looked good. I also tried just scripting the orig.mgz and I get a wonderful strip. How can I move forward with the recon-all process?
Thanks, Vina
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