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 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
