Nick, List:
Still no luck with this data. See attached as an example. To get to this point I had run: recon-all -all This ran to the error: mri_watershed Error: GLOBAL region of the brain empty ! Then I followed your recommendation below recon-all -s <subjid> -skullstrip -no-wsgcaatlas, which had no errors and then recon-all -s <subjid> -autorecon2 -autorecon3 This produced the result attached. I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine. Then I ran recon-all -s <subjid> -autorecon1 This fails with the mri_watershed error. Then I ran recon-all -s <subjid> -skullstrip -no-wsgcaatlas. This runs without error but when I look at the brainmask.mgz it looks just like the attached image. Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly less than usual, but it doesn't seem particularly noisy. Darren
<<attachment: FS_error.jpg>>
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