Darren, I forgot to mention that you'll need to add
-clean-bm after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be retained and the new one will be saved as brainmask.auto.mgz. Nick On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote: > 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 > > > > _______________________________________________ > 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
