Bruce I used the following version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522
Is that the same as the one you are using or are you referring to an internal development version? I will try Nick's suggestion as well. Darren On Wed, Sep 5, 2012 at 4:05 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > I'm running it now with the current dev version and it's passed the skull > stripping stage and it seems to have worked fine... > > On Wed, > 5 Sep 2012, Nick Schmansky wrote: > > > 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. > > -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073
_______________________________________________ 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.
