Glad to hear it worked out Bruce > On Feb 24, 2017, at 5:01 PM, Rockers, Elijah D. > <edrock...@houstonmethodist.org> wrote: > > OK, sorry for spamming the list. I fixed the the faulty skullstrip by using > > recon-all -skullstrip -clean-bm -no-wsgcaatlas -subjid <subject name> > > Currently redoing the surface reconstructions, but it should be OK now. > Thanks for the nice documentation. > Eli > > >> On Fri, 2017-02-24 at 15:30 -0600, Elijah Rockers wrote: >> As far as I can tell, everything looks OK up until brainmask.mgz. The >> skullstrip step seems to have cropped out the brain and left the neck... >> >> On Fri, 2017-02-24 at 12:58 -0600, Elijah Rockers wrote: >> > Hello all, >> > >> > I recon-all'd ~40 different subjects. I have been going through all the >> > images to make sure they were processed correctly. Most required no no >> > editing and recon-all did a very good job. >> > >> > But for one scan in particular, it looks like Freesurfer thinks the top >> > of the spinal cord is the brain. Several vertebrae are very nicely >> > segmented... :P >> > >> > Just wondering if you have any suggestions for reprocessing this >> > subject? The error is reproducible with default recon-all settings. >> > >> > Subject has some pathology in the white matter which might be causing >> > the problem? >> > >> > Screenshot of T1.mgz + lh.pial at the following link: >> > http://imgur.com/a/uwyaq >> > >> > Thanks, >> > Eli >> > > Houston Methodist. Leading Medicine. > > U.S. News & World Report has recognized Houston Methodist as one of the > nation’s top 20 hospitals, placing it for the second time on the magazine’s > prestigious Honor Roll. It is also designated as a Magnet hospital for > excellence in nursing. Visit us at houstonmethodist.org. Follow us at > twitter.com/MethodistHosp and facebook.com/HoustonMethodist. > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist > and/or its relevant affiliates and may contain restricted and privileged > material for the sole use of the intended recipient(s). Any review, use, > distribution or disclosure by others is strictly prohibited. If you are not > the intended recipient (or authorized to receive for the recipient), please > contact the sender and delete all copies of the message. Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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