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.
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