well, something is really wrong. Did you happen to change the voxel type of brain.finalsurfs.mgz? Can you run mri_info on it and send us the results? If not, then upload the tarred and gzipped subject dir and I'll take a look. I don't think it will be hard to fix
On Thu, 28 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: > A) Log attached. > B) That was my next step but I wanted to check first to see if there was > something obvious I was missing. > > I actually ran "recon-all -autorecon-pial -subjid subject_name" twice. I > thought the first time, that it was the result of some process failing/not > completing along the way without entirely crashing freesurfer. I ran it > again in the hopes that it was some crazy fluke but the result is exactly > the same. > > -Ronny > >> eek, that's pretty bad. No idea why that would happen. Can you send us >> the recon-all.log? If you rerun with the original brain.finalsurfs.mgz >> does it restore good surfaces? >> On Thu, 28 Mar 2013, >> preci...@nmr.mgh.harvard.edu wrote: >> >>> Hello Freesurfers, >>> >>> I ran recon-all on a subject's structural data like so: >>> recon-all -autorecon-all -subjid subect_name >>> >>> The resulting pial surface looked pretty good except that there were a >>> few >>> voxels of dura and cerebellum that were included in the pial surface. >>> not >>> a big deal. I deleted some voxels of dura from brainmask.mgz and deleted >>> voxels of from the cerebellum by creating and saving a copy of >>> brain.finalsurfs.mgz. >>> /subject_name/mri/ >>> cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz >>> >>> >>> Then I ran recon all to regenerate the pial surface: >>> recon-all -autorecon-pial -subjid subject_name >>> >>> >>> The results from the pial surface redrawing are now totally wrong and >>> completely underestimated. The weird thing is that it looked perfectly >>> fine before and removing some problematic voxels caused this result. >>> >>> Any insights as to how/why this occurred and how to fix it? Images of >>> the >>> AFTER picture attached. >>> >>> Thanks! >>> -Ronny >> >> >> > _______________________________________________ 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.
