mri_info for both attached. Interestingly enough, brain.finalsurfs.manedit.mgz is significantly larger in size. If it was a copy of the other, shouldn't it be the same size? Also, brain.finalsurfs.manedit.mgz shows a time/date stamp from the last time I edited it and brain.finalsurfs.mgz has a time/date stamp from the last time I executed recon-all -autorecon-pial...
-rw-rw-r-- 1 preciado birn 1416877 Mar 26 22:23 brain.finalsurfs.manedit.mgz -rw-rw-r-- 1 preciado birn 16605 Mar 27 09:39 brain.finalsurfs.mgz A more basic question, I am assuming that -autorecon-pial defaults to using brain.finalsurfs.manedit.mgz and then proceeds to use brain.finalsurfs.mgz if there is no manual edit volume, is that correct? -Ronny > 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 >>> >>> >>> >> > > >
brain.finalsurfs.mgz.mri_info
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brain.finalsurfs.manedit.mgz.mri_info
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