[Freesurfer] Corrupted T1 file (?) but segmentation look fine
External Email - Use Caution Hello all, I have been running into a curious problem with a couple brains (8 out of 150 seem to have this problem) running through the recon-all pipeline. Upon loading brainmask.mgz, T1.mgz, and corresponding white matter and pial surfaces in Freeview, my colleague and I received an error that T1.mgz failed to load. Segmentation and parcellation seemed to run smoothly and accurately, however, the size of the T1.mgz file was 0. Assuming the file had been corrupted somehow (our server through which we run recon-all and store our data has tons of available memory), we reran the brains affected. Upon loading up the same re-run surfaces, T1.mgz loaded into the GUI as white, washed out voxels, displaying no brain at all. The size of this file is large, as well as all other surface and volume files. Curiously, the brainmask file seems normalized/stripped fine and surfaces displayed over the T1 look accurately segmented. I attached a screenshot displaying the T1.mgz file and surfaces that I'm referring to. I have a few concerns and questions. Because T1.mgz doesn't seem to be necessary for downstream manual editing and processing, can we proceed as normal, only displaying and using the brainmask file to make edits? Will our surface and volume metrics export properly without a usable T1 file? Lastly, any clues to how this might have occurred are welcomed. It seems like the mri_normalize step is the culprit, although the nu.mgz files corresponding to these brains seem normally sized. Best, Anneliis Sartin-Tarm Associate Research Specialist Neurocircuitry of Trauma and PTSD Study UW-Madison Dept. Psychiatry 608-262-6375 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Could not read curvature from curv
External Email - Use Caution Hello all, I noticed that after I ran recon-all -autorecon2-wm -autorecon3 to incorporate manual edits from a white matter surface inspection, many abnormal hard failures occurred. First, upon checking to see if my subject successfully ran through recon-all via tail scripts/recon-all.log, I received neither "finished without errors" or "finished with errors," but instead, this: SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 singular matrix in quadratic form I then checked the subject's status via tail scripts/recon-all-status.log and received this: #@# Smooth2 lh Tue May 22 16:41:17 CDT 2018 #@# Smooth2 rh Tue May 22 16:41:24 CDT 2018 #@# Inflation2 lh Tue May 22 16:41:30 CDT 2018 #@# Inflation2 rh Tue May 22 16:42:10 CDT 2018 #@# Curv .H and .K lh Tue May 22 16:42:56 CDT 2018 #@# Curv .H and .K rh Tue May 22 16:44:22 CDT 2018 #@# Curvature Stats lh Tue May 22 16:45:40 CDT 2018 #@# Curvature Stats rh Tue May 22 16:45:43 CDT 2018 #@# Sphere lh Tue May 22 16:45:47 CDT 2018 #@# Sphere rh Tue May 22 17:20:21 CDT 2018 I then attempted to view the subject in Freeview, which only loaded the surface edges and not the inflated 3-D surface, and this message appeared in my terminal -- which is the same message in the subject's error.log folder: MRISreadNewCurvature: incompatible vertex number in file /Volumes/Vol2/cisler/freesurfer/ testing/annewuwu/surf/lh.curv No such file or directory could not read curvature from curv No such file or directory mpatible vertex number in file /Volumes/Vol2/cisler/freesurfer/testing/annewuwu/surf/lh.curv MRISreadNewCurvature: incompatible vertex number in file /Volumes/Vol2/cisler/freesurfer/ testing/annewuwu/surf/lh.curv No such file or directory could not read curvature from curv No such file or directory mpatible vertex number in file /Volumes/Vol2/cisler/freesurfer/testing/annewuwu/surf/lh.curv MRISreadNewCurvature: incompatible vertex number in file /Volumes/Vol2/cisler/freesurfer/ testing/annewuwu/surf/rh.curv No such file or directory could not read curvature from curv No such file or directory mpatible vertex number in file /Volumes/Vol2/cisler/freesurfer/testing/annewuwu/surf/rh.curv MRISreadNewCurvature: incompatible vertex number in file /Volumes/Vol2/cisler/freesurfer/ testing/annewuwu/surf/rh.curv No such file or directory could not read curvature from curv No such file or directory mpatible vertex number in file /Volumes/Vol2/cisler/freesurfer/testing/annewuwu/surf/rh.curv It looks like I most likely have to rerun the subject through recon-all, but does anybody have any tips to prevent this from happening again? Thank you for your time! Anneliis Sartin-Tarm Associate Research Specialist Neurocircuitry of Trauma and PTSD Study UW-Madison Dept. Psychiatry 608-263-5756 ___ 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.
