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