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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