Can you attach recon-all.log of a failing subject?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Carly McIntyre-Wood Sent: Tuesday, January 16, 2024 4:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Issue with mri_brainvol_stats for only some participants
External Email - Use Caution Hi there,
I've come across a strange issue while running some new participants through Freesurfer 7.3.
A portion of participants (30%) are missing their stats files, although I have visually inspected the segmentation using Freeview and they look great. I have rerun autorecon3 and it only fixes the problem for select subjects. The exact error is below:
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness
Update not needed
\n mri_brainvol_stats 1096 \n
Segmentation fault
I found one instance of this in the archives where someone recommended running:
recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 -wmparc -balabels
However, this command exits at the same point with the same error.
Thanks so much, Carly
mri_brainvol_stats reads the following files:
mri/aseg.mgz surf/lh.white surf/rh.white surf/lh.pial surf/rh.pial mri/brainmask.mgz mri/transforms/talairach.xfm $FREESURFER_HOME/ASegStatsLUT.txt
Can you check if they all exist for your subjects?
Any errors if you run 'mri_brainvol_stats <subjid>' at prompt?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Carly McIntyre-Wood Sent: Tuesday, January 16, 2024 4:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Issue with mri_brainvol_stats for only some participants
External Email - Use Caution Hi there,
I've come across a strange issue while running some new participants through Freesurfer 7.3.
A portion of participants (30%) are missing their stats files, although I have visually inspected the segmentation using Freeview and they look great. I have rerun autorecon3 and it only fixes the problem for select subjects. The exact error is below:
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness
Update not needed
\n mri_brainvol_stats 1096 \n
Segmentation fault
I found one instance of this in the archives where someone recommended running:
recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 -wmparc -balabels
However, this command exits at the same point with the same error.
Thanks so much, Carly
freesurfer@nmr.mgh.harvard.edu