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