Error loading mri/aseg.mgz

1

Hi, I got this error running FMRIPrep on this this dataset. Does anyone have experience with this?

Started at Fri Oct 19 09:20:54 UTC 2018
Ended at Fri Oct 19 09:21:06 UTC 2018
Apas2aseg-Run-Time-Sec 12

apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Fri Oct 19 09:21:06 UTC 2018
/data/aca16mha/freesurfer/sub-01

mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-01

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd
cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-01
sysname Linux
hostname sharc-node060.shef.ac.uk
machine x86_64
user aca16mha
UseRobust 0
atlas_icv (eTIV) = 1455509 mm^3 (det: 1.338436 )
mghRead(mri/aseg.mgz): could not read 262144 bytes at slice 40
Computing euler number
orig.nofix lheno = -30, rheno = -74
orig.nofix lhholes = 16, rhholes = 38
Loading mri/aseg.mgz
No such file or directory
ERROR: loading mri/aseg.mgz
Linux sharc-node060.shef.ac. uk 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-01 exited with ERRORS at Fri Oct 19 09:21:13 UTC 2018

2

Looks like similar issue to Could not read error : while file ":/out/freesurfer/sub-001/mri/T2.prenorm.mgz" exist

3

I’m also getting this error (“ERROR: loading mri/aseg.mgz”, see log below) on about 10-15 percent of subjects.

It’s seems to be typially resolved simply by rerunning.

This was also raised as an issue on Github in multiple closed issues. Is there a theory about why this occurs on a random fraction of cases?

also related:

crash log:

ERROR: loading mri/aseg.mgz
Linux gra730 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-2020 exited with ERRORS at Tue Nov 20 21:38:33 UTC 2018

For more details, see the log file /project/6019291/brad/weeks_retrocue/prepped/freesurfer/sub-2020/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:

mv: cannot move ‘/project/6019291/brad/weeks_retrocue/prepped/freesurfer/sub-2020/scripts/recon-all.env’ to ‘/project/6019291/brad/weeks_retrocue/prepped/freesurfer/sub-2020/scripts/recon-all.env.bak’: No such file or directory

Return code: 1

4

Hi @bbuchsbaum, could you finally resolve these issues?

5

No, but I haven’t run anything in awhile or upgraded fmriprep from 1.18.

6

Could you give 1.3.1 a go on a subject you know it failed this way?