Fmriprep _autorecon31 error

fmriprep

#1

Hi All,

I have processed a batch of subjects using fmriprep:

singularity run --cleanenv ${HOME}/singularity_images/fmriprep-1.2.5.simg \
    ${data_folder}/trfep/raw ${data_folder}/trfep/processed  \
    participant \
    --participant-label ${file} \
    --fs-license-file ${HOME}/license.txt
    --low-mem

Most of these have completed successfully, but for a few no /fmfriprep/func folder has been generated and there is an error in the .html report:

Node Name: _autorecon31

The log for the subject shows the following:

ERROR: loading mri/wmparc.mgz
Linux nanlnx16.iop.kcl.ac.uk 3.10.0-862.14.4.el7.x86_64 #1 SMP Tue Sep 25 14:32:52 CDT 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-TRFEP24A exited with ERRORS at Sat Jan 12 09:42:30 UTC 2019

For more details, see the log file /home/k1201869/dcm/data/trfep/processed/freesurfer/sub-TRFEP24A/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:
mv: '/home/k1201869/dcm/data/trfep/processed/freesurfer/sub-TRFEP24A/scripts/recon-all.env' and '/home/k1201869/dcm/data/trfep/processed/freesurfer/sub-TRFEP24A/scripts/recon-all.env.bak' are the same file
Return code: 1

Any advice appreciated

Many thanks

Rob


#2

Hi Rob,

A first guess when FreeSurfer has trouble loading files is that the filesystem may not be synced, and all that needs doing is a re-run to resolve it. You should check for and remove any freesurfer/<subject>/scripts/IsRunning* before proceeding. If that still happens, perhaps you could post the most recent log (it should also be found in scripts/), and we could see if there’s something more serious happening.

Chris


#3

Thanks! Rerunning solved it (A couple subjects needed to be rerun 2 times before they got all the way through)

Rob