Summary of what happened:
Dear Community,
I have successfully run fmriprep for most of my participants. However, two participants show the same error. I wonder what the issue is here. Can anyone kindly tell me what was wrong please?
Thank you
Wendy
Command used (and if a helper script was used, a link to the helper script or the command generated):
PASTE CODE HERE
Version:
Environment (Docker, Singularity / Apptainer, custom installation):
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
This is the error in the log:
Fri Feb 9 08:10:20 GMT 2024
tmpdir is transforms/tmp.talairach.3928214
/data/project/CannTeen/CannTeen_longitudinal_fMRI/SST_11/output/sub-274/sourcedata/freesurfer/sub-274/mri
mri_convert orig_nu.mgz transforms/tmp.talairach.3928214/src.mnc
mri_convert orig_nu.mgz transforms/tmp.talairach.3928214/src.mnc
reading from orig_nu.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -5.82077e-10, -1.86265e-09)
j_ras = (0, 3.72529e-09, -1)
k_ras = (-5.82077e-10, 1, 0)
writing to transforms/tmp.talairach.3928214/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir /opt/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.3928214/src.mnc transforms/talairach.auto.xfm
mritotal: Command not found.
ERROR: mritotal failed, see transforms/talairach.log
Linux grid07.nan.kcl.ac.uk 4.18.0-513.11.1.el8_9.x86_64 #1 SMP Wed Jan 17 02:00:40 EST 2024 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-274 exited with ERRORS at Fri Feb 9 08:10:22 GMT 2024
For more details, see the log file /data/project/CannTeen/CannTeen_longitudinal_fMRI/SST_11/output/sub-274/sourcedata/freesurfer/sub-274/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Stderr:
Traceback:
RuntimeError: subprocess exited with code 1.
240209-08:10:25,230 cli ERROR:
Preprocessing did not finish successfully. Errors occurred while processing data from participants: 274 (1). Check the HTML reports for details.
240209-08:10:26,251 nipype.workflow INFO:
[Node] Finished "07_fill_gm", elapsed time 19.691168s.