Hello,
I’m gotten a series of errors for a participant that I’ve tried to run through fmriprep three separate times using the following command:
export SINGULARITYENV_TEMPLATEFLOW_HOME=/N/dcwan/projects/irf/templateflow
unset PYTHONPATH; singularity run -B /N/dcwan/projects/irf/templateflow:/opt/templateflow /N/dcwan/projects/irf/containers/fmriprep-1.5.0.simg \
$bids_root_dir $bids_root_dir/derivatives \
participant \
--skip-bids-validation \
--participant-label $s \
--fs-license-file $FREESURFER_HOME/license.txt \
--ignore slicetiming \
--use-aroma \
--aroma-melodic-dimensionality 100 \
--output-spaces T1w fsnative fsaverage MNI152NLin6Asym:res-2 \
--nthread $nthreads \
--fd-spike-threshold 0.5 \
--dvars-spike-threshold 5 \
--stop-on-first-crash \
--resource-monitor \
--low-mem \
--mem_mb $mem_mb \
--use-plugin $bids_root_dir/fmriprep_plugin_${s}.yml \
--verbose \
-w $bids_root_dir/derivatives
I’m attaching the error log, since it’s rather long, but I’m wondering if it has something to do with nipype. Nothing else about the data suggests that it should fail. fmriprep_errors.txt (31.4 KB)
Thanks for the help