Hello,
I’m running version 1.5.0rc2 on a batch of subjects, and am noticing that my jobs are taking ~21 hours to complete, even though I ran freesurfer’s recon-all beforehand and that data is in $bids_root_dir/derivatives/freesurfer. My command is:
unset PYTHONPATH; singularity run -B /N/dcwan/projects/irf/templateflow:/opt/templateflow /N/dcwan/projects/irf/containers/fmriprep-1.5.0rc2.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 8 \
--fd-spike-threshold 0.2 \
--dvars-spike-threshold 5 \
--stop-on-first-crash \
--resource-monitor \
--low-mem \
--mem_mb 45000 \
--use-plugin $bids_root_dir/fmriprep_plugin_${s}.yml \
--verbose \
-w $bids_root_dir/derivatives
I realize that requesting multiple output-spaces and aroma increases time, but I was wondering if this amount of time to completion seems reasonable, especially given that freesurfer was run prior?
Furthermore, in the logs I see things like this, so I’m unsure if freesurfer is being run again for some reason.
190826-16:23:34,904 nipype.interface INFO:
recon-all complete : Not running
190826-16:23:35,331 nipype.workflow INFO:
[LegacyMultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 43.63/48.83, Free processors: 0/8.
Currently running:
* fmriprep_wf.single_subject_1000_wf.anat_preproc_wf.surface_recon_wf.autorecon1
Thanks for the help!