summary of what happened:
I had some issues with the brainmasks that were generated with fmriprep and followed the advice found here: Brain mask generation in fmriprep - #10 by effigies , i.e. I ran fmriprep with --level minimal, fixed up the mask, and then passed the first round of derivatives to a new run with --derivatives However, somehow this does not seem to work as fmriprep always gets stuck after or during resampling:
Command used (and if a helper script was used, a link to the helper script or the command generated):
#!/bin/bash
subs=('sub-103')
for sub in "${subs[@]}"; do
echo "Processing $sub"
singularity run \
--cleanenv \
/data/pt_02771/software/my_images/fmriprep-24.1.1.simg \
/data/pt_02771/data/derivatives/nordic/ \
/data/pt_02771/data/derivatives/fMRIPrep/ \
participant \
--participant-label $sub \
--task-id auditory \
--fs-license-file /data/pt_02771/software/license.txt \
--output-spaces fsnative \
--cifti-output 170k \
--fs-subjects-dir /data/pt_02771/data/derivatives/freesurfer/ \
--derivatives /data/pt_02771/data/derivatives/fMRIPrep/
done
Version
24.1.1
Environment (Docker, Singularity / Apptainer, custom installation):
singularity
Output Logs
From the logfiles, it seems like the confounds files are not being produced:
Node: fmriprep_24_1_wf.sub_103_wf.bold_ses_01_task_auditory_run_01_wf.bold_confounds_wf.add_rmsd_header
Working directory: /data/pt_02771/software/cfmapping/preprocessing/work/fmriprep_24_1_wf/sub_103_wf/bold_ses_01_task_auditory_run_01_wf/bold_confounds_wf/add_rmsd_header
Node inputs:
columns = ['rmsd']
in_file = <undefined>
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 722, in _run_command
result = self._interface.run(cwd=outdir, ignore_exception=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 388, in run
self._check_mandatory_inputs()
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 275, in _check_mandatory_inputs
raise ValueError(msg)
ValueError: AddTSVHeader requires a value for input 'in_file'. For a list of required inputs, see AddTSVHeader.help()
When creating this crashfile, the results file corresponding
to the node could not be found.
Data formatted according to a validatable standard? Please provide the output of the validator:
Yes, it passes the bids validator
Any clues on what may be going on here?