Participant was previously ran on full fmriprep but I wanted to rerun. I ran fmriprep 23.1.4 on this one subject first with the –anat-only flag and it gave me an error. I went into the node’s scratch space and the folder it is looking for doesn’t exist. Scratch space is only 5% used. How do you fix that?
Command:
singularity run
–cleanenv
-B {MAINDIR}:{MAINDIR}
-B {BIDSDIR},{PREPROCDIR},{SCRATCHDIR} \ -B /optnfs/freesurfer:/optnfs/freesurfer {IMAGE}
{BIDSDIR} {OUTDIR} participant
–participant_label {SUBJ} \ --ignore slicetiming \ --resource-monitor \ --bold2t1w-dof 9 \ --dummy-scans 6 \ --notrack \ --nprocs 32 \ --omp-nthreads 8 \ --nthreads 12 \ --mem_mb 280000 \ --fs-license-file /optnfs/freesurfer/6.0.0/license.txt \ --cifti-output 91k \ --output-spaces T1w MNI152NLin2009cAsym fsnative fsaverage6 \ --skull-strip-fixed-seed \ -w {WORKDIR}
–random-seed 42
–stop-on-first-crash
–force-syn
–use-syn-sdc
–skip_bids_validation
–anat-only
exception calling callback for <Future at 0x2b0067e8d270 state=finished raised FileNotFoundError>
concurrent.futures.process._RemoteTraceback:
“”"
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 497, in run
self._get_hashval()
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 548, in _get_hashval
self._get_inputs()
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 607, in _get_inputs
output_value = evaluate_connect_function(
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/utils.py”, line 697, in evaluate_connect_function
output_value = func(first_arg, *list(args))
File “”, line 24, in fix_multi_T1w_source_name
IndexError: list index out of rangeDuring handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/concurrent/futures/process.py”, line 246, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py”, line 70, in run_node
result[“result”] = node.result
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 223, in result
return _load_resultfile(
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/utils.py”, line 291, in load_resultfile
raise FileNotFoundError(results_file)
FileNotFoundError: /scratch/f003z4j/fmriprep-work/work-SID000002/fmriprep_23_1_wf/single_subject_SID000002_wf/bids_info/result_bids_info.pklz
“”"The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/concurrent/futures/_base.py”, line 342, in _invoke_callbacks
callback(self)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py”, line 159, in _async_callback
result = args.result()
File “/opt/conda/envs/fmriprep/lib/python3.10/concurrent/futures/_base.py”, line 451, in result
return self.__get_result()
File “/opt/conda/envs/fmriprep/lib/python3.10/concurrent/futures/_base.py”, line 403, in __get_result
raise self._exception
FileNotFoundError: /scratch/f003z4j/fmriprep-work/work-SID000002/fmriprep_23_1_wf/single_subject_SID000002_wf/bids_info/result_bids_info.pklz