Summary of what happened:
Running fmriprep on a single subject runs into an error during ‘unwarp_wf.resample’. The dataset contains 1 BOLD run, 1 T1w image, 2 fieldmap magnitude and 1 fieldmap phasediff image.
Running with ‘–ignore fieldmap’ tag works fine without errors. Applying fieldmap correction outside of fmriprep (FSL) works fine as well.
Command used (and if a helper script was used, a link to the helper script or the command generated):
Command was used with fmriprep-docker wrapper:
/opt/conda/envs/fmriprep/bin/fmriprep /data /out participant --participant_label control01 --fs-no-reconall --nthreads 8 --stop-on-first-crash --dummy-scans 3 --mem_mb 21000 -v -w /scratch
Version:
fmriprep version 23.1.3 (based on Nipype 1.8.6)
Environment (Docker, Singularity, custom installation):
Docker (v4.21.1)
Data formatted according to a validatable standard? Please provide the output of the validator:
Bids valid.
Relevant log outputs (up to 20 lines):
File: /out/sub-control01/log/20230718-145946_f2d342cc-ea27-4eee-8490-4454be856bdb/crash-20230718-193542-root-resample-ef79e793-bdec-450a-8ff9-467d5ec5b0cb.txt
Working Directory: /scratch/fmriprep_23_1_wf/single_subject_control01_wf/func_preproc_task_socialrewardlearning_wf/unwarp_wf/resample
Inputs:
in_coeff:
in_data:
in_xfms:
num_threads: 4
pe_dir:
ro_time:
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 527, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node resample.
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/sdcflows/interfaces/bspline.py", line 395, in _run_interface
) = zip(*outputs)
File "/opt/conda/envs/fmriprep/lib/python3.10/concurrent/futures/process.py", line 575, in _chain_from_iterable_of_lists
for element in iterable:
File "/opt/conda/envs/fmriprep/lib/python3.10/concurrent/futures/_base.py", line 621, in result_iterator
yield _result_or_cancel(fs.pop())
File "/opt/conda/envs/fmriprep/lib/python3.10/concurrent/futures/_base.py", line 319, in _result_or_cancel
return fut.result(timeout)
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
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.