🐛 `fsl_prepare_fieldmap` crashing

[shnizzedy]

Describe the bug

Working directory: /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare

Node inputs:

args = <undefined>
delta_TE = 4.760000000000002
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
in_magnitude = /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/distcor_phasediff_bet_skullstrip_190/sub-NDARCA186WGH_magnitude1_brain.nii.gz
in_phase = /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/fcp-indi/data/Projects/HBN/MRI/Site-SI/sub-NDARCA186WGH/fmap/sub-NDARCA186WGH_phasediff.nii.gz
nocheck = False
out_fieldmap = /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared.nii.gz
output_type = NIFTI_GZ
scanner = SIEMENS

Traceback (most recent call last):
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/pipeline/plugins/linear.py", line 47, in run
    node.run(updatehash=updatehash)
  File "/code/CPAC/pipeline/nipype_pipeline_engine/engine.py", line 474, in run
    return super().run(updatehash)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/usr/share/fsl/6.0/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 prepare.

Cmdline:
	fsl_prepare_fieldmap SIEMENS /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/fcp-indi/data/Projects/HBN/MRI/Site-SI/sub-NDARCA186WGH/fmap/sub-NDARCA186WGH_phasediff.nii.gz /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/distcor_phasediff_bet_skullstrip_190/sub-NDARCA186WGH_magnitude1_brain.nii.gz /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared.nii.gz 4.760000
Stdout:
	Loading volumes
	Phase loaded
	Magnitude loaded
	Mask loaded
	Done. Created /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared for use with FEAT.
Stderr:
	/usr/share/fsl/6.0/bin/fsl_prepare_fieldmap: 1: bc: not found
	/usr/share/fsl/6.0/bin/fsl_prepare_fieldmap: 1: bc: not found
	/usr/share/fsl/6.0/bin/fsl_prepare_fieldmap: 1: bc: not found
	/usr/share/fsl/6.0/bin/fsl_prepare_fieldmap: 1: bc: not found
	/usr/share/fsl/6.0/bin/fsl_prepare_fieldmap: 1: bc: not found
	/usr/share/fsl/6.0/bin/fsl_prepare_fieldmap: 1: bc: not found
	/usr/share/fsl/6.0/bin/fsl_prepare_fieldmap: 1: bc: not found
	/usr/share/fsl/6.0/bin/fsl_prepare_fieldmap: 1: bc: not found
	/usr/share/fsl/6.0/bin/fsl_prepare_fieldmap: 1: bc: not found
	/usr/share/fsl/6.0/bin/fsl_prepare_fieldmap: 1: bc: not found
	ERROR: input phase image exceeds allowable phase range.
	Allowable range is 6.283 radians.  Image range is: 12.5265 radians.
	Aborting.
	/usr/share/fsl/6.0/bin/fsl_prepare_fieldmap: 1: bc: not found
	Image Exception : #63 :: No image files match: /tmp/fsl_595dkmr9_tmp_ph_radians_unwrapped
	terminate called after throwing an instance of 'std::runtime_error'
	  what():  No image files match: /tmp/fsl_595dkmr9_tmp_ph_radians_unwrapped
	Aborted (core dumped)
	Image Exception : #63 :: No image files match: /tmp/fsl_595dkmr9_tmp_ph_rps
	Image Exception : #22 :: Failed to read volume /tmp/fsl_595dkmr9_tmp_ph_rps
	Error : No image files match: /tmp/fsl_595dkmr9_tmp_ph_rps
	terminate called after throwing an instance of 'std::runtime_error'
	  what():  Failed to read volume /tmp/fsl_595dkmr9_tmp_ph_rps
	Error : No image files match: /tmp/fsl_595dkmr9_tmp_ph_rps
	Aborted (core dumped)
	Image Exception : #63 :: No image files match: /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared
	terminate called after throwing an instance of 'std::runtime_error'
	  what():  No image files match: /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared
	Aborted (core dumped)
	Image Exception : #63 :: No image files match: /tmp/fsl_595dkmr9_tmp_fmapmasked
	Image Exception : #22 :: Failed to read volume /tmp/fsl_595dkmr9_tmp_fmapmasked
	Error : No image files match: /tmp/fsl_595dkmr9_tmp_fmapmasked
	Failed to read volume /tmp/fsl_595dkmr9_tmp_fmapmasked
	Error : No image files match: /tmp/fsl_595dkmr9_tmp_fmapmasked
	Image Exception : #63 :: No image files match: /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared
	terminate called after throwing an instance of 'std::runtime_error'
	  what():  No image files match: /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared
	Aborted (core dumped)
	Image Exception : #63 :: No image files match: /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared
	Image Exception : #22 :: Failed to read volume /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared
	Error : No image files match: /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared
	terminate called after throwing an instance of 'std::runtime_error'
	  what():  Failed to read volume /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared
	Error : No image files match: /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared
	Aborted (core dumped)
	Image Exception : #63 :: No image files match: /tmp/fsl_595dkmr9_tmp_fmapfilt
	terminate called after throwing an instance of 'std::runtime_error'
	  what():  No image files match: /tmp/fsl_595dkmr9_tmp_fmapfilt
	Aborted (core dumped)
	Image Exception : #63 :: No image files match: /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared
	terminate called after throwing an instance of 'std::runtime_error'
	  what():  No image files match: /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared
	Aborted (core dumped)
Traceback:
	Traceback (most recent call last):
	  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nibabel/loadsave.py", line 100, in load
	    stat_result = os.stat(filename)
	FileNotFoundError: [Errno 2] No such file or directory: '/ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared.nii.gz'

	During handling of the above exception, another exception occurred:

	Traceback (most recent call last):
	  File "/code/CPAC/pipeline/nipype_pipeline_engine/monkeypatch.py", line 40, in run
	    runtime = self._run_interface(runtime)
	  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/interfaces/fsl/epi.py", line 120, in _run_interface
	    im = nb.load(out_file)
	  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nibabel/loadsave.py", line 102, in load
	    raise FileNotFoundError(f"No such file or no access: '{filename}'")
	FileNotFoundError: No such file or no access: '/ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/default/SI/sub-NDARCA186WGH/working/pipeline_cpac-default-pipeline/cpac_pipeline_cpac-default-pipeline_sub-NDARCA186WGH_ses-1/_scan_rest/prepare/sub-NDARCA186WGH_phasediff_fslprepared.nii.gz'

To reproduce

I discovered this issue testing 2df6cb4 (a2c3d2f 🔀 #2230 🔀 #2241 🔀 #2246 🔀 #2247)

Preconfig

• default
• ccs-options
• fmriprep-options
• fx-options
• benchmark-FNIRT

Run command

singularity run \
  --cleanenv \
  -B "$OUTPUT":"$OUTPUT" \
  "$IMAGE" \
  "$INPUT" \
  "$OUTPUT" \
  participant \
  --skip_bids_validator \
  --n_cpus 1 \
  --mem_gb 7.0 \
  --participant_label "$PARTICIPANT" \
  --preconfig "$CONFIG_NAME"

Expected behavior

No crashes in preconfigs.

Acceptance criteria

• fsl_prepare_fieldmap runs successfully

C-PAC version

v1.8.8-dev @ 2df6cb4

Container platform

Singularity

Docker and/or Singularity version(s)

Apptainer v1.4.1-1.el8

[shnizzedy]

This issue might be because I accidentally ran this with the lite instead of the full image