🐛 `input mask must have at least 1 voxel`

[shnizzedy]

Describe the bug

Node: cpac_pipeline_cpac_abcd-options_sub-3884955_ses-1.cal_DVARS_762
Working directory: /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/abcd-options/KKI/sub-3884955/working/pipeline_cpac_abcd-options/cpac_pipeline_cpac_abcd-options_sub-3884955_ses-1/_scan_rest_run-1_acq-2/cal_DVARS_762

Node inputs:

args = <undefined>
environ = {}
in_file = /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/abcd-options/KKI/sub-3884955/working/pipeline_cpac_abcd-options/cpac_pipeline_cpac_abcd-options_sub-3884955_ses-1/_scan_rest_run-1_acq-2/cal_DVARS_762/sub-3884955_ses-1_task-rest_acq-2_run-1_bold_resample_calc_mcf.nii.gz
mask = /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/abcd-options/KKI/sub-3884955/working/pipeline_cpac_abcd-options/cpac_pipeline_cpac_abcd-options_sub-3884955_ses-1/xfm_from-template_to-bold_mask_224/_scan_rest_run-1_acq-2/apply_warp_xfm_from-template_to-bold_mask_224/wmparc_maths_fill_holes_maths_warp_trans_trans.nii.gz
method = dvars
num_threads = 1
out_file = <undefined>
outputtype = AFNI

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 cal_DVARS_762.

Cmdline:
	3dTto1D -input /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/abcd-options/KKI/sub-3884955/working/pipeline_cpac_abcd-options/cpac_pipeline_cpac_abcd-options_sub-3884955_ses-1/_scan_rest_run-1_acq-2/cal_DVARS_762/sub-3884955_ses-1_task-rest_acq-2_run-1_bold_resample_calc_mcf.nii.gz -mask /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/abcd-options/KKI/sub-3884955/working/pipeline_cpac_abcd-options/cpac_pipeline_cpac_abcd-options_sub-3884955_ses-1/xfm_from-template_to-bold_mask_224/_scan_rest_run-1_acq-2/apply_warp_xfm_from-template_to-bold_mask_224/wmparc_maths_fill_holes_maths_warp_trans_trans.nii.gz -method dvars -prefix sub-3884955_ses-1_task-rest_acq-2_run-1_bold_resample_calc_mcf_3DtoT1.1D
Stdout:

Stderr:
	++ reading mask dset from /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/abcd-options/KKI/sub-3884955/working/pipeline_cpac_abcd-options/cpac_pipeline_cpac_abcd-options_sub-3884955_ses-1/xfm_from-template_to-bold_mask_224/_scan_rest_run-1_acq-2/apply_warp_xfm_from-template_to-bold_mask_224/wmparc_maths_fill_holes_maths_warp_trans_trans.nii.gz...
	** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /ocean/projects/med250004p/shared/regression_outputs_v1.8.8/2025-06-20/abcd-options/KKI/sub-3884955/working/pipeline_cpac_abcd-options/cpac_pipeline_cpac_abcd-options_sub-3884955_ses-1/xfm_from-template_to-bold_mask_224/_scan_rest_run-1_acq-2/apply_warp_xfm_from-template_to-bold_mask_224/wmparc_maths_fill_holes_maths_warp_trans_trans.nii.gz to FLOAT32
	     Warnings of this type will be muted for this session.
	     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
	** ERROR: input mask must have at least 1 voxel
Traceback:
	RuntimeError: subprocess exited with code 1.

To reproduce

No response

Preconfig

• default
• abcd-options
• anat-only
• blank
• ccs-options
• fmriprep-options
• fx-options
• monkey
• monkey-ABCD
• ndmg
• nhp-macaque
• preproc
• rbc-options
• rodent

Custom pipeline configuration

No response

Run command

singularity run \
  --cleanenv \
  -B "/ocean/projects/med250004p/jclucas/C-PAC/CPAC":"/code/CPAC" \
  -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 crash

Acceptance criteria

• DVARS nodes don't crash

Screenshots

No response

C-PAC version

v1.8.8-dev @ 0ec8206

Container platform

Singularity

Docker and/or Singularity version(s)

Apptainer v1.4.1-1.el8

Additional context

No response