Fmriprep 3dvolreg error in bold_t1_trans_wf.bold_reference_wf.gen_avg

[dlevitas]

What happened?

This is cross-post from NeuroStars. I repeatedly encounter this issue even when restarting fmriprep with clean working and freesurfer directories. I've included a screenshot that demonstrates the poor alignment of my functional to anatomical data.

What command did you use?

unset PYTHONPATH; singularity run \
		    -B ${bids_root_dir}:${bids_root_dir} \
		    -B /N/dcwan/projects/irf/templateflow:/opt/templateflow
		    -B ${work_dir}:${work_dir} \
		    -B ${output_dir}:${output_dir} \
		    /N/dcwan/projects/irf/containers/fmriprep-${fmriprep_version}.simg 			\
		    $bids_root_dir $output_dir													\
			participant															\
			--participant-label $s 													\
			--skip-bids-validation 													\
			--md-only-boilerplate													\
			--fs-license-file $FREESURFER_HOME/license.txt							\
			--fs-subjects-dir $output_dir/sourcedata/freesurfer/sub-${s} 			\
			--output-spaces MNI152NLin6Asym:res-2									\
			--nthreads $cores														\
			--stop-on-first-crash 													\
			--resource-monitor 														\
			--low-mem 																\
			--mem_mb $reduced_mem 													\
			--use-plugin $bids_root_dir/fmriprep_plugin_${s}.yml 					\
			--use-aroma 															\
			--aroma-melodic-dimensionality 100 										\
			--dummy-scans $dummy_scans 												\
			--verbose 																\
			--bids-filter-file ${bids_root_dir}/code/bids_filter_file.json 			\
			--output-layout bids 													\
			-w $work_dir/sub-${s}

What version of fMRIPrep are you running?

21.0.2

How are you running fMRIPrep?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

Inputs:

    in_file:
    mc_method: AFNI
    nonnegative: True
    t_mask:

Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/legacymultiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
    runtime = self._run_interface(runtime)
  File "/opt/conda/lib/python3.8/site-packages/niworkflows/interfaces/images.py", line 322, in _run_interface
    res = Volreg(
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
    runtime = self._run_interface(runtime)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/afni/base.py", line 124, in _run_interface
    return super(AFNICommandBase, self)._run_interface(
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface
    self.raise_exception(runtime)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 749, in raise_exception
    raise RuntimeError(
RuntimeError: Command:
3dvolreg -Fourier -twopass -1Dfile vol0000_xform-00000_clipped_merged_sliced.1D -1Dmatrix_save vol0000_xform-00000_clipped_merged_sliced.aff12.1D -prefix vol0000_xform-00000_clipped_merged_sliced_volreg.nii.gz -zpad 4 -maxdisp1D vol0000_xform-00000_clipped_merged_sliced_md.1D /N/scratch/dlevitas/fmriprep-21.0.2_temp/sub-41/fmriprep_wf/single_subject_41_wf/func_preproc_task_pacpal_run_2_wf/bold_t1_trans_wf/bold_reference_wf/gen_avg/vol0000_xform-00000_clipped_merged_sliced.nii
Standard output:

Standard error:
++ 3dvolreg: AFNI version=AFNI_22.1.02 (Apr  6 2022) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=4 (INT16) in file /N/scratch/dlevitas/fmriprep-21.0.2_temp/sub-41/fmriprep_wf/single_subject_41_wf/func_preproc_task_pacpal_run_2_wf/bold_t1_trans_wf/bold_reference_wf/gen_avg/vol0000_xform-00000_clipped_merged_sliced.nii 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.
++ Coarse del was 10, replaced with 5

Fatal Signal 11 (SIGSEGV) received
       fft_shift2
      apply_zshear
     apply_3shear
    THD_rota_vol
   mri_3dalign_one
  3dvolreg main
 Bottom of Debug Stack
** Command line was:
3dvolreg -Fourier -twopass -1Dfile vol0000_xform-00000_clipped_merged_sliced.1D -1Dmatrix_save vol0000_xform-00000_clipped_merged_sliced.aff12.1D -prefix vol0000_xform-00000_clipped_merged_sliced_volreg.nii.gz -zpad 4 -maxdisp1D vol0000_xform-00000_clipped_merged_sliced_md.1D /N/scratch/dlevitas/fmriprep-21.0.2_temp/sub-41/fmriprep_wf/single_subject_41_wf/func_preproc_task_pacpal_run_2_wf/bold_t1_trans_wf/bold_reference_wf/gen_avg/vol0000_xform-00000_clipped_merged_sliced.nii
** AFNI version = AFNI_22.1.02  Compile date = Apr  6 2022
** [[Precompiled binary linux_openmp_64: Apr  6 2022]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /N/u/dlevitas/Carbonate/.afni.crashlog
Return code: 1

Additional information / screenshots

[dlevitas]

This issue appears to be related to the new SDC workflow changes implemented starting fmriprep version 21. I've left a comment in #2830 since it is the core problem (SDC) I've encountered with the newer fmriprep versions. I'll therefore close this issue.