topup post-processing failure on 21.0.0RC2

[Lestropie]

What happened?

First test of 21.0.0RC2 on data that has proven problematic thus far (combined multi-echo fMRI and spin-echo EPIs for susceptibility field estimation, which was non-functional in RC0: #2558). topup executes successfully, but subsequent "fix_coeff function throws an unhandled Exception.

What command did you use?

singularity run --cleanenv \
    --bind /projects/hb93:/projects/hb93,/scratch/hb93:/scratch/hb93 \
    /scratch/hb93/fmriprep-21.0.0rc2.sif /scratch/hb93/rob_testing_fmri/BIDS /scratch/hb93/rob_testing_fmri/rc2 participant \
    --participant_label sub-01 \
    --nthreads 4 --omp-nthreads 4 --mem_mb 16384 \
    --output-spaces T1w MNI152NLin6Asym:res-2 fsaverage5 \
    --fs-license-file /projects/hb93/freesurfer_license.txt \
    --fs-subjects-dir /scratch/hb93/rob_testing_fmri/freesurfer \
    -w /scratch/hb93/rob_testing_fmri/work

What version of fMRIPrep are you running?

21.0.0RC2

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.

211123-13:51:16,697 nipype.workflow WARNING:
	 [Node] Error on "fmriprep_wf.single_subject_01_wf.fmap_preproc_wf.wf_auto_00000.fix_coeff" (/scratch/hb93/rob_testing_fmri/work/fmriprep_wf/single_subject_01_wf/fmap_preproc_wf/wf_auto_00000/fix_coeff)
211123-13:51:16,779 nipype.workflow ERROR:
	 Node fix_coeff failed to run on host m3i037.
211123-13:51:16,792 nipype.workflow ERROR:
	 Saving crash info to /scratch/hb93/rob_testing_fmri/rc2/sub-01/log/20211123-130706_d88ce07e-b99b-4ca1-b83e-037638e6872b/crash-20211123-135116-robertes-fix_coeff-5bdb8b27-2b61-4223-9b25-5be1f020e564.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
    self.procs[jobid].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/sdcflows/interfaces/bspline.py", line 420, in _run_interface
    self._results["out_coeff"] = [
  File "/opt/conda/lib/python3.8/site-packages/sdcflows/interfaces/bspline.py", line 422, in <listcomp>
    _fix_topup_fieldcoeff(
  File "/opt/conda/lib/python3.8/site-packages/sdcflows/interfaces/bspline.py", line 480, in _fix_topup_fieldcoeff
    raise ValueError(
ValueError: Shape of coefficients file [72 72 44] does not meet the expectation given the reference's shape [72 72 44].

### Additional information / screenshots

_No response_

[oesteban]

I think this is a duplicate of #2628 (comment), and we are following up in nipreps/sdcflows#250.

We have pushed a Docker image including a patch to dockerhub (tag: nipreps/fmriprep:pepolar-2628), just in case you could give it a try - please let us know if the patch is working.

To follow up on this bug, please head to the sdcflows issue linked in the first paragraph.