Fmriprep 21.0.2 failing during fmap_preproc_wf bs_filter in SDC

zachladwig · April 26, 2023, 5:33pm

Summary of what happened:

I am receiving the below error using fmriprep version 21.0.2. I have used this version successfully before, but this data is from a new scanner which we haven’t preprocessed before, so it’s probably related to that.

Command used (and if a helper script was used, a link to the helper script or the command generated):

singularity run --cleanenv -B /projects/b1081:/projects/b1081 \
    -B ${WORK_DIR}:/quest_scratch \
    /projects/b1081/singularity_images/fmriprep-21.0.2.simg \
    ${BIDS_DIR} \
    ${BIDS_DIR}/${DERIVS_DIR} \
    participant --participant-label ${subject} \
    -w /quest_scratch --omp-nthreads 8 --nthreads 16 \
    --fs-license-file /projects/b1081/singularity_images/freesurfer_license.txt \
    --fs-subjects-dir ${BIDS_DIR}/${DERIVS_DIR}/sourcedata/freesurfer \
    --output-spaces MNI152NLin6Asym:res-2 \
    --ignore slicetiming --fd-spike-threshold 0.2 --me-output-echos --resource-monitor

Version: 21.0.2

Environment (Docker, Singularity, custom installation): singularity

Data formatted according to a validatable standard? Please provide the output of the validator:

Yes, validated w BIDS validator.

Relevant log outputs (up to 20 lines):

Node: fmriprep_wf.single_subject_HUBS02_wf.fmap_preproc_wf.wf_auto_00003.bs_filter
Working directory: /quest_scratch/fmriprep_wf/single_subject_HUBS02_wf/fmap_preproc_wf/wf_auto_00003/bs_filter

Node inputs:

bs_spacing = [(100.0, 100.0, 40.0), (16.0, 16.0, 10.0)]
extrapolate = True
in_data = <undefined>
in_mask = <undefined>
recenter = mode
ridge_alpha = 0.01

Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.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/sdcflows/interfaces/bspline.py", line 141, in _run_interface
    data -= mode(data[mask], axis=None)[0][0]
IndexError: boolean index did not match indexed array along dimension 2; dimension is 4 but corresponding boolean dimension is 54

Screenshots / relevant information:

Steven · April 26, 2023, 6:01pm

Hi @zachladwig,

SDC workflows have been updated a lot since that version. Does this error persist on the most recent version 23.0.2?

Best,
Steven

zachladwig · April 27, 2023, 3:30pm

Hi Steven! Nice to see your face pop up. I hope you are well.

Yeah, I tried 23.0.2 and got this similar error

Node: fmriprep_23_0_wf.single_subject_HUBS02_wf.fmap_preproc_wf.wf_auto_00003.bs_filter
Working directory: /quest_scratch/fmriprep_23_0_wf/single_subject_HUBS02_wf/fmap_preproc_wf/wf_auto_00003/bs_filter

Node inputs:

bs_spacing = [(100.0, 100.0, 40.0), (16.0, 16.0, 10.0)]
debug = False
extrapolate = True
in_data = <undefined>
in_mask = <undefined>
recenter = mode
ridge_alpha = 0.01
zooms_min = 4.0

Traceback (most recent call last):
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.9/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 bs_filter.

Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 397, in run
	    runtime = self._run_interface(runtime)
	  File "/opt/conda/lib/python3.9/site-packages/sdcflows/interfaces/bspline.py", line 191, in _run_interface
	    center = np.squeeze(mode(data[mask]).mode)
	IndexError: boolean index did not match indexed array along dimension 2; dimension is 2 but corresponding boolean dimension is 32

effigies · April 28, 2023, 2:56am

With a dimension mismatch, this seems likely to be an orientation issue. Are you able to narrow it down to a single task and fieldmap? auto_00003 means that you’ve got fieldmaps that aren’t specified with B0FieldIdentifier. You should be able to singularity exec <container> sdcflows-find-estimators <bids-dir> to see what files are used to estimate each fieldmap.

zachladwig · April 28, 2023, 8:28pm

ah helpful thanks @effigies
Does auto_0003 mean that it is failing while working on sub-HUBS01 session 3? It is strange because I meant to only run fMRIprep for sub-HUBS02? (in initial command i specificy participant as sub-HUBS02).

zachladwig · April 28, 2023, 8:53pm

Subjects 1 and 2 were collected on two different scanners… could that be contributing to the issue

zachladwig · April 28, 2023, 9:11pm

in the actual log it looks like auto_00003 was session 4 of HUBS02