Fieldmap SDC from v24.0.0 seems to introduce artifact for some participants

[michael-s-cohen-2]

What happened?

There seem to be line-like artifacts appearing in the data as a result of field map distortion correction for some participants. I tried re-running the pipeline using --ignore fmap-jacobian, as suggested by @effigies , and the data visually seemed better. However, the HTML output still showed a distortion in the "corrected" data, so I'm not sure if the issue is entirely fixed just by disabling that feature. In any case, it seems very problematic that there are major distortions introduced via at the default behavior.

Final image, after processing with standard v24 pipeline:

Same image with ignore fmap-jacobian applied:

HTML output after using ignore fmap-jacobian:
Fieldmap reference vs. EPI reference (appears misaligned):

What command did you use?

srun singularity run --cleanenv -B /project/decety -B /scratch/midway3/mscohen /project/decety/my_images/fmriprep-24.0.0.simg --participant_label=3404017 --fs-license-file="/project/decety/freesurfer_license.txt" -v -v --nthreads 8 --output-spaces MNI152NLin6Asym:res-2 --bold2anat-dof 6 --fd-spike-threshold 0.9 --dvars-spike-threshold 3 --skull-strip-template OASIS30ANTs -w /scratch/midway3/mscohen /project/decety/VAD_BIDS /project/decety/VAD_BIDS/derivatives/fmriprep_v24 participant

What version of fMRIPrep are you running?

24.0.0

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.

For some participants who had this issue (though not all of them!), the default workflow generates an error. But for other participants, and with --ignore fmap-jacobian applied, there was not an error.

This was the last part of the log output when it did generate an error:

240725-23:14:54,92 nipype.workflow ERROR:
	 could not run node: fmriprep_24_0_wf.sub_3404017_wf.bold_task_VAD_run_2_wf.bold_fit_wf.func_fit_reports_wf.sdecreg_report
240725-23:14:54,96 nipype.workflow INFO:
	 crashfile: /project/decety/VAD_BIDS/derivatives/fmriprep_v24/sub-3404017/log/20240725-132523_1e68b72e-557f-4dc6-8368-a2f8ceb85726/crash-20240725-190730-jchen28-sdecreg_report-9ed96f78-61de-489d-bf56-ba363f6fab24.txt
240725-23:14:54,96 nipype.workflow INFO:
	 ***********************************
240725-23:14:54,142 nipype.workflow CRITICAL:
	 fMRIPrep failed: Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmriprep/lib/python3.11/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 sdecreg_report.

Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 398, in run
	    runtime = self._post_run_hook(runtime)
	              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/interfaces/mixins/reporting.py", line 50, in _post_run_hook
	    self._generate_report()
	  File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/sdcflows/interfaces/reportlets.py", line 103, in _generate_report
	    abs(np.percentile(fmapdata[maskdata], 99.8)),
	                      ~~~~~~~~^^^^^^^^^^
	IndexError: boolean index did not match indexed array along dimension 1; dimension is 84 but corresponding boolean dimension is 130

Additional information / screenshots

No response