ds002338-fmriprep: "Found usable B0-map (fieldmap) estimator(s) <auto_00000> to correct"

[jbwexler]

Only for sub-xp210. The run exited immediately after this:

220501-13:08:50,551 nipype.workflow IMPORTANT: Building fMRIPrep's workflow:

• BIDS dataset path: /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds002338-fmriprep/sourcedata/raw.
• Participant list: ['xp210'].
• Run identifier: 20220501-130705_34309072-3c00-4451-aa52-f651e05c56f2.
• Output spaces: MNI152NLin2009cAsym:res-2 anat func fsaverage:den-10k.
• Pre-run FreeSurfer's SUBJECTS_DIR: /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds002338-fmriprep/sourcedata/freesurfer. 220501-13:08:54,298 nipype.workflow INFO: B0 field inhomogeneity map will be estimated with the following 1 estimators: [<EstimatorType.ANAT: 5>]. 220501-13:08:54,463 nipype.workflow INFO: No single-band-reference found for sub-xp210_task-2dNF_run-01_bold.nii.gz. 220501-13:08:54,463 nipype.workflow INFO: Found usable B0-map (fieldmap) estimator(s) to correct </scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds002338-fmriprep/sourcedata/raw/sub-xp210/func/sub-xp210_task-2dNF_run-01_bold.nii.gz> for susceptibility-derived distortions. 220501-13:08:55,837 nipype.workflow INFO: No single-band-reference found for sub-xp210_task-2dNF_run-02_bold.nii.gz. 220501-13:08:55,837 nipype.workflow INFO: Found usable B0-map (fieldmap) estimator(s) to correct </scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds002338-fmriprep/sourcedata/raw/sub-xp210/func/sub-xp210_task-2dNF_run-02_bold.nii.gz> for susceptibility-derived distortions.

[jbwexler]

Process Process-2: Traceback (most recent call last): File "/opt/conda/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/opt/conda/lib/python3.8/multiprocessing/process.py", line 108, in run self._target(*self._args, *self._kwargs) File "/opt/conda/lib/python3.8/site-packages/fmriprep/cli/workflow.py", line 118, in build_workflow retval["workflow"] = init_fmriprep_wf() File "/opt/conda/lib/python3.8/site-packages/fmriprep/workflows/base.py", line 85, in init_fmriprep_wf single_subject_wf = init_single_subject_wf(subject_id) File "/opt/conda/lib/python3.8/site-packages/fmriprep/workflows/base.py", line 370, in init_single_subject_wf func_preproc_wf = init_func_preproc_wf(bold_file, has_fieldmap=has_fieldmap) File "/opt/conda/lib/python3.8/site-packages/fmriprep/workflows/bold/base.py", line 167, in init_func_preproc_wf if nb.load( File "/opt/conda/lib/python3.8/site-packages/nibabel/loadsave.py", line 55, in load raise ImageFileError(f'Cannot work out file type of "{filename}"') nibabel.filebasedimages.ImageFileError: Cannot work out file type of "/scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds002338-fmriprep/sourcedata/raw/sub-xp210/func/sub-xp210_task-2dNF_run-03_bold.nii.gz" ...skipping... Process Process-2: Traceback (most recent call last): File "/opt/conda/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/opt/conda/lib/python3.8/multiprocessing/process.py", line 108, in run self._target(self._args, **self._kwargs) File "/opt/conda/lib/python3.8/site-packages/fmriprep/cli/workflow.py", line 118, in build_workflow retval["workflow"] = init_fmriprep_wf() File "/opt/conda/lib/python3.8/site-packages/fmriprep/workflows/base.py", line 85, in init_fmriprep_wf single_subject_wf = init_single_subject_wf(subject_id) File "/opt/conda/lib/python3.8/site-packages/fmriprep/workflows/base.py", line 370, in init_single_subject_wf func_preproc_wf = init_func_preproc_wf(bold_file, has_fieldmap=has_fieldmap) File "/opt/conda/lib/python3.8/site-packages/fmriprep/workflows/bold/base.py", line 167, in init_func_preproc_wf if nb.load( File "/opt/conda/lib/python3.8/site-packages/nibabel/loadsave.py", line 55, in load raise ImageFileError(f'Cannot work out file type of "{filename}"') nibabel.filebasedimages.ImageFileError: Cannot work out file type of "/scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds002338-fmriprep/sourcedata/raw/sub-xp210/func/sub-xp210_task-2dNF_run-03_bold.nii.gz"

[effigies]

Looks like a failure to datalad get. I'm able to fetch and load this file in nibabel locally.

[jbwexler]

Rerunning didn't fix. My script should be datalad getting but going to do this manually and rerun another time just in case.