I have BIDS valid data that consist (amongst others) of a fieldmap file named fmap/sub-003_ses-mri01_acq-fieldmap2p0iso68slices_run-1_magnitude1.nii.gz. If I run fmriprep I get this error message:
Process Process-2:
Traceback (most recent call last):
File "/opt/conda/lib/python3.8/site-packages/sdcflows/fieldmaps.py", line 340, in __attrs_post_init__
FieldmapFile(
File "<attrs generated init sdcflows.fieldmaps.FieldmapFile>", line 11, in __init__
__attr_validator_path(self, __attr_path, self.path)
File "/opt/conda/lib/python3.8/site-packages/sdcflows/fieldmaps.py", line 203, in check_path
raise FileNotFoundError(
FileNotFoundError: File path </project/3015089.01/deep-brain_EPI/bids_GEmap_mb3me2/sub-003/ses-mri01/fmap/sub-003_ses-mri01_acq-magnitude2p0iso68slices_run-1_magnitude1.nii.gz> does not exist, is a broken link, or it is not a file
During handling of the above exception, another exception occurred:
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 324, in init_single_subject_wf
fmap_estimators = find_estimators(
File "/opt/conda/lib/python3.8/site-packages/sdcflows/utils/wrangler.py", line 281, in find_estimators
e = fm.FieldmapEstimation(
File "<attrs generated init sdcflows.fieldmaps.FieldmapEstimation>", line 7, in __init__
self.__attrs_post_init__()
File "/opt/conda/lib/python3.8/site-packages/sdcflows/fieldmaps.py", line 348, in __attrs_post_init__
raise ValueError(
ValueError: A fieldmap or phase-difference estimation type was found, but an anatomical reference (magnitude1 file) is missing.
However, the error disappears and everything runs normally if I simply change/remove the fieldmap substring in the fmap filename (i.e. change the acq label), e.g. to fmap/sub-003_ses-mri01_acq-2p0iso68slices_run-1_magnitude1.nii.gz.
What happened?
I have BIDS valid data that consist (amongst others) of a fieldmap file named
fmap/sub-003_ses-mri01_acq-fieldmap2p0iso68slices_run-1_magnitude1.nii.gz
. If I run fmriprep I get this error message:However, the error disappears and everything runs normally if I simply change/remove the
fieldmap
substring in the fmap filename (i.e. change the acq label), e.g. tofmap/sub-003_ses-mri01_acq-2p0iso68slices_run-1_magnitude1.nii.gz
.What command did you use?
What version of fMRIPrep are you running?
21.0.1
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.
No response
Additional information / screenshots
No response