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Raise error if two-echo data are provided #3570

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Merged
merged 1 commit into from
Nov 25, 2025
Merged

Raise error if two-echo data are provided #3570

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10 changes: 10 additions & 0 deletions fmriprep/workflows/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -834,6 +834,16 @@ def init_single_subject_wf(
fieldmap_id = estimator_map.get(bold_file)
jacobian = False

if len(bold_series) == 2:
# This should only be reached if two-echo data are provided and echo-idx is not.
# Raise an error in this case, until we figure out how to support two-echo data.
bold_series_str = '\n\t'.join(bold_series)
raise RuntimeError(
'This BOLD series contains two echoes, which fMRIPrep does not support:\n'
f'\t{bold_series_str}\n'
'Please set "--echo-idx" to process one echo at a time.'
)

if fieldmap_id:
if 'fmap-jacobian' in config.workflow.force:
jacobian = True
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