ValueError: Fieldmap-less (SyN) estimation was requested, but PhaseEncodingDirection information appears to be absent. fMRIprep v. 22.0.2

jsein · November 4, 2022, 9:01pm

A long topic but I learnt something in the process.

This DatasetType defined in dataset_description.json defines the “scope” and how pipeline with interact with the dataset.

If we look here:

github.com

nipreps/sdcflows/blob/master/sdcflows/utils/wrangler.py

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line: 271:

    base_entities = {
        "subject": subject,
        "extension": [".nii", ".nii.gz"],
        "scope": "raw",  # Ensure derivatives are not captured
    }

This may suggest that SDCFlows does not deal with datasets whose “scope” (The "DataType" defined in dataset_description.json) is "derivative"`.

PyBIS seems to be involved in this too. Well, a whole new world…