fMRIprep on a dataset without json files

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i would like to run fMRIprep on this dataset. This dataset comes with phase and magnitude field maps for distortion correction. However, it does not come with any .json files. I figure i have to create these .json files on my own from scratch.

So how do i go about doing that? which parameters should be included in the *bold.json *magnitude1.json *magnitude2.json and *phasediff.json files?

is it necessary to include a json file (*T1w.json) for the structural scan?

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Hi @gerardyu,

Required JSON metadata are described in the BIDS specification (for example, the fmap fields are here: Magnetic Resonance Imaging - Brain Imaging Data Structure v1.9.0).

The BIDS validator will error if you do not, but I do not believe it is used at all during processing, so I think in a pinch a dummy json will allow you to continue.

Best,
Steven

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Na I don’t think it will.

We have many BIDS examples where there is no json for the T1w:

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Yes, looking at the specification there is no required metadata for anatomical images, thanks for the catch.

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yeah eventhough most of us would actually like to get all the metadata, one has to admit it that lowering the requirement bar makes it easier to convert old datasets¹ to BIDS.

1 datasets whose DICOM are lost somewhere on a hard drive gathering dust “in the bottom of a locked filing cabinet stuck in a disused lavatory with a sign on the door saying ‘Beware of the Leopard.'”

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