fMRIprep on a dataset without json files

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?

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.


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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.

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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