How should the transformation files generated during preprocessing be named? Is there any BIDS specification for that similar to the one for derivatives here: BIDS derivatives? For example, how to name the registration matrix (.lta) that is generated when co-registering PET volumes to corresponding MR images (using freesurfer’s MRICoreg()) so that it is in accordance with BIDS specifications?**
This is currently unspecified in BIDS, though BEP 014 exists. Note that the latest work on that predates the BIDS derivatives release, so whenever there’s a conflict, the BIDS standard takes precedence.
Right now, fMRIPrep translates all transforms into ITK formats, for whatever that’s worth, though this is not something that is likely to be required by future versions of the spec. See Outputs of fMRIPrep — fmriprep version documentation for what the naming conventions look like in practice.
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