FIX: Implement B0FieldIdentifier / B0FieldSource
#247
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Start with the implementation of the new BIDS metadata entries, to facilitate more reliable estimation and correction with fieldmaps. Resolves: #246.
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I suggested some additional query arguments to ensure we only grab subject relevant files.
Will this require us to make changes to the current fmriprep / nibabies way of handling the B0* metadata?
Co-authored-by: Mathias Goncalves <mathiasg@stanford.edu>
| estimators.append(e) | ||
| b0_ids = tuple() | ||
| with suppress(BIDSEntityError): | ||
| b0_ids = layout.get_B0FieldIdentifiers(**base_entities) |
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Do we want to specify extension and scope? I think only subject is relevant. Possibly session.
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I don't think extension would be required, yes. But, in the case of a weird dataset where pybids finds a json without its NIfTI this would fail for very little gain.
scope is necessary, because derivatives/ will definitely have B0FieldIdentifier defined if processed with SDCFlows.
subject is necessary, of course,
and session should not be there - the user may want to use fieldmaps with data from another session and save time in others (e.g., My Connectome).
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Okay, as long as extension doesn't break things, that's fine.
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scopeis necessary, becausederivatives/will definitely haveB0FieldIdentifierdefined if processed with SDCFlows.
But suppose I have a qMRI sequence where I quantify B0, which would be a derivative, and want to use that to correct raw BOLD series?
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If it is preprocessed, and in Hz, then you don't need an estimator for that - this function finds data that potentially can be used to estimate a fieldmap.
If, on the contrary, some preprocessing is needed (e.g., you will want to approximate some B-Spline coefficients to properly integrate with the correction workflows), then SDCFlows does not support that type of fieldmap. You would definitely pick up some sdcflows.interfaces but essentially, you have to build the workflow yourself. Also, our Fieldmap and FieldmapEstimator objects do not support other types of fieldmaps.
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The responsibility of this function is merely implementing the best we can those heuristics we used to have in fMRIPrep, for convenience across the board (dMRIPrep, babies, rodents, etc.).
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Before I merge, I guess I didn't explicitly give an answer to the actual question.
But suppose I have a qMRI sequence where I quantify B0, which would be a derivative, and want to use that to correct raw BOLD series?
Then, (i) you want it to have a B0FieldIdentifier in it, or at the least the IntendedFor so that the code to find fieldmap matches locates it, (ii) if you want to use SDCFlows' unwarp workflow, then you need to make sure that an anatomical reference is given and B-Spline coefficients representation available - if not, that's something you'll write on your own, (iii) invoke the unwarp workflow.
As you will see with the links, both (i) and (iii) take place within the downstream library (i.e., not implemented in SDCFlows proper).
Start with the implementation of the new BIDS metadata entries, to
facilitate more reliable estimation and correction with fieldmaps.
Resolves: #246.