[ENH][SCHEMA] Allow .bval and .bvec files for pepolar fmaps

[mattcieslak]

Closes #1724

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[tsalo]

I think the other approach I mentioned (adding .bval and .bvec to pepolar and override the extensions in pepolar_m0scan) might be easier to integrate in the schema.

EDIT: Can you also update the derivative rules for field maps?

https://github.com/bids-standard/bids-specification/blob/bd08602760d2fa0fd61e8f579a2677ea9bda8588/src/schema/rules/files/deriv/preprocessed_data.yaml#L100-L105

[tsalo]

Thanks! I think you just need to address the issues in the remark job (misaligned bars in the contributors table and trailing space from my suggestion).

[effigies]

Started having a look yesterday. It's not clear why this isn't showing up in the rendered examples.

[tsalo]

I'm seeing .bval and .bvec in the filename templates for field map case 4: https://bids-specification--1754.org.readthedocs.build/en/1754/modality-specific-files/magnetic-resonance-imaging-data.html#case-4-multiple-phase-encoded-directions-pepolar

Should it be showing up somewhere else?

[effigies]

Ah, no. Sorry, it turned out I opened the wrong PR's render.

[tsalo]

And do we want to add a check for epi.bval there must be at least one 0 value?

I think datasets can have non-zero, but low, b-values in these images. In QSIPrep there's a b0-threshold parameter that determines which volumes to treat as b=0.

[effigies]

I think datasets can have non-zero, but low, b-values in these images. In QSIPrep there's a b0-threshold parameter that determines which volumes to treat as b=0.

What are typical thresholds? 1, 1e-2, 1e2?

[effigies]

Just looked, the default is 100. Maybe let's make the check that there is at least one volume with b<100. cc @oesteban @arokem for a sanity check.

[oesteban]

Just looked, the default is 100. Maybe let's make the check that there is at least one volume with b<100. cc @oesteban @arokem for a sanity check.

I believe in DIPY it is 50.

That said, it may be necessary to define it in terms of the number of orientations: to fit the simplest model (DTI), you need at least 6 DWIs and one low-b. So, in practical terms, an EPI sequence with 5 b=1000 and 1 b=0 is, in reality, not a DWI (this is to say, it would fit best in fmap)

Anyways, this is a bit of splitting hairs, so happy to +1 the overall effort.

[effigies]

Yeah, this is just EPI that may have b-values, not DWI, so that doesn't seem like a problem here.

@mattcieslak @tsalo Do you want to make a schema check? Or need guidance?

[tsalo]

I agree. The actual content hasn't changed since @arokem and I approved, so I think we can say that there are still three approvals.