[ENH] Expand fieldmaps section to include B1 maps, including qMRI maps

[tsalo]

Closes #2181. This is just a first attempt. I'm happy to hand it over to someone else if anyone's interested.

Changes proposed:

• Remove [T|R]B1map from parametric anatomical suffixes table.
• Split field map section into B0, B1+, and B1- subsections.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.71%. Comparing base (6bbd951) to head (f7b96e2).

Additional details and impacted files

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  Coverage   82.71%   82.71%           
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  Files          20       20           
  Lines        1608     1608           
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  Hits         1330     1330           
  Misses        278      278           

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[tsalo]

Pinging @effigies @Remi-Gau and @agahkarakuzu for your opinions.

[agahkarakuzu]

Thank you @tsalo looks great to me! Early on this was premature, but now it is a timely change as qMRI concepts are less unfamiliar.

[effigies]

I'm good with this. We probably need a little more text in the new sections (I haven't looked at the rendering, so feel free to refute me with a screenshot), but this makes sense to me.

[Remi-Gau]

2 things:

• this leads to duplication with sections of the qmri section: https://bids-specification--2183.org.readthedocs.build/en/2183/appendices/qmri.html#field-maps
• the qmri section has an extra table specifying what metadata is required for certain fieldmaps.

I would suggest: moving table to the main MRI page under the relevant section (@agahkarakuzu why are some lines of that table empty - can we just remove the lines?)
I would suggest that in the qmri page the field map section just says: see section foo and bar in the main MRI page.

[effigies]

I agree that moving specification details out of the appendix and into the main spec is good. qMRI is a bit of an outlier in providing additional rules inside the appendix (and they are easy to skip over while working on the schema and/or validator).

[tsalo]

I tried to move the fieldmap-related information out of the appendix. I think it looks fairly good.

One thing I just realized I don't know- is any metadata used to link B1 fieldmaps to specific scans? The sections on IntendedFor and B0FieldIdentifier (we'd want a B1FieldIdentifier I'm guessing) are nested under the B0 fieldmap section, and I don't know if I should move them.

[effigies]

One thing I just realized I don't know- is any metadata used to link B1 fieldmaps to specific scans? The sections on IntendedFor and B0FieldIdentifier (we'd want a B1FieldIdentifier I'm guessing) are nested under the B0 fieldmap section, and I don't know if I should move them.

Adding something now requires getting it right, so I would only do it if we're absolutely sure. We can clarify in the future.

Instinctively, I'd say that we want to put a Fieldmap metadata section above the B0/B1 sections where we outline IntendedFor and B[0|1]FieldIdentifier. The main thing I'd worry about getting wrong is whether B1FieldIdentifier is sufficient, or if B1PlusIdentifier and B1MinusIdentifier would be needed.

[effigies]

Yeah, looks like we need https://mrkeo.github.io/reference/mathjax/. I think it might be good to do, but out of scope for this PR. Will open an issue.

[effigies]

@Remi-Gau @bthirion does this address your concerns at this point?

https://bids-specification--2183.org.readthedocs.build/en/2183/modality-specific-files/magnetic-resonance-imaging-data.html#radiofrequency-rf-field-mapping

[bthirion]

LGTM AFAICT

[Remi-Gau]

Good with me.
thanks @tsalo that's much better that anything I could have done!

[tsalo]

This just reorganizes the documentation really, so @effigies do you think it merits a 5 day waiting period or should I just merge now?

[effigies]

Let's merge.