Staging BEP16 into an upstream branch #2257
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This PR splits the tractography section from the diffusion derivatives document, so that #5 is easier to merge. The new ``05-diffusion-derivatives-tractography.md`` file will remain orphaned, but kept there as a base for the time we tackle tractography. It shouldn't be merged into the derivatives branch until it is ready.
[FIX] Split out tractography
- More clarity of distinction between requisite and optional files in output directory. - Try using 3 spaces rather than 4 in non-code indentation; partly to try to get tables within dot point lists to render correctly, partly to improve editor software syntax highlighting.
- Various small re-wordings. - Slightly more use of hyperlinks. - Short introductions to "parameter terminology" and "data representations" sections. - Be more explicit about normalised vs. non-normalised 3-vectors, so that structure more clusely mimics that of description of spherical coordinate representation. - Rename hyperlink names to "parameter terminology" section to better separate from later "intrinsic / extrinsic model parameters" sections.
Based on suggestion in #5. If all model intrinsic parameters are incorporated into a single file, rather than dropping the "_parameter-<param>" field, instead enforce that parameter name "all" be used.
When introducing the file naming convention, give an example of the "_<model>" field.
Re-arranged descriptions of intrinsic and extrinsic model parameters within the file naming section, and corrected a discordance in one dot point that was using an intrinsic model parameter filename path but discussing extrinsic model parameters.
Provide information on specification of orientation data after the various models and model parameters have been explained.
[ENH] Restructuring of DWI derivatives
Revised based on MRtrix3/mrtrix3#1635. Manual merge / cherry-pick of: c6539851, 8b278282, c6539851, ebbf0d3d, d7b4731d, 99e92e0a, 6bfc7849 due to unresolvable conflict in bids-standard/bids-bep016#8.
[FIX] Formatting conformity to pass CI
Conflicts: src/05-derivatives/05-diffusion-derivatives.md
- Provide basic instructions rather than elaborating on rare use cases. - Remove JSON dictionary on preprocessing steps utilised as these relate to provenance and are therefore out of scope. Proposal for addressing bids-standard/bids-bep016#25.
…cale. This diverges from the usual recommendation to use SI units, but makes sense in this field, where values of mm^2/s are used to describe diffusivity in many different places.
I didn't use any references so the glossary links will be broken.
Add metadata fields to schema
Fix yamllint and remark warnings
arokem
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Lestropie,
erdalkaraca,
francopestilli and
oesteban
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This PR will stage work done so far on BEP16 into a branch on the upstream repo (i.e., bids-standard/bids-specification, rather than arokem/bids-specification) so that maintainers can do work on the branch (this was specifically requested by @tsalo).