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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
[FIX] Formatting conformity to pass CI
Conflicts: src/05-derivatives/05-diffusion-derivatives.md
…ructure-f2d4b981e8
…actions-infrastructure-f2d4b981e8 chore(deps): bump the actions-infrastructure group across 1 directory with 5 updates
Conflicts: src/derivatives/05-diffusion-derivatives.md
Use of "order" has been adopted across the documentation.
- Rename exemplar data and metadata files encoding the FSL bedpostx ball-and-sticks model from "_model-bs" to "_model-ballsticks" to avoid negative acronym connotation. - Rename permissble value for "Reference" metadata from "bvec" to "fsl": this axis reference convention is not specific to the "bvec" file format but is a convention utilised throughout the FSL software.
New appendix page: spherical harmonics
Conflicts: src/derivatives/05-diffusion-derivatives.md
BEP016: Renaming relevant to FSL
Bumps the actions-infrastructure group with 2 updates: [actions/upload-artifact](https://github.com/actions/upload-artifact) and [actions/download-artifact](https://github.com/actions/download-artifact). Updates `actions/upload-artifact` from 5 to 7 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](actions/upload-artifact@v5...v7) Updates `actions/download-artifact` from 6 to 8 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](actions/download-artifact@v6...v8) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions-infrastructure - dependency-name: actions/download-artifact dependency-version: '8' dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions-infrastructure ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 5 to 6. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v5...v6) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [tabulate](https://github.com/astanin/python-tabulate) from 0.9.0 to 0.10.0. - [Changelog](https://github.com/astanin/python-tabulate/blob/master/CHANGELOG) - [Commits](astanin/python-tabulate@v0.9.0...v0.10.0) --- updated-dependencies: - dependency-name: tabulate dependency-version: 0.10.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [pymdown-extensions](https://github.com/facelessuser/pymdown-extensions) from 10.15 to 10.21.3. - [Release notes](https://github.com/facelessuser/pymdown-extensions/releases) - [Commits](facelessuser/pymdown-extensions@10.15...10.21.3) --- updated-dependencies: - dependency-name: pymdown-extensions dependency-version: 10.21.3 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [myst-parser](https://github.com/executablebooks/MyST-Parser) from 4.0.1 to 5.1.0. - [Release notes](https://github.com/executablebooks/MyST-Parser/releases) - [Changelog](https://github.com/executablebooks/MyST-Parser/blob/master/CHANGELOG.md) - [Commits](executablebooks/MyST-Parser@v4.0.1...v5.1.0) --- updated-dependencies: - dependency-name: myst-parser dependency-version: 5.1.0 dependency-type: direct:development update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [sphinx](https://github.com/sphinx-doc/sphinx) from 8.2.3 to 9.0.4. - [Release notes](https://github.com/sphinx-doc/sphinx/releases) - [Changelog](https://github.com/sphinx-doc/sphinx/blob/v9.0.4/CHANGES.rst) - [Commits](sphinx-doc/sphinx@v8.2.3...v9.0.4) --- updated-dependencies: - dependency-name: sphinx dependency-version: 9.0.4 dependency-type: direct:development update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [myst-nb](https://github.com/executablebooks/myst-nb) from 1.2.0 to 1.4.0. - [Release notes](https://github.com/executablebooks/myst-nb/releases) - [Changelog](https://github.com/executablebooks/MyST-NB/blob/main/CHANGELOG.md) - [Commits](executablebooks/MyST-NB@v1.2.0...v1.4.0) --- updated-dependencies: - dependency-name: myst-nb dependency-version: 1.4.0 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.5.1 to 6.5.6. - [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst) - [Commits](tornadoweb/tornado@v6.5.1...v6.5.6) --- updated-dependencies: - dependency-name: tornado dependency-version: 6.5.6 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com>
chore(deps): bump tornado from 6.5.1 to 6.5.6
…actions-infrastructure-985357984d chore(deps): bump the actions-infrastructure group with 2 updates
…codecov/codecov-action-6 chore(deps): bump codecov/codecov-action from 5 to 6
chore(deps): bump tabulate from 0.9.0 to 0.10.0
Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.5.6 to 6.5.7. - [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst) - [Commits](tornadoweb/tornado@v6.5.6...v6.5.7) --- updated-dependencies: - dependency-name: tornado dependency-version: 6.5.7 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com>
--- updated-dependencies: - dependency-name: aiohttp dependency-version: 3.14.1 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com>
…nsions-10.21.3 chore(deps): bump pymdown-extensions from 10.15 to 10.21.3
…5.1.0 chore(deps-dev): bump myst-parser from 4.0.1 to 5.1.0
chore(deps-dev): bump sphinx from 8.2.3 to 9.0.4
chore(deps-dev): bump myst-nb from 1.2.0 to 1.4.0
chore(deps): bump tornado from 6.5.6 to 6.5.7
chore(deps): bump aiohttp from 3.12.13 to 3.14.1
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This is a replacement of #6 as the BEP is being reinvested in.
The PR is not for merging, but to show the current state of the difference between the BEP and an up-to-date
masterof the BIDS specification.