Current state of the BEP (NOT FOR MERGING) #24
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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
In order to better disambiguate the various types of "parameters" defined, change "model parameters" to "model fit parameters".
BEP016: Adopt "model fit parameters" terminology
BEP016: Remove references to removed "pdf" data representation
Specification requests field "ModelDescription", but exemplars at end of document instead erroneously used key "Model".
DWI derivatives: Fix ModelDescription in exemplars
This commit/PR updates the bids-BEP016 repository to incorporate the changes/current state in the bids-specification repo.
synch bids-bep016 with current state of bids-specification [MISC]
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Looks like there are still a lot of unrelated things even after merging #78 in here. |
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Ok - now merged with the specification |
arokem
reviewed
Mar 14, 2023
| <pipeline_name>/ | ||
| sub-<participant_label>/ | ||
| dwi/ | ||
| <source_keywords>[_space-<space>]_model-<label>_param-<param1>_model.nii[.gz] |
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Should we change this suffix to _mfp, along the lines of the ongoing work on dimensionality reduction networks?
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I think this change was agreed on the dimensionality reduction BEP after we last discussed with @Lestropie so Rob did know. Let's change it here too. Happy to get started when I back or Peer perhaps can?
arokem
reviewed
Apr 25, 2023
| - Mapping between image volume *V* and spherical harmonic basis | ||
| function coefficient *Y<sub>l,m</sub>*: | ||
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| *V<sub>l,m</sub>* = (*l*(*l*+1) / 2) + *m* |
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@arokem needs to write this for the Descoteaux SH basis as well
Adds the descoteaux 2007 convention.
Change from strange html encoding to "<" and ">"
Fix codespell-detected British spellings.
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Updated with current master branch on the upstream fork of the spec. |
Replace the latin "etc" with ellipses.
DWI derivatives: Make tensor a data representation
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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.