Add older processing scripts to clarify provenance of PAM50 atlas files #47
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This should be everything that's needed to run the script. :)
Previously it was too difficult to tell what part of the script you were in (since it takes a long time, it's important to know what steps we're on).
These files probably shouldn't be committed to the PAM50 repo, but I'm adding them to this branch just to make reproduction easier for anyone else checking out my branch.
Making it more discoverable -- though this doesn't fully document the exact procedures used. Instead, the CHANGES.md file should be used for this purpose.
jcohenadad
approved these changes
Sep 4, 2025
This reverts commit 4b85d81.
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Description
Prior to my investigation in #32 (comment), it was unclear which scripts were used to generate the WM atlas files.
This PR adds what I believe to be the necessary files (though there are multiple "atlas creation scripts" so I may have the wrong one). This PR also adds links to the README pointing to the archival locations of the scripts.
We can use this as a baseline for further re-generation of the atlas (e.g. for #41).
Discussion
We can probably safely drop commit 4b85d81 from this PR, since we don't really want to commit unnecessary binary files to the repo, and the files are also backed up in the
spinalcordtoolboxrepo (and linked to in the "Depencencies" section of thecreate_atlas.mscript).But, I wanted to add them initially just for ease of access...
Related Issues/PRs
Fixes #46.
Part of #32.