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docs: Add guide for updating Rica without rerunning tedana#111

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eurunuela merged 2 commits intoME-ICA:masterfrom
eurunuela:docs/update-open-rica-report
Mar 3, 2026
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docs: Add guide for updating Rica without rerunning tedana#111
eurunuela merged 2 commits intoME-ICA:masterfrom
eurunuela:docs/update-open-rica-report

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@eurunuela eurunuela commented Mar 3, 2026

Summary

  • Adds docs/updating-rica.md: a dedicated guide explaining how to update the open_rica_report.py that tedana generates without having to rerun tedana
  • Adds a concise "Updating Rica Without Rerunning Tedana" section to README.md with links to the full guide
  • Registers the new page in mkdocs.yml so it appears in the documentation site navigation

What the guide covers

  • Why you might want to update Rica independently (tedana runs are expensive; Rica releases bug fixes and new features separately)
  • The simplest path: using the always-up-to-date online app
  • Step-by-step: downloading the latest index.html + rica_server.py from a release and dropping them into an existing tedana output folder
  • What open_rica_report.py does and why rica_server.py is a drop-in replacement
  • Bulk-update recipe for multiple tedana output directories
  • Troubleshooting (port conflicts, missing files)

Test plan

  • Verify the new docs page renders correctly with MkDocs (mkdocs serve)
  • Confirm the README section links resolve correctly
  • Check that the new page appears in the site nav under "Updating Rica"

🤖 Generated with Claude Code

Copilot AI review requested due to automatic review settings March 3, 2026 16:36
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Pull request overview

This PR adds documentation for updating Rica independently of tedana runs, and also introduces runtime changes to improve large-NIfTI handling and local-server file discovery.

Changes:

  • Add a new MkDocs page plus README section describing how to update index.html/rica_server.py in existing tedana outputs.
  • Update the app to optionally load NIfTI data via URL (including extracting TR from a small header slice / HTTP Range request) to better support very large files.
  • Update rica_server.py file discovery patterns/filters (including registry.json) to improve auto-discovery from tedana output directories.

Reviewed changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 4 comments.

Show a summary per file
File Description
src/utils/niftiUtils.js Adjust gzip header decompression flow to avoid deadlock with large inputs.
src/index.js Add niftiUrl state and plumb it into major tabs.
src/Tree/DecisionTreeTab.js Pass niftiUrl through to the Decision Tree view.
src/Tree/DecisionTree.js Gate BrainViewer rendering based on NIfTI buffer-or-URL availability.
src/PopUps/IntroPopUp.js Extract TR from header slice/Range request; set niftiUrl and attempt full buffer load with fallback.
src/Plots/Plots.js Update interactive view gating and pass niftiUrl to BrainViewer.
src/Plots/BrainViewer.js Support loading the stat map from URL (prefer URL over Blob) and update cleanup logic.
scripts/rica_server.py Add registry.json and refine _components.nii.gz discovery filtering.
mkdocs.yml Register the new “Updating Rica” page in site navigation.
docs/updating-rica.md Add a new guide page describing how to update Rica without rerunning tedana.
README.md Add a concise “Updating Rica Without Rerunning Tedana” section linking to the full guide.
claude-progress.txt Add session notes documenting the changes made.

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eurunuela and others added 2 commits March 3, 2026 09:45
Add a new documentation page (docs/updating-rica.md) and a README
section explaining how users can update the open_rica_report.py that
tedana generates by replacing it with the latest index.html and
rica_server.py from a Rica release.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
The script already auto-downloads the latest Rica from GitHub on every
run. Update the docs and README to reflect the real workflow:
- Just running the script is enough to get the latest version
- --force-download bypasses the cache check
- TEDANA_RICA_PATH env var pins a local/custom build
- Falls back to cache automatically when offline

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@eurunuela eurunuela force-pushed the docs/update-open-rica-report branch from fd2bcb4 to 933833f Compare March 3, 2026 16:45
@eurunuela eurunuela merged commit b282a9a into ME-ICA:master Mar 3, 2026
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2 participants