Update freesurfer #4
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GitHK
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GitHK
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looks OK, just remove the todo's if you are done with them. Don't keep them in the code, open an issue
| <!-- TODO'S | ||
| - DONE fix build process | ||
| - bump version to 2.2.0 after bump in FreeSurfer + make sure pipeline Fariba runs end to end | ||
| - add version details in the README | ||
| - add badges | ||
| - then keep going through modernization plan (reduce image size, build time etc); add these learning to my Obsidian notes | ||
| - in future, download FreeSurfer 8.1.0 .deb and put in filesrv and fetch from there (like in ASCENT service) so we can have the latest version without increasing build time | ||
| --> |
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Please address this TODO and remove it
|
Im not done with them, that is why I kept them. But was prioritizing making the CI green, will tackle those in a subsequent PR |
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Pull request overview
This PR updates the FreeSurfer installation to version 7.4.1 and modernizes the Docker build process by implementing a multi-stage build that copies FreeSurfer from its official Docker image instead of downloading from slow FTP servers. Additionally, it adds version pinning for Python dependencies and improves build efficiency with a new .dockerignore file.
Key Changes:
- Upgraded FreeSurfer from version 6.0.0 to 7.4.1 using multi-stage Docker build
- Pinned all Python package versions in
requirements.inwith release dates for reproducibility - Added comprehensive
.dockerignorefile to optimize Docker build context
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 4 comments.
| File | Description |
|---|---|
| Dockerfile | Implements multi-stage build to copy FreeSurfer 7.4.1 from official image; updates Qt5 dependencies; improves wxPython installation process |
| requirements.in | Adds version pins for all packages (nibabel, pyvista, PyOpenGL, fsleyes, etc.) with release date comments |
| README.md | Documents FreeSurfer version 7.4.1; adds TODO comments for future work; comments out Spinal Cord Toolbox reference |
| .dockerignore | New file excluding Git files, documentation, test data, and build artifacts from Docker context |
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Co-authored-by: Copilot <[email protected]>
…/jupyter-medimproc into update-freesurfer
pcrespov
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pcrespov
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Not sure why am i owner of a repo I never saw before :-)
At first sight, it LGTM
thx
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