Fix NaNs in lh_holes, rh_holes, and cc_size #92
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Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4 to 5. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](actions/upload-artifact@v4...v5) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 4 to 6. - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](actions/download-artifact@v4...v6) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 6. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v4...v6) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5 to 6. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v5...v6) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
…/upload-artifact-5 Bump actions/upload-artifact from 4 to 5
…/download-artifact-6 Bump actions/download-artifact from 4 to 6
…/checkout-6 Bump actions/checkout from 4 to 6
…/setup-python-6 Bump actions/setup-python from 5 to 6
Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 5 to 6. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](actions/upload-artifact@v5...v6) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 6 to 7. - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](actions/download-artifact@v6...v7) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
…/upload-artifact-6 Bump actions/upload-artifact from 5 to 6
…/download-artifact-7 Bump actions/download-artifact from 6 to 7
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Pull request overview
This PR addresses NaN value issues in the computation of lh_holes, rh_holes, and cc_size metrics that occurred with FastSurfer versions >= 2.3.0 due to changes in logging and output formats. The fix involves computing hole counts directly from surface mesh files rather than parsing log files, and improving the pattern matching for intracranial volume extraction.
Changes:
- Computation of hemisphere holes now uses direct mesh analysis via lapy's TriaMesh instead of log file parsing
- Corpus callosum size calculation updated with more specific pattern matching for intracranial volume and improved NaN handling
- Version bumped from 2.1.4 to 2.1.5
- GitHub Actions dependencies updated and Dependabot configuration enabled for automated dependency management
Reviewed changes
Copilot reviewed 8 out of 8 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
| fsqc/checkTopology.py | Adds direct computation of lh_holes and rh_holes from surface files using TriaMesh.euler() instead of parsing log files |
| fsqc/checkCCSize.py | Improves pattern matching for intracranial volume extraction and adds proper NaN handling when volume is missing |
| VERSION | Version bump from 2.1.4 to 2.1.5 |
| .github/workflows/publish.yml | Updates actions/checkout to v6 and actions/setup-python to v6 |
| .github/workflows/doc.yml | Updates actions to v6/v7 and configures artifact upload/download |
| .github/workflows/code-style.yml | Updates actions/checkout to v6 and actions/setup-python to v6 |
| .github/workflows/build.yml | Updates actions/checkout to v6 and actions/setup-python to v6 |
| .github/dependabot.yml | Configures Dependabot for automated GitHub Actions updates |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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This PR fixes issues in the computation of lh_holes and rh_holes as well as cc_size, which were returned as NaN for FastSurfer versions >= 2.3.0 due to logigng and output format differences.