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Bumps [actions/setup-python](https://github.com/actions/setup-python) from 6 to 7. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v6...v7) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
Wrap the mesh/profile/hull rendering calls in qcPlots() in try/except so a rendering backend failure (e.g. kaleido 1.x requiring Chrome) logs a warning and skips that image instead of aborting a successful surface reconstruction run. Fixes #24
…radation Gracefully degrade QC plot rendering failures
kaleido>=1.0 dropped its bundled Chromium and now requires an external Chrome/Chromium binary to render QC plots, which the Docker image did not provide (Kaleido requires Google Chrome to be installed). Install Chrome via plotly_get_chrome into a fixed, world-readable location and point to it via BROWSER_PATH, since the image is meant to be run with an arbitrary --user; also default HOME to a writable directory, since Chrome needs a writable profile/user-data directory. Verified by building the image from this Dockerfile and running the full pipeline (mesh/profile/hull QC stages) both as root and as an arbitrary non-root --user, producing valid PNGs in all three cases with no warnings. Refs #24
Segmentations at ~1 mm rather than the ~0.33 mm this method is designed for fail checkSurface with "Surface contains holes", which sends users toward manual editing even though the segmentation is usually fine. The mask filters are parameterised in voxels, not mm, so their physical strength scales with the input voxel size. - Warn at startup when the input voxel edge length exceeds a threshold, and for --lut freesurfer additionally point out the .FSvoxelSpace. variant, which is the common way to hit this. - Add the voxel size to the "Surface contains holes" message when the input is coarse, so the error itself suggests checking the resolution before editing the segmentation. - Log when --upsample is a no-op, which it silently is for isotropic input, since reaching for it is the natural response to the error. - Document the two FreeSurfer output files and the resolution dependency in the tutorial and documentation. Refs #25
Per review feedback, split the single voxel-size warning into two independent checks: coarseness (min voxel edge > threshold, expect failures regardless of --upsample) and anisotropy (voxels unequal, --upsample recommended). checkSurface's gate is updated to match the coarseness definition (min-based instead of max-based).
Warn about coarse input voxel size and clarify resolution requirements
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