Version the FreeSurfer data volume so image updates re-seed it (fixes #123)#131
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The FreeSurfer install is shared into the simnibs container via a Docker named volume. Docker only seeds a volume once (when empty), so the fixed volume name pinned the first install forever and never picked up updated freesurfer images — users who installed before the image gained the MATLAB runtime kept an MCR-less volume, breaking thalamic/hippocampal segmentation (issue #123). Version the volume name by the freesurfer image tag and make it compose-managed (not external) so compose creates and seeds it automatically. Launchers derive the name from the image tag, pass it as FREESURFER_VOLUME, and prune stale older-version volumes.
…unchers
Address review findings on the volume-versioning change:
- Non-destructive fallback (all 3 launchers): when the freesurfer image tag
cannot be parsed, get_freesurfer_volume_name()/computeFreesurferVolume() now
returns None/null instead of the bare "ti-toolbox_freesurfer_data" prefix.
Callers then leave FREESURFER_VOLUME unset (so compose's versioned
${FREESURFER_VOLUME:-ti-toolbox_freesurfer_data_v7.4.1} default seeds the
correct volume) and skip pruning. Previously a parse miss both regressed to
the never-re-seeded issue #123 and deleted the good versioned volume.
- Unmount before prune (Python loaders): run "docker compose down" before
prune_old_freesurfer_volumes() so containers from a previous (older-image)
run release the old volume and it can actually be removed. This mirrors the
Electron cleanupExistingContainers -> pruneOldVolumes ordering.
- Anchor JS regex (docker-manager.js): match /^\s*image:.../m so commented-out
"# image:" lines are skipped and only the first real image line wins,
matching the Python re.match(^\s*...) semantics.
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Problem
The FreeSurfer install is shared into the simnibs container via a Docker named volume. Docker only seeds a volume once (on first creation). With a fixed name (
ti-toolbox_freesurfer_data), pulling a newer freesurfer image never refreshed it — so users who installed before the image gained the MATLAB runtime (MCR) kept an MCR-less volume, breakingsegmentThalamicNuclei.sh/segmentHA_T1.sh(#123).Fix
ti-toolbox_freesurfer_data_v7.4.1) — bumping the image bumps the name → a fresh volume is created and re-seeded.external) sodocker compose upcreates/seeds it; a baredocker compose upworks too.FREESURFER_VOLUME, and prune stale older-version volumes (best-effort, scoped to the FreeSurfer prefix, never the current one).Consistent across all three launchers (
loader.py,dev/loader/loader_dev.py,package/src/backend/docker-manager.js) and three compose files. Seedev/freesurfer-volume-versioning.md.Notes
docker compose downkeeps the volume; onlydown -vremoves it. Existing users' old volume is pruned + re-seeded on next launch.${FREESURFER_VOLUME:-…}default in all three compose files.