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- Add download_checkpoints.py/sh to pre-download all model checkpoints for offline/portable deployment across machines and cloud - Add volume mounts in docker-compose.yml for persistent checkpoints and HF cache (avoids re-downloading on every container restart) - Make MedGemma loading optional via ENABLE_MEDGEMMA env var to support GPUs with less than 35GB VRAM- Read HF_TOKEN from environment instead of hardcoded empty string - Fix DICOM SEG export being disabled for non-reconstructable series by relaxing the is Reconstructable check in PanelSegmentation - Add .env.example, .gitattributes, and update .gitignore- Update start.sh with pre-flight checkpoint validation
- Relax isReconstructable constraint from required to optional in all 7 hanging protocol presets (MPR, 3D four up, 3D main, 3D only, 3D primary, Axial Primary, MPR + 3D Volume) - Add isPreset and icon to mprAnd3DVolumeViewport so it appears in the layout selector Advanced menu - Rename mprAnd3DVolumeViewport display name from 'mpr' to 'MPR + 3D' for clarity - Allow CT series with variable slice spacing to use MPR and 3D volume rendering layouts
- Add medsam2-anatomy Python package (TotalSegmentator priors + MedSAM2) - Add frontend UI: model selector, modality/CT-window dropdowns, anatomy text input - Add backend bridge (medsam2_anatomy_infer.py) and dispatch in basic_infer.py - Add entrypoint.sh for TotalSegmentator model pre-download and nnUNet env setup - Update Dockerfile to install medsam2-anatomy package - Update docker-compose.yml with TotalSegmentator cache volume mount - Update start.sh to create checkpoint directories on host - Fix flipped flag encoding (bool vs string) for correct Z-axis slice mapping
…d enforce full-mode mask prompts: - Add smart regional scan detection (Z-extent < 500mm) to skip doomed ROI-subset cropping on partial-body volumes, saving ~20-40s per request - Keep ROI-subset with automatic fallback for full-body scans - Enforce ts_fast=False default in medsam2_anatomy_infer.py for full-resolution 1.5mm TotalSegmentator - Add detailed per-slice and majority-vote logging for MedSAM2 segmentation diagnostics - Clean up temp directories after reading TS prior masks
…nt false timeouts on large volumes
… nginx timeouts to 600s
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