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Improved embedding extraction in README for smoother workflow #9

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6 changes: 4 additions & 2 deletions README.md
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Expand Up @@ -84,10 +84,10 @@ To extract vision embeddings using the CT models, please refer to the example me
```bash
uv run rate-extract \
--model pillar0 \
--dataset rve_chest_ct \ # rve_abd_ct, rve_brain_ct, rve_chest_ct
--dataset rve_chest_ct \
--split train \
--batch-size 4 \
--model-repo-id YalaLab/Pillar0-ChestCT \ # YalaLab/Pillar0-AbdomenCT, YalaLab/Pillar0-BrainCT, YalaLab/Pillar0-ChestCT
--model-repo-id YalaLab/Pillar0-ChestCT \
--ct-window-type all \
--output-dir /path/to/cache \
data.train_json=/path/to/json \
Expand All @@ -101,6 +101,8 @@ uv run rate-extract \
- `train.json`: JSON file with sample metadata (e.g., `{"sample_name": "EXAMPLE_ACCESSION", "nii_path": null, "report_metadata": "FINDINGS: ..."}`)
- `manifest.csv`: CSV mapping samples to cached volumes (columns: `sample_name`, `image_cache_path`)
- Volume directories: Each volume should be in a directory with `volume.mp4` and `metadata.json`
3. **Dataset options include**: `rve_abd_ct`, `rve_brain_ct`, `rve_chest_ct`
4. **Model repo options include**: `YalaLab/Pillar0-AbdomenCT`, `YalaLab/Pillar0-BrainCT`, `YalaLab/Pillar0-ChestCT`

## Troubleshooting
### Common Issues
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