diff --git a/README.md b/README.md index 434333f..8abf129 100644 --- a/README.md +++ b/README.md @@ -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 \ @@ -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