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| Repo | Input | Output | Recommended use |
|---|---|---|---|
ricklisz/FlexiCT-2D | [B, 1, 512, 512] CT slices | CLS and patch tokens | Slice-level feature extraction, classification, visualization, registration features |
ricklisz/FlexiCT-3D | [B, 1, 160, 160, 160] CT volumes | CLS and patch tokens | Whole-volume feature extraction and downstream 3D workflows |
ricklisz/FlexiCT-3D-VLM | CT volumes plus text | Image/text embeddings and similarity scores | Report-aligned retrieval and zero-shot text-image scoring |
default is recommended for whole-volume 3D and 3D-VLM inference. It orients/resamples path inputs to LPS at 2 mm spacing when spacing is available, clips HU to [-1000, 1000], z-score normalizes, pads with the tensor minimum to at least 160^3, then center crops to 160^3. This best matches the released VLM evaluation path because it preserves physical scale better than globally resizing the anatomy.local_path is a forgiving demo preset for arbitrary local CT files. It orients/resamples path inputs, clips, normalizes, pads to a cube, then trilinear-resizes to 160^3. It is robust to heterogeneous scans but less faithful to the VLM inference scripts because it globally rescales anatomy.retrieval_roi is retrieval-specific. It orients/resamples, clips, normalizes, crops an ROI cube from coordinates, a mask, or a bounding box, pads if the crop hits an image boundary, then resizes to 160^3.1@misc{li2026universalctrepresentations,
2 title = {Universal CT Representations from Anatomy to Disease Phenotype through Agglomerative Pretraining},
3 author = {Yuheng Li and Yuan Gao and Haoyu Dong and Yuxiang Lai and Shansong Wang and Mojtaba Safari and James E. Baciak and Xiaofeng Yang},
4 year = {2026},
5 eprint = {2605.21906},
6 archivePrefix = {arXiv},
7 primaryClass = {cs.CV},
8 doi = {10.48550/arXiv.2605.21906},
9 url = {https://arxiv.org/abs/2605.21906}
10}