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Clarify output labels and training mixture

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Explain aggregate spine annotations without presenting them as checkpoint channels, and direct readers to the paper for training mixture proportions.

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  1. README.md +13 -14
README.md CHANGED
@@ -141,11 +141,11 @@ resample back to the original image size.
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  ## Output labels
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- 61 channels: `background` at index 0, then 60 anatomical structures in the
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- order stored in `label_schema.json`. The training protocol
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- (`all_structures_flexray_v4`) has 62 foreground labels; its two coarse region
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- labels, `lumbar_spine` and `thoracolumbar_spine`, only harmonize datasets that
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- label those regions as a block and are not predicted.
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  - **Skull / shoulder girdle:** skull, scapulae, clavicles
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  - **Upper limb:** humeri, radii, ulnae, carpals, metacarpals, phalanges
@@ -168,17 +168,16 @@ architecture is in `config.yml`.
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  ## Training data
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  The model was trained on three source types unified under the FleXray label
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- protocol (mixing proportions in parentheses):
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- - **Real X-ray masks:** HandBones (0.01), FootBones (0.01), MURA forearm
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- (0.01) and MURA humerus (0.01) with our own annotations.
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- - **Generated FluXray images (0.375):** digitally reconstructed radiographs from
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- the MOOSE CTs, generatively edited toward real X-ray appearance, with exact
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  overlapping masks for every protocol structure.
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- - **Online CT->DRR rendering:** MOOSE / ENHANCE-PET 1.6k (0.375), Shoulder-CT
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- (0.05), HaN-Seg (0.05), PedsCT (0.04), RSNA cervical-spine fracture CTs
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- (0.04), and ElbowCT (0.03), rendered to DRRs at random poses during training
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- with per-label attenuation jitter.
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  Training used AdamW (lr 3e-4, cosine schedule), a Dice + binary cross-entropy
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  loss routed per dataset (partially labeled sources ignore unlabeled channels),
 
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  ## Output labels
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+ FleXray outputs 60 foreground masks (61 channels including `background`). The
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+ broader dataset/evaluation protocol also recognizes aggregate `lumbar_spine` and
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+ `thoracolumbar_spine` annotations; these are evaluated by combining the relevant
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+ per-vertebra outputs and are not checkpoint channels. Channel order is stored in
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+ `label_schema.json`.
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  - **Skull / shoulder girdle:** skull, scapulae, clavicles
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  - **Upper limb:** humeri, radii, ulnae, carpals, metacarpals, phalanges
 
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  ## Training data
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  The model was trained on three source types unified under the FleXray label
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+ protocol. For training mixture proportions, please refer to the paper:
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+ - **Real X-ray masks:** HandBones, FootBones, MURA forearm, and MURA humerus,
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+ with our own annotations.
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+ - **Generated FluXray images:** digitally reconstructed radiographs from the
176
+ MOOSE CTs, generatively edited toward real X-ray appearance, with exact
177
  overlapping masks for every protocol structure.
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+ - **Online CT->DRR rendering:** MOOSE / ENHANCE-PET 1.6k, Shoulder-CT, HaN-Seg,
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+ PedsCT, RSNA cervical-spine fracture CTs, and ElbowCT, rendered to DRRs at
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+ random poses during training with per-label attenuation jitter.
 
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  Training used AdamW (lr 3e-4, cosine schedule), a Dice + binary cross-entropy
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  loss routed per dataset (partially labeled sources ignore unlabeled channels),