Publish MRI staging images, prompts and labels

L3/extensions/N400/labels.jsonl

@@ -0,0 +1,400 @@
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+{"id": "L3-N400:mri-3255ceeb81f2447b", "n_stage": "N2"}
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+{"id": "L3-N400:mri-0e5e20c106254524", "n_stage": "N2"}
+{"id": "L3-N400:mri-4f6375babb14457d", "n_stage": "N2"}
+{"id": "L3-N400:mri-a2fb4a2a35834f6b", "n_stage": "N2"}
+{"id": "L3-N400:mri-743e318975d34ab9", "n_stage": "N2"}
+{"id": "L3-N400:mri-d2f33f081de9485f", "n_stage": "N2"}
+{"id": "L3-N400:mri-d62f919d528d4002", "n_stage": "N2"}
+{"id": "L3-N400:mri-a49f8b2de31e4f3a", "n_stage": "N2"}
+{"id": "L3-N400:mri-534f8cc8355f4b49", "n_stage": "N2"}
+{"id": "L3-N400:mri-de3729bafb634685", "n_stage": "N2"}
+{"id": "L3-N400:mri-a1408824124e4e13", "n_stage": "N2"}
+{"id": "L3-N400:mri-ee815a539e0a41f6", "n_stage": "N2"}
+{"id": "L3-N400:mri-bce9936c6c004bc7", "n_stage": "N2"}
+{"id": "L3-N400:mri-99d8f740d58747e8", "n_stage": "N2"}
+{"id": "L3-N400:mri-be9e453a7d484349", "n_stage": "N2"}
+{"id": "L3-N400:mri-41c41f6198cc49e8", "n_stage": "N2"}
+{"id": "L3-N400:mri-919e6d91ce834876", "n_stage": "N2"}
+{"id": "L3-N400:mri-214ad00d5e494005", "n_stage": "N2"}
+{"id": "L3-N400:mri-8224cee299ff41d9", "n_stage": "N2"}
+{"id": "L3-N400:mri-9fecab65c6a54c7f", "n_stage": "N2"}
+{"id": "L3-N400:mri-3c1c01838aba4d80", "n_stage": "N2"}
+{"id": "L3-N400:mri-a7eda23cfc734574", "n_stage": "N2"}
+{"id": "L3-N400:mri-ad37d9b346ea4372", "n_stage": "N2"}
+{"id": "L3-N400:mri-e065dcd53a574e90", "n_stage": "N2"}
+{"id": "L3-N400:mri-5414e3c1351c41ec", "n_stage": "N2"}
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+{"id": "L3-N400:mri-7ff33360bf9c416e", "n_stage": "N2"}
+{"id": "L3-N400:mri-c8ccf7492e4f4f2e", "n_stage": "N2"}
+{"id": "L3-N400:mri-617eea39b01a469d", "n_stage": "N2"}
+{"id": "L3-N400:mri-33324e3410034be6", "n_stage": "N2"}
+{"id": "L3-N400:mri-f9118aa8c8fc4f14", "n_stage": "N2"}
+{"id": "L3-N400:mri-d13ed00ac1c842a3", "n_stage": "N2"}
+{"id": "L3-N400:mri-b534ccfdf29b4f7f", "n_stage": "N2"}
+{"id": "L3-N400:mri-f31877fce1334a6f", "n_stage": "N2"}
+{"id": "L3-N400:mri-0b1062e25528452c", "n_stage": "N2"}
+{"id": "L3-N400:mri-6fb2ca10cb6d468d", "n_stage": "N2"}
+{"id": "L3-N400:mri-e5add086c60e44b3", "n_stage": "N2"}
+{"id": "L3-N400:mri-6dc39018ed90416a", "n_stage": "N2"}
+{"id": "L3-N400:mri-00f13b7337e14932", "n_stage": "N2"}
+{"id": "L3-N400:mri-3cc5920871d24a0f", "n_stage": "N2"}
+{"id": "L3-N400:mri-2a7a5d213a574d06", "n_stage": "N2"}
+{"id": "L3-N400:mri-dc5a195c5dcb40c6", "n_stage": "N2"}
+{"id": "L3-N400:mri-9dc9775b8ed746bf", "n_stage": "N2"}
+{"id": "L3-N400:mri-a9d8d6118f81483d", "n_stage": "N2"}
+{"id": "L3-N400:mri-454ed46837944685", "n_stage": "N2"}
+{"id": "L3-N400:mri-988fe99eac654d20", "n_stage": "N2"}
+{"id": "L3-N400:mri-ec77ee5162684942", "n_stage": "N2"}
+{"id": "L3-N400:mri-45357ae7789740bd", "n_stage": "N2"}
+{"id": "L3-N400:mri-ff2c5fb485424315", "n_stage": "N2"}
+{"id": "L3-N400:mri-9d4dd892ed8d4416", "n_stage": "N2"}
+{"id": "L3-N400:mri-ef0347f0fc6e4aee", "n_stage": "N2"}
+{"id": "L3-N400:mri-b530bf9cb3cf4a5d", "n_stage": "N2"}
+{"id": "L3-N400:mri-14b883dc27254eac", "n_stage": "N2"}
+{"id": "L3-N400:mri-936bf64e3b2b446f", "n_stage": "N2"}
+{"id": "L3-N400:mri-29c63d153863406f", "n_stage": "N2"}
+{"id": "L3-N400:mri-5baeff97757d498b", "n_stage": "N3"}
+{"id": "L3-N400:mri-3da8511cbf0b41ef", "n_stage": "N3"}
+{"id": "L3-N400:mri-1dcfc4c301ec452b", "n_stage": "N3"}
+{"id": "L3-N400:mri-23c28bac08644593", "n_stage": "N3"}
+{"id": "L3-N400:mri-acf3634094c54c18", "n_stage": "N3"}
+{"id": "L3-N400:mri-e49896e15a4347f0", "n_stage": "N3"}
+{"id": "L3-N400:mri-ec7e021964b4495b", "n_stage": "N3"}
+{"id": "L3-N400:mri-89cfcee7f93e4a8b", "n_stage": "N3"}
+{"id": "L3-N400:mri-3a4d41d4a3054dae", "n_stage": "N3"}
+{"id": "L3-N400:mri-f0bb6ee344d54ac1", "n_stage": "N3"}
+{"id": "L3-N400:mri-e5c52483f45542c7", "n_stage": "N3"}
+{"id": "L3-N400:mri-499e80ae2b0e46a3", "n_stage": "N3"}
+{"id": "L3-N400:mri-5c36d293b52c4ee2", "n_stage": "N3"}
+{"id": "L3-N400:mri-db301548e56f4e7e", "n_stage": "N3"}
+{"id": "L3-N400:mri-e5b2997898b04824", "n_stage": "N3"}
+{"id": "L3-N400:mri-48c844b14f5549ab", "n_stage": "N3"}
+{"id": "L3-N400:mri-11fcc29e174f48bf", "n_stage": "N3"}
+{"id": "L3-N400:mri-57ddacfab99f4080", "n_stage": "N3"}
+{"id": "L3-N400:mri-49d003d2f76d4d6c", "n_stage": "N3"}
+{"id": "L3-N400:mri-258f53dd6b954ff9", "n_stage": "N3"}
+{"id": "L3-N400:mri-3fecd97676864a16", "n_stage": "N3"}
+{"id": "L3-N400:mri-ba2fd623c6f9437a", "n_stage": "N3"}
+{"id": "L3-N400:mri-11927c9335f045b9", "n_stage": "N3"}
+{"id": "L3-N400:mri-0eec12e9c67541db", "n_stage": "N3"}
+{"id": "L3-N400:mri-10283ca6c2444a09", "n_stage": "N3"}
+{"id": "L3-N400:mri-1af0354f3c124a94", "n_stage": "N3"}
+{"id": "L3-N400:mri-bac19540f0754074", "n_stage": "N3"}
+{"id": "L3-N400:mri-a1fca0b294444a90", "n_stage": "N3"}
+{"id": "L3-N400:mri-372cbb7b83a24a8f", "n_stage": "N3"}
+{"id": "L3-N400:mri-efdec9c8d79c4678", "n_stage": "N3"}
+{"id": "L3-N400:mri-849fd71001c94ff8", "n_stage": "N3"}
+{"id": "L3-N400:mri-9e9c2a077a2342d0", "n_stage": "N3"}
+{"id": "L3-N400:mri-bd55e9f814684eed", "n_stage": "N3"}
+{"id": "L3-N400:mri-029220f4ef254c02", "n_stage": "N3"}
+{"id": "L3-N400:mri-528138d89c174c27", "n_stage": "N3"}
+{"id": "L3-N400:mri-52946a7db8fb4e36", "n_stage": "N3"}
+{"id": "L3-N400:mri-4d26bfb29f824a9d", "n_stage": "N3"}
+{"id": "L3-N400:mri-96b2dc1591614228", "n_stage": "N3"}
+{"id": "L3-N400:mri-732bdb409afd4ce6", "n_stage": "N3"}
+{"id": "L3-N400:mri-14ec0eb189d44d55", "n_stage": "N3"}
+{"id": "L3-N400:mri-4ff5c58f003c4523", "n_stage": "N3"}
+{"id": "L3-N400:mri-38062c15dbe74729", "n_stage": "N3"}
+{"id": "L3-N400:mri-445f745cac264aaa", "n_stage": "N3"}
+{"id": "L3-N400:mri-48630004d8dd4f52", "n_stage": "N3"}
+{"id": "L3-N400:mri-315bc8f8912b4f66", "n_stage": "N3"}
+{"id": "L3-N400:mri-7ddc879e7cdf4ad4", "n_stage": "N3"}
+{"id": "L3-N400:mri-0f81d3b1e90c4fa9", "n_stage": "N3"}
+{"id": "L3-N400:mri-820d6370fe604b87", "n_stage": "N3"}
+{"id": "L3-N400:mri-97796b3c7edd420c", "n_stage": "N3"}
+{"id": "L3-N400:mri-2be0a9325162419a", "n_stage": "N3"}
+{"id": "L3-N400:mri-f55583b958f042d1", "n_stage": "N3"}
+{"id": "L3-N400:mri-96568525a2b14fe6", "n_stage": "N3"}
+{"id": "L3-N400:mri-54d674a472bc433c", "n_stage": "N3"}
+{"id": "L3-N400:mri-9468961926634fdd", "n_stage": "N3"}
+{"id": "L3-N400:mri-58cf64ac1d2440de", "n_stage": "N3"}
+{"id": "L3-N400:mri-ee8be7ba49ae4b0e", "n_stage": "N3"}
+{"id": "L3-N400:mri-eb6e8835c88f4bd7", "n_stage": "N3"}
+{"id": "L3-N400:mri-737cb6258c5046ed", "n_stage": "N3"}
+{"id": "L3-N400:mri-33030b0efc2f46c1", "n_stage": "N3"}
+{"id": "L3-N400:mri-a185a2e383804c0e", "n_stage": "N3"}
+{"id": "L3-N400:mri-cb9b5f7a135f4bd2", "n_stage": "N3"}
+{"id": "L3-N400:mri-cf85e43636134247", "n_stage": "N3"}
+{"id": "L3-N400:mri-fce3d9661b564100", "n_stage": "N3"}
+{"id": "L3-N400:mri-979b8558f54a454a", "n_stage": "N3"}
+{"id": "L3-N400:mri-b75a98b53b78430b", "n_stage": "N3"}
+{"id": "L3-N400:mri-2851eee410e141de", "n_stage": "N3"}
+{"id": "L3-N400:mri-90703c29e9484056", "n_stage": "N3"}
+{"id": "L3-N400:mri-56491de3aa6d4b24", "n_stage": "N3"}
+{"id": "L3-N400:mri-58f0bb032a164706", "n_stage": "N3"}
+{"id": "L3-N400:mri-8839afbd6e0d4aab", "n_stage": "N3"}
+{"id": "L3-N400:mri-aac5d0ef07ee44e1", "n_stage": "N3"}
+{"id": "L3-N400:mri-a742ee67f3b2440c", "n_stage": "N3"}
+{"id": "L3-N400:mri-b193700652bb4abf", "n_stage": "N3"}
+{"id": "L3-N400:mri-16cb459d984242b3", "n_stage": "N3"}
+{"id": "L3-N400:mri-fb8f9aac4af7446f", "n_stage": "N3"}
+{"id": "L3-N400:mri-0b9e6c5f475f4363", "n_stage": "N3"}
+{"id": "L3-N400:mri-64db89bf3cbe4fb6", "n_stage": "N3"}
+{"id": "L3-N400:mri-36dfc5d473c34e37", "n_stage": "N3"}
+{"id": "L3-N400:mri-a523ca589f684931", "n_stage": "N3"}
+{"id": "L3-N400:mri-93377512d50c4ef4", "n_stage": "N3"}

L3/extensions/README.md

@@ -1,26 +1,23 @@
-# T300 and N400 MRI extension
-
-| Cohort | Cases | Reference-stage distribution |
-|---|---:|---|
-| T300 | 300 | T1: 35; T2: 35; T3: 115; T4: 115 |
-| N400 | 400 | N0: 80; N1: 160; N2: 80; N3: 80 |
-
-Both use AJCC/UICC edition 8 and explicitly documented cM0. T300 extends the
-original T100; N400 is patient-disjoint from their combined T400 cohort. Original
-T100 includes patients with cM1 or unspecified M status, so combined T400 is not
-an all-M0 cohort. Original T100 results retain their original visual condition.
-
-The extension uses five sequences: axial T1, axial T2, axial enhanced T1,
-coronal enhanced fat-suppressed T1, and coronal precontrast non-fat-suppressed T1.
-Matched axial and coronal planes form separate ordered image groups, jointly
-supplied in each model request. A clinical display tile is 512 × 512 pixels.
-
-Target axial coverage is suprasellar cistern to inferior C3 for T staging and
-skull base to inferior sternoclavicular joint for N staging. The reviewed example
-bounds are confirmed; patient-specific boundary review is not complete across
-the extension. Image OCR screening is complete, with findings adjudication and
-visual review still open. Consequently this directory currently contains the
-cohort description only, not the 700-case image download or a final score table.
-
-See the [evaluation guide](https://github.com/pidneuralode/NPCBench/blob/main/docs/mri_extension.md)
-for the actual model-specific context, image encoding and sampling conditions.
+# MRI sequence-group data
+
+This directory contains the group-format inputs for 300 T-stage and 400 N-stage patients. Together with the 100-patient structure-card panel in `L3/primary_l3_inputs/`, these form T400 and N400. Both tasks use AJCC/UICC edition 8; the T and N cohorts are patient-disjoint.
+
+## Files
+
+- `images-01.tar` through `images-07.tar`: seven 100-case image shards, containing 45,829 lossless PNG groups.
+- `requests.jsonl`: prompts and ordered image paths for all 700 patients.
+- `requests_gpt41.jsonl`: at most 50 groups per case, sampled within the axial/coronal groups with both endpoints retained.
+- `requests_internvl.jsonl`: the groups selected for the model's 40,960-token context.
+- `T300/labels.jsonl`, `N400/labels.jsonl`: report-derived reference stages.
+
+Extract every shard into this directory. Image paths in these request files are relative to this directory. The complete T400 and N400 labels are one level above, in `L3/T400.jsonl` and `L3/N400.jsonl`.
+
+## Layout and coverage
+
+Axial groups stack T1, T2 and enhanced T1 from the same physical plane. Coronal groups stack enhanced fat-suppressed T1 and precontrast non-fat-suppressed T1. Each clinical display tile is 512×512 pixels. Group dimensions are 512×1644 and 512×1096 pixels, including sequence labels.
+
+T coverage runs from the suprasellar cistern to inferior C3; N coverage extends from the skull base to the inferior sternoclavicular joint. The study team reviewed the anatomical bounds. All selected images for a patient enter one model request. Model-specific sampling, tiling and spatial merging are documented in the [evaluation code](https://github.com/pidneuralode/NPCBench/blob/main/docs/mri_extension.md).
+
+The 300 group-format T cases and all 400 N cases have explicit clinical M0 status. The combined T400 set includes 374 M0, 14 M1 and 12 cases with unspecified M status. T and N labels are reference labels for their own tasks; the T300 set does not provide independent structure-invasion annotations.
+
+Images are rendered derivatives without DICOM headers or patient-identity maps. The files contain anonymous case IDs and sequence labels. Clinical pixels are retained.

L3/extensions/T300/labels.jsonl

@@ -0,0 +1,300 @@
+{"id": "L3-T300:mri-d4c892f0b7e3423f", "t_stage": "T1"}
+{"id": "L3-T300:mri-1a77d0c1afdc43b7", "t_stage": "T1"}
+{"id": "L3-T300:mri-e75b60d1d083428e", "t_stage": "T1"}
+{"id": "L3-T300:mri-e3d8eb4d531d4fcf", "t_stage": "T1"}
+{"id": "L3-T300:mri-76a6988d1e084bab", "t_stage": "T1"}
+{"id": "L3-T300:mri-492555690ebc4338", "t_stage": "T1"}
+{"id": "L3-T300:mri-6075270c70db4d72", "t_stage": "T1"}
+{"id": "L3-T300:mri-a822794800b24433", "t_stage": "T1"}
+{"id": "L3-T300:mri-524c6754989f4a43", "t_stage": "T1"}
+{"id": "L3-T300:mri-43a46f6923804318", "t_stage": "T1"}
+{"id": "L3-T300:mri-0f97d76a51a040a4", "t_stage": "T1"}
+{"id": "L3-T300:mri-4eff6559f14148d5", "t_stage": "T1"}
+{"id": "L3-T300:mri-7cb304a3ddd04efa", "t_stage": "T1"}
+{"id": "L3-T300:mri-d2d9da67055048e2", "t_stage": "T1"}
+{"id": "L3-T300:mri-c4103868bea44f56", "t_stage": "T1"}
+{"id": "L3-T300:mri-a3351c647eb34a73", "t_stage": "T1"}
+{"id": "L3-T300:mri-91686de02cb64fc2", "t_stage": "T1"}
+{"id": "L3-T300:mri-93a27965e6ad4525", "t_stage": "T1"}
+{"id": "L3-T300:mri-02211a5df28b41c8", "t_stage": "T1"}
+{"id": "L3-T300:mri-aafde48fd76947e0", "t_stage": "T1"}
+{"id": "L3-T300:mri-e62cf64b75ea4c8c", "t_stage": "T1"}
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