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synthseg/LICENSE

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synthseg/NOTICE

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+SynthSeg assets for Neurodesk webapps
+Model: SynthSeg 2.0, Copyright Benjamin Billot and contributors, Apache-2.0,
+https://github.com/BBillot/SynthSeg. The ONNX file is a lossless re-export of
+the FreeSurfer 8.1.0 checkpoint synthseg_2.0.h5; no retraining.
+Validation images: T1-weighted scans of Chris Rorden, defaced, public domain.
+Golden segmentations: produced with FreeSurfer 8.1.0 mri_synthseg.

synthseg/README.md

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+# SynthSeg assets for Neurodesk
+
+SynthSeg 2.0 model and validation data for `exes/synthseg` (native CLI) and
+`apps/synthseg` (browser) in https://github.com/neurodesk/webapps.
+
+| File | SHA-256 | Bytes |
+| --- | --- | --- |
+| `synthseg/models/synthseg-2.0.onnx` | `94412cd4ece229cee1ec21ac05d9aa6f084ea7b600303d2e598707d86a9a9b13` | 52983030 |
+| `synthseg/models/synthseg_2.0.h5` | `f190bfd742f450ef3ca2c9df9ed4d2e0232b3a74471da5e51b7770bacdf80c3e` | 53079152 |
+| `synthseg/validation/T1_head.nii.gz` | `58220b40d179b7a93dd3ce231dd7afaa39989c75658b2b8e4c2f34abf8f16416` | 5176902 |
+| `synthseg/validation/T1_head_2mm.nii.gz` | `e4c1bb988b6b6efe0966b1bf09869f12151d75ad31e64097dcd14fa0c717aadd` | 1568247 |
+| `synthseg/validation/T1_head_2mm_default.nii.gz` | `3fd14829d1503c9179255e9c485bb04ddddd02a0f87a81d1a2aaeea41ba6ac0a` | 720479 |
+| `synthseg/validation/T1_head_2mm_fast.nii.gz` | `12f020cf5d0c8b4ffb744d7e21405b71ddd35651f1ab8e041e4576e77459f7e7` | 722688 |
+| `synthseg/validation/T1_head_default.nii.gz` | `8fea403662eb3f422ff9b942b667ef5cce454cb79c8177e55e14aa9427f4c81a` | 706242 |
+| `synthseg/validation/T1_head_fast.nii.gz` | `80f6822d2f445fd0f8791eb2e1abd3349168c6ec99f25253423cf21c2309a8ec` | 712028 |
+
+## Models
+
+- `synthseg_2.0.h5` — upstream Keras checkpoint, byte-identical to FreeSurfer 8.1.0 `models/synthseg_2.0.h5`. SynthSeg is Apache-2.0 (https://github.com/BBillot/SynthSeg); see LICENSE.
+- `synthseg-2.0.onnx` — float32 ONNX rebuilt from that checkpoint by `exes/synthseg/scripts/export_model.py` (neuron U-Net topology via `onnx.helper`, no retraining, no quantization). Layout NCDHW, batch 1, channel 1 in, 33 label classes out; spatial dimensions multiples of 32 and at least 128. Keras vs ONNX max abs diff 2e-5 (`scripts/check_onnx.py`).
+
+## Validation
+
+- `T1_head.nii.gz` (1 mm) and `T1_head_2mm.nii.gz` (2 mm): T1-weighted head scans of Chris Rorden, facial features removed, released to the public domain. `T1_head.nii.gz` is also the browser app's default image.
+- `T1_head_default.nii.gz`, `T1_head_fast.nii.gz`, `T1_head_2mm_default.nii.gz`, `T1_head_2mm_fast.nii.gz`: FreeSurfer 8.1.0 `mri_synthseg --i IN --o OUT` outputs (`--fast` for the fast variants), int32 label maps on the 1 mm grid. These are the parity goldens: the native and browser ports must reproduce geometry and header exactly and differ in at most 2e-6 of voxels (`exes/synthseg/tests/parity.rs`).
+- `native-report.json`: the last native parity run (device, mode, mismatches, seconds on named hardware).
+
+Consumers pin a commit revision and verify SHA-256. Files are immutable; a new model or golden gets a new name.
+
+Citation: Billot B, Greve DN, Puonti O, et al. (2023). SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining. Medical Image Analysis 86:102789. https://doi.org/10.1016/j.media.2023.102789

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synthseg/validation/native-report.json

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+}