| # SimCortex v2 Model Card |
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| ## Model overview |
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| SimCortex v2 is a deep-learning pipeline for reconstructing four cortical surfaces from T1-weighted structural MRI: |
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| - left pial surface |
| - left white-matter surface |
| - right pial surface |
| - right white-matter surface |
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| The pipeline operates in MNI152 space and combines volumetric segmentation, cortical-surface initialization, and simultaneous deformation of the four cortical surfaces. |
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| ## Intended use |
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| The released models are intended for research use in cortical surface reconstruction and downstream morphometric analysis. |
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| They are not intended for standalone clinical diagnosis or treatment decisions. |
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| ## Pipeline stages |
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| 1. T1-weighted MRI preprocessing into MNI152 space. |
| 2. Nine-class 3D U-Net segmentation. |
| 3. Initial cortical-surface generation. |
| 4. Simultaneous deformation of left/right white and pial surfaces. |
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| ## Released checkpoints |
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| ### Segmentation |
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| File: |
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| `seg/seg_best_dice.pt` |
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| Role: |
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| Final segmentation checkpoint used by the released pipeline. |
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| SHA256: |
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| `2cea6dc1606958dbdb2aea50748b73ff73e604b0c367b3b1588cef7a112c8e06` |
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| ### Primary deformation checkpoint |
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| File: |
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| `deform/deform_best_rmse.pth` |
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| Role: |
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| Recommended deformation checkpoint used for the final SimCortex v2 paper evaluation. |
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| SHA256: |
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| `3fb84c917953e479e72d59291837bd6b08f40fb197534046b95dc5a452e86b95` |
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| ### Secondary deformation checkpoint |
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| File: |
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| `deform/deform_best_model.pth` |
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| Role: |
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| Alternative deformation checkpoint retained for reproducibility and comparison. |
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| SHA256: |
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| `d30d3218069a6eb395dacd3ff0dd085a93f6f0102616eed809b90c362b885b40` |
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| ## Model file format |
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| The released `.pt` and `.pth` files are PyTorch state dictionaries intended for inference. |
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| Training-resume checkpoints, optimizer states, and scheduler states are not included. |
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| ## Training data split |
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| The released training split contains 515 subjects from HCP-YA and OASIS-1: |
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| - training: 361 |
| - validation: 77 |
| - test: 77 |
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| By dataset: |
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| HCP-YA: |
| - 70 train |
| - 15 validation |
| - 15 test |
| - 100 total |
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| OASIS-1: |
| - 291 train |
| - 62 validation |
| - 62 test |
| - 415 total |
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| The exact split is stored in: |
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| `splits/dataset_split.csv` |
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| SHA256: |
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| `68f42ef3ed09373685de5d1dd144c7d3d72b7f8083850057dcccd5780756188d` |
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| ## Evaluation cohort |
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| The public evaluation cohort definition is stored in: |
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| `splits/evaluation_sample40.csv` |
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| It contains: |
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| - 560 cases |
| - 14 datasets |
| - 40 cases per dataset |
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| SHA256: |
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| `2c41b21afea327756c8d7fccc30bd03e461670d59dc00f941e8cba06fcf59842` |
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| ## Configuration files |
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| The archive includes the YAML configurations used by the released pipeline: |
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| - `configs/seg/train.yaml` |
| - `configs/seg/inference.yaml` |
| - `configs/seg/eval.yaml` |
| - `configs/initsurf/generate.yaml` |
| - `configs/deform/train.yaml` |
| - `configs/deform/inference.yaml` |
| - `configs/deform/eval.yaml` |
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| ## Surface ordering |
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| The deformation implementation uses the following four-surface order: |
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| ```text |
| lh_pial |
| lh_white |
| rh_pial |
| rh_white |
| ``` |
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| ## Input and output |
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| Input: |
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| T1-weighted MRI processed into the reference space expected by the SimCortex pipeline. |
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| Output: |
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| Left/right white-matter and pial cortical surface meshes. |
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| ## Data availability |
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| The MRI datasets themselves are not included in this model archive. |
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| The associated dataset release is hosted separately in the Federated Research Data Repository (FRDR). |
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| FRDR dataset DOI: |
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| `10.20383/103.01769` |
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| ## Limitations |
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| The released models were developed and evaluated using the datasets and processing conventions described in the SimCortex v2 study. |
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| Performance may vary for data acquired with different scanners, protocols, populations, preprocessing pipelines, or image quality. |
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| The models are provided for research use and should be independently validated before use in new settings. |
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| ## Reproducibility |
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| The archive includes: |
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| - pretrained model state dictionaries |
| - frozen YAML configurations |
| - training/validation/test split |
| - final evaluation cohort definition |
| - provenance metadata |
| - SHA256 checksums |
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| The source-code repository should be used together with this archive for inference and reproduction of the released pipeline. |
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