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| title: README | |
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| # SimCortex | |
| **Deep Learning for Cortical Surface Reconstruction from Brain MRI** | |
| [Website](https://simcortex.app) · [GitHub](https://github.com/Neuro-iX/SimCortex) · [3D Slicer Extension](https://github.com/Kaveh-Moradkhani/SlicerSimCortex) | |
| ## About | |
| SimCortex is an open-source research project focused on fast, accurate, and topologically consistent cortical surface reconstruction from structural T1-weighted magnetic resonance imaging (MRI). | |
| The framework reconstructs four cortical surfaces: | |
| - Left hemisphere white matter surface | |
| - Left hemisphere pial surface | |
| - Right hemisphere white matter surface | |
| - Right hemisphere pial surface | |
| SimCortex combines deep learning, geometric modeling, and topology-aware surface reconstruction to produce anatomically meaningful cortical meshes while minimizing self-intersections and inter-surface collisions. | |
| ## Research Focus | |
| Our work explores deep learning for neuroimaging, 3D geometric modeling, cortical mesh reconstruction, diffeomorphic surface deformation, and anatomically constrained learning. | |
| ## Open-Source Ecosystem | |
| **SimCortex Framework:** Core implementation, inference tools, and research code. | |
| **SlicerSimCortex:** A 3D Slicer extension that integrates SimCortex through Docker, enabling cortical surface reconstruction and visualization directly within 3D Slicer. | |
| **Pretrained Models:** The SimCortex v2 pretrained weights, configuration files, and reproducibility resources are publicly available on [Hugging Face](https://huggingface.co/SimCortexAI/simcortex-v2) and archived on [Zenodo](https://doi.org/10.5281/zenodo.22710781). | |
| **Research Data:** The associated research dataset is archived in the [Federated Research Data Repository (FRDR)](https://doi.org/10.20383/103.01769). | |
| ## Resources | |
| - **Paper:** [SimCortex v2 — arXiv:2610.07378](https://doi.org/10.48550/arXiv.2610.07378) | |
| - **Website:** https://simcortex.app | |
| - **Source Code:** https://github.com/Neuro-iX/SimCortex | |
| - **Pretrained Models:** https://huggingface.co/SimCortexAI/simcortex-v2 | |
| - **Model Archive (Zenodo):** https://doi.org/10.5281/zenodo.22710781 | |
| - **Research Dataset (FRDR):** https://doi.org/10.20383/103.01769 | |
| - **3D Slicer Extension:** https://github.com/Kaveh-Moradkhani/SlicerSimCortex | |
| ## Research and Collaboration | |
| SimCortex is developed as part of academic research on deep learning and medical image analysis at École de technologie supérieure (ÉTS), Montréal, Canada. | |
| We welcome research collaboration, reproducibility efforts, and community contributions. |