Surfa: Medical Imaging and Surface Processing ============================================= Surfa is a collection of Python utilities for medical image analysis and mesh-based surface processing. It provides tools that operate on 3D image arrays and triangular meshes with consideration of their representation in a world (or scanner) coordinate system. **Citing Surfa in a Publication** Surfa was originally built in part for the development of learning-based cortical surface reconstruction and it is a derivation of the FreeSurfer software suite. If you find this package useful in your analysis, please cite: - Andrew Hoopes et al. **"TopoFit: Rapid Reconstruction of Topologically-Correct Cortical Surfaces."** *Medical Imaging with Deep Learning*. 2021. - Bruce Fischl. **"FreeSurfer."** *NeuroImage* vol. 62,2 (2012): 774-81. **Acknowledgments** While broad in scope, surfa is an derivative of the [FreeSurfer](https://surfer.nmr.mgh.harvard.edu) brain analysis software suite. Further, the implementation of many mesh-based algorithms were inspired by the [open-source](https://github.com/mikedh/trimesh/blob/main/LICENSE.md) [trimesh](https://github.com/mikedh/trimesh) python library. ```{toctree} --- maxdepth: 1 hidden: caption: User Guide --- guide/installation guide/images guide/meshes guide/visualization guide/coordinates ``` ```{toctree} --- maxdepth: 1 hidden: caption: API Reference --- reference/image reference/mesh reference/geometry reference/affine reference/io reference/visualization reference/system ```