Evaluate whether FreeSurfer's `surfa` could replace or simplify some of our custom code

[hoechenberger]

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. While broad in scope, surfa is developed with particular emphasis on neuroimaging applications.

• Documentation

• Code

• surfa is a Python package derived from FreeSurfer. Some of its outputs and inputs directly overlap with MNE’s use of FreeSurfer I/O (meshes, surfaces, coordinate systems transformations).

• It has built-in coordinate system awareness (scanner / RAS).

• It's actively developed by the FreeSurfer team.

• It uses Cython and compiled extensions for performance-critical operation (which can also be a con, I haven't checked whether they provide up-to-date binary wheels).

• Since it provides a Python API, we don't need to piece together and call shell commands to run FS operations.

Any thoughts?

[larsoner]

It uses Cython and compiled extensions for performance-critical operation (which can also be a con, I haven't checked whether they provide up-to-date binary wheels).

Doesn't look like it:

Would be great to switch to this if/when they provide binary wheels. I'll look in their repo and offer to set up cibuildwheel

[larsoner]

xref freesurfer/surfa#64

[hoechenberger]

Thanks for looking into this, @larsoner!