mne-tools
Evaluate whether FreeSurfer's `surfa` could replace or simplify some of our custom code
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.
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surfais 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).
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It's actively developed by the FreeSurfer team.
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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).
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Since it provides a Python API, we don't need to piece together and call shell commands to run FS operations.
Any thoughts?
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
