rcruces
commented
1 year ago We hear you! and we are working in the incorporation of fastsurfer as well as other CNN based strategies to decrease the processing time of the pipeline and accuracy. We still have some issues to solve and it will take some time for this future release. Currently you can follow the implementation on our development branch.
What is the current behaviour?
Freesurfer is slow and fix_topology is a problem.
What is the motivation / use case for changing the behaviour?
Speedup, no vertex correction issues in fix_topology
Other information
FastSurfer https://deep-mi.org/research/fastsurfer/ would be a great alternative to Freesurfer cortical parc. and segmentation. https://github.com/deep-mi/FastSurfer Drawbacks: It resamples T1w images to 1mm iso if they are hires - could include an option for choosing either stream (free vs fastsurfer)