I am a undergraduate student new in the research of brain-mapping. I am currently switching from FreeSurfer to FastSurfer to speed up the brain-mapping process.
I am using a MacBook with Apple Silicon. When I tried to run FastSurfer with Docker, the speed was really slow. When I tried to run it natively, run_fastsurfer.sh didn't seem to be running properly. However, it seems that running FastSurfer natively on Apple Silicon should be feasible based on my online research.
Could anyone familiar with this topic give me any suggestions?
Thank you so much for your time in advance.
Essentially, transitioning to FastSurfer alone is not feasible, as FastSurfer relies on Freesurfer in the background for recon-all. To ensure proper functionality, both FastSurfer and Freesurfer must be installed. I personally run FastSurfer and Freesurfer on my Android tablet. The specific device is not a limiting factor; as long as your device supports a Chrome browser, you can leverage cloud servers for the setup.
here is how to run freesurfer and fastsurfer on any device using chrome:
https://colab.research.google.com/drive/1aT9Eae3d2dJBD2OOqlgxbUjzrdHOwqpO?usp=sharing
consider using GPU sessions for GPU supported functions of fastsurfer
the function packages() installs reqiured packages
the function freesurfer() installs freesurfer
the function fastsurfer() installs fastsurfer
the function FreeSurfer(input,subject,subdir) do recon-all
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