pycortex
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align.automatic isn't too useful (have fix)
Current align.automatic
My version using bbregister, has no pre-alignment either
If you'd like me to commit my way I'm assuming it should be a separate function. Any suggestion for a name or any conventions I should follow, if there are any?
Sure, a commit would be great. Can you create a pull request with your branch, and we'll take a quick look? We'd be happy to replace the existing FSL-based BBR coregistration with the Freesurfer one if it reliably works better!