ENH Add more options for freesurfer's automatic alignment, move code for FSL's automatic alignment #528
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This change will allow using volumes with T1 contrast as a reference for automatic alignment. It will also allow passing a registration file for initialization.
I moved the code for the automatic alignment using FSL to
cortex.align.automatic_fsl. I doubt it will be used because freesurfer's bbregister works very well, but it's there.