Hi AFNI team,
I am running a resting state analysis with a pipeline consisting of SSwarper, reconall, and proc.py following example 11. Would you recommend that we use the intensity uniformized output from SSwarper (ex. anatU.sub) or the original anat as input to reconall?
Thanks,
Jenna
I would recommend using the original anat for Freesurfer’s recon-all. They have their own normalization scheme that suits their segmentation quite well.
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