Hi, As mentioned in a previous message, running the subcortical segmentation takes 10-15 hours, primarily because of the Cannonical Registration (mri_ca_register) step. However, one the freesurfer papers (Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain) states on the very first page that it takes only 30 minutes to label the brain. How essential is the Cannonical Registration part? Can one leave it out and still get a good subcortical segmentation? Thanks, Eli
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