#!/bin/sh

# fsl_anat will clean up the T1w image & normalize it to standard space
# including bias correction, tissue segmentation & subcortical 
# segmentation (FIRST), though it creates the image in 2mm MNI space.
# Output is generated in a subdirectory named for the image but with the 
# extension .anat (e.g., T1w.anat)

# Do all processing
fsl_anat -i T1w 

# Do not run reorient, segmentation or FIRST subcortical segmentation
fsl_anat -i T1w --noreorient --noseg --nosubcortseg