fsl reorient
#!/bin/sh
# fslreorient2std is an FSL tool for reorienting the image to match the
# approximate orientation of the standard template images (MNI152).
# It only applies 0, 90, 180 or 270 degree rotations.
# It is not a registration tool.
# It requires NIfTI images with valid orientation information
# in them (seen by valid labels in FSLeyes). This tool
# assumes the labels are correct - if not, fix that before using this.
# Specify the input and output name!
fslreorient2std T1w T1w