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Hi Alex
you better use afni to do this! look at the script fat_proc_axialize_anat

Francesco Sammartino MD

On Aug 25, 2017 11:03 AM, "Alexandre Boutet" <[log in to unmask]> wrote:
Dear Fsl users,

I would like to align FSPGR T1s scans with isotropic voxels to the ac-pc axial plane.

Would anyone be able to direct me to an fsl command that does this? Or would anyone have a script that they could share?

Thank you

Alex