You can do this with these steps (most of them beneficial for later analyses too):
bet - brain extract your T1
flirt - register your T1 (brain extracted) to the MNI (brain extracted) with 12 DOF
aff2rigid - create a 6 DOF matrix that will align the original T1 so that the mid-plane and ac-pc lines are aligned with the axes (using information from the MNI registration)
flirt or applyXFM - apply the 6 DOF matrix from aff2rigid in order to resample your T1
All the best,
> On 25 Aug 2017, at 15:52, 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