match one anatomical dataset to the other anatomical dataset

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1

Dear,
I’ve tried to match anatomical dataset to MNI space, yet I get a little confused with how to match one anatomical dataset to the other anatomical dataset, could anyone help me with this one?
Thanks for your precious time and looks forward to your reply!
Yours,
Peng

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Lots of choices:

auto_warp.py (affine, nonlinear
@auto_tlrc (affine only)
align_epi_anat.py (affine only, for two anatomical datasets, use -dset1 templateset and -dset2 mydset -dset2to1)
3dQwarp (nonlinear only)
@SSwarper (MNI-2009 template only, affine, nonlinear)