I tried using 3dallineate and had a little trouble. To clarify I want the following:
Input: roi+tlrc
output: roi+orig
master: anat_ns+orig
1Dmatrix_apply: anat_ns.Xaff12.1D
This means that I want to convert roi from TT space to subject space modeled after anat_ns (which maintains the high resolution image, but just changes the spatial orientation of the image. Given that, would the following command make sense:
3dAllineate -verb -1Dmatrix_apply anat_ns.Xaff12.1D -1Dmatrix_save roi -prefix roi+orig -input roi+tlrc -master anat_ns+orig
Thanks.