We have a sagittal 1 mm isotropic whole-brain 3D T1 mprage (morphometry protocol suggested on Freesurfer's page) and a coronal anisotropic (0.4mm inplane, 2mm thickness, similar to ADNI protocol) T2 measurement acquired perpendicular to the hippocampus. We'd like to use both measurements simultaneously in the segmentation. However, on the fswiki it is suggested that T2 should be coarsely aligned to the main T1 scan, but I'm not sure about how to understand it, especially since our 3D T1 is acquired in sagittal plane, while T2 is in coronal.

(a) Should T1 and T2 acquired in the same (e.g. coronal plane) with the same or little angulation? 

or

(b) Is it enough if they are just aligned based on the physical/anatomical coordinate system (which is automatically ensured if both images were  acquired in the same session with no repositioning and little or no head movement of the subject between the two measurements)?

Best,

Gabor