[Freesurfer] Incorporating hi-res T2w image in longitudinal pipeline

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Good afternoon,

We are collecting hi-resolution T1w and T2w images (0.8mm3) in a pre-/post- design. I am using Freesurfer 7.4.1 to process the data and have been successful in ingressing the T2w images in the cross-sectional recon-all runs with -T2 <path> and -T2pial.

Two questions:

1. When creating the base image, is there any value to using the T2s and, if so, is there a way to do that? 2. When running the -long step, I know that -T2pial is an option but do I need to pass -T2 <path> with it? If I need the path, should it point to the original image or something from the cross/mri folder?

Thanks

Adam C. Raikes, PhD

Imaging Projects Manager

Center for Innovation in Brain Science

University of Arizona