T1 and DWI are already aligned - should I skip registration and transform steps in MRtrix pipeline?

[adsouza]

@WilliamFCB

Also, make sure that, for example, the T1 images you are using are not corrected for gradient distortions.

What are the potential implications of using gradient distortion–corrected T1-weighted images?

@pyotrfrancois

these masks primarily serve as constraints or seed points for the tract orientation rather than rigid anatomical boundaries

This depends on how the masks have been defined in the 5TT image and the selected seeding mechanism in tckgen

@pyotrfrancois as for registration method, I’m a fan of epi_reg with the white-matter mask option (here’s an example that might be helpful). In saying that, I’ve seen flirt do a good job, too. It might be worth trying both approaches and visually inspecting the results.

Hope this helps
Arkiev