4. Registration: Single Stage and Multi-Stage Applications (Reg E4)

Single Stage and Multi-Stage Applications

[@Michael-il8ls]

I am trying to align rat brain fMRI to P56 Atlas template. And I'm not quite satisfied with the result. What are the tips for rat brains? And more importantly, how can I manually edit transformation matrices, delete skulls etc?

[@zahraroozbehi5454]

Thank you for your valuable explanations.
What is the file-name of the final 4D MRI that has been registered in MNI space?

[@Michael-il8ls]

I have some problems with flirt/fnirt for rat fMRI. Also I cannot import P56 Allen atlas for rat brain. Why is that?

[@angelalee5903]

Thanks for your helpful videos! If I am trying to do two step registration with the first step being linear registration of a T1 image to a T2 image, is it OK to use the FEAT tool and upload the T2 image where you have uploaded the functional data? Then subsequently use FNIRT to perform spatial normalization to MNI space?

[@tamseelnaveed3876]

did you ever figure this out?