Transforming 5TT image to different space


I have a subject scanned twice (time 1 and time 2). Because the time 2 structural scans are poor quality while time 1 structural scans are isotropic voxels I would like to use this subject’s time 1 T1 scan to perform ACT tractography at time 2.

I have already generated a 5TT image from the time 1 T1 scan which works great for ACT tractography at time 1.

Is there a way to register the time 1 5TT image to the time 2 DWI image so I can run tractography?

I have tried to register the time 1 T1 scan to time 2 DWI using ANTS and then running 5ttgen fsl on my transformed image. Although the transformation works very well (first image), the result of 5ttgen fsl is very strange- see attached (bottom image):