I’d second that, the mean squared metric is likely not suitable for cross-modality registration. I’ve managed to linearly (affine) register across modalities using combinations of manually fine-tuned contrasts to give similar contrast and intensity ranges but the results of nonlinear registration are unusable more often than not.
@EricMoulton_ICM If you want, you can send me a link with a subject’s FOD, tensor (dwi2tensor) and b0 (dwiextract) image and I can give it a try.
No near future plan but we definitely should… If anyone wants to take this on, I’d start in the mrreg branch.
Cheers,
Max