Hi,
Yes, I think I got the wrong end of the stick…
This tripped me up. Did you use mrtransform for this? If not, the first check would be to transform the template image to subject space with mrtransform and the warp warp_def.nii.gz. I suspect this does not work.
Assuming your warp_mni2diff.nii.gz is the output of fnirt and you did not use mrtransform, I think you’ll need to convert that warp to MRtrix format as described in the docs. I’d not use warpconvert but use warpinit, use the fsl tool to warp these images (applywarp I think) and then use warpcorrect to sanitise the warp.
I have no experience with fnirt but you might not need to do the conversion and be fine with the warpconvert command depending on the image strides of the images used in fnirt (I’d try -1,2,3 first).
If my assumptions are off again, please provide the full commands you used.
Cheers,
Max