Hi Mrtrix community,
I seem to be running into some trouble transforming tractography that was done in native space into MNI common space.
i am using a warp file made with fsl FNIRT. based on previous threads here, I used:
warpconvert warp_mni2diff.nii.gz displacement2deformation warp_def.nii.gz
tcktransform tracts warp_def.nii.gz tracts2template.tck
the result is not only not registered to the template image, but also seems to be pretty much the same as the original tracts, but with less tracts. Weirdly, the original tracts seem to fit the template better than the transformed ones.
the original tracts on the template:
the transformed tracts on the template:
obviously, I’m doing something wrong. I know the warp is fine because I used it to transform the template atlas to native space and it worked perfectly, so any input as to what is wrong in my process would be helpful.
thanks a lot in advance!