I am trying to warp a tractogram which I have run on an individual (using MRtrix) from the third release into the extended 40 week template space. However the streamlines are not being transformed correctly. I know that you need to use the inverse transform to warp the tracts (so use the warp from the template to the individual), and I believe(?) that it needs to be converted to a deformation field. I used the following commands:
warpconvert ./sub-CC00656XX13_ses-217601_from-extdhcp40wk_to-dwi_mode-image.nii.gz displacement2deformation ./warp_sub-CC00656XX13_ses-217601_2extdhcp40wk.nii.gz
tcktransform ./tracts.tck ./warp_sub-CC00656XX13_ses-217601_2extdhcp40wk.nii.gz ./extdhcp40wk_tracts.tck
and got this:
I have tried using the warps directly (i.e., not running warpconvert on them), using the non-inverted warps and none of these work.
I know the warps should work because I have used them with FSL’s img2imgcoord to correctly convert coordinates, so I presume there is some small trick I am missing or if I am using the wrong file? Looking at the first image, I feel like there is some mathematical transform that needs to be performed to get the tracts aligned? Am a bit stumped!