FSL mask registration to diffusion space

Hello! I’m trying to coregister a VTA mask (in T2 space) developed with Lead DBS to DWI scans. This is a binary mask. When I apply the transformation matrix from T2 to DTI the output results in voxels with the value 0.
This is the command I use: flirt -in VTA_R.nii -ref nodif_brain.nii -applyxfm -init T2_to_DTI.mat -interp nearestneighbour
Does anyone know what could be going wrong and how I can fix it? Thanks!

Have you verified that the registration succeeded? i.e. what does a regular T2 image look like when you transform it to DTI space?