Can you please describe what you would like to do? The image analysis of diffusion tensors is done by BDP and TrackConnect and you would not need coregistration of the results to the MNI space.
If you do need to transform your data to a common MNI space,
you can apply inverse map generated by svreg as follows:
Use svreg_apply_map.sh binary provided with svreg. Here is how I would do this on Linux, though the corresponding binaries are available in Linux, Windows and Mac, so similar command will work.
/home/ajoshi/BrainSuite16a1/svreg/bin/svreg_apply_map.sh subname.svreg.inv.map.nii.gz fa_map.nii.gz out_fa.nii.gz /home/ajoshi/BrainSuite16a1/svreg/BrainSuiteAtlas1/mri.bfc.nii.gz