Dear Freesurfer community,

I am relatively new to this community.

I was trying to register the CT image and the MRI images (MRI as a the target volume and CT as the movable volume). I used the mri_robust_register to to do the registration as below:

mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit

The problem is that: after register, the new image (v1to2.nii) is not exactly aligned with the original MRI image (vol2.nii). It gives a very different output. I wonder if I am missing anything here or I need to do some extra steps after the above command in order to get the correct alignment of the two images. I was hoping to get the resultant image should be well orient with the target volume image (vol2.nii image in my case).

I really appreciate any help here.

Hari Guragain