I was working on to automatically register the CT (with electrodes) and MRI images. Here MRI image is the reference image and CT is the one to register. Also, I used the cost function: Normalized Mutual Information which is for the intermodel case. The number of histogram bin used is 200 and the Model/dof =Rigid Body (6 parameter model). 

Following are the informations for image's FOV and resolution: 

 CT: Rows->512 Column-> 512, pixel spacing= 0.48828 X0.48828;

I used the:

 flirt -in <mob file> -ref <reference file (in my case it is MRI>  -out <outpur>, used -cost normni -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 6  -interp nearestneighbour

The result I am getting is not good. The resulted image is rotated and not showing all the benchmark of the images. Just to clarify: the CT image have electrodes in it. The MRI doesn't have. It is for the same subject. 

My apology if I miss something here as I am new to the FSL.

Any help in dealing with such images will be greatly appreciated.

Thank you,