Hi,
If your CT has electrodes in it and the MRI does not, and these are obvious features (I'm not familiar with CT and I don't know quite what kind of electrodes you are talking about) then this might be the cause of your problems. Have you tried running brain extraction first and then registration? As I'm not familiar with CT I'm not sure how well that will work either.
It would also be helpful if you could put an illustrative picture on a website somewhere and post a link to it so that we could see what the images look like (note that you cannot attach pictures or images to these emails).
All the best,Mark
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Hari Guragain <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Monday, 13 June 2016 at 23:31
To: "[log in to unmask]" <[log in to unmask]>
Subject: [FSL] Registration of CT and MRI images in FSL
Dear FSL experts,
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;for MRI: Rows->256 Column-> 256, pixel spacing= 0.9375 X0.9375;
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,Hari Guragain