I have to register two MRIs that represent the same patient (who is always in the same position). Note that one image is larger than the other as it represents a larger portion of the body.
I roto-translated the larger image in order to obtain an “initial manual registration” and everything is fine until this point.
Then, I applied the General Registration (BRAINS) to refine the initial registration. The results is a cropped image: the larger image is cropped to the same size as the smaller one. This is undesired since I would need the extra portion of the body originally provided by my larger image.
I’ve experienced many times that otherwise very stable registration methods (such as Elastix with default bspline parameter set) failed to converge if one image covered a significantly larger portion of the patient than the other. I would recommend to crop the images to cover approximately the same anatomical region. You can still apply the computed transformation to the entire original image.
How can I visualize the computed transform? I cannot find it after applying the registration (BRAIN). I expect to find a 4x4 matrix.
Moreover, will this transformation matrix refer also to the initial roto-translation (“initial manual alignment” mentioned above)? In other words, shall I apply the transformation matrix to the original volume or to the volume which I obtained after the “initial manual alignment”? If it is the second case, how does the matrix change?
You can see all transforms in Transforms module. If you computed a composite transform (e.g., linear+bspline) then you need to open “Information” section. To edit linear component of a composite transform, you need to split it first then choose the linear transform node.
