Align pre- and post- scans using imregister

I am trying to align pre- and post treatment scans in order to highlight the differences. After adding a contrast agent there are more structures visible and I want to display just these ones that occur in the post scan, but not in the pre scan. I have attached both scans. Eventually I will work with 3D matrices. I am rotating the post scan and get close to a match, but despite using the command imregister I can't get the two pictures to fully match. I am using the following commands and am happy for any hints and recommendations. Thanks.

A= imread('11Tpre (296).jpg');  
A = rgb2gray (A);
A = imcrop (A,[345 390 1179 1179]); %cropping image to a 1180 x 1180

B= imread('11Tpost (272).jpg');
B = rgb2gray (B);
B = imcrop (B,[435 370 1179 1179]); %cropping image to a 1180 x 1180
B = imrotate (B, 27.2,'bilinear', 'crop')

figure
imshow (A)
figure
imshow(B)

   % View misaligned images
    imshowpair(A,B,'Scaling','joint');

    % Get a configuration suitable for registering images from different
    % sensors.
    [optimizer, metric] = imregconfig('multimodal')

    % Tune the properties of the optimizer to get the problem to converge
    % on a global maxima and to allow for more iterations.
    optimizer.InitialRadius = 0.009;
    optimizer.Epsilon = 1.5e-4;
    optimizer.GrowthFactor = 1.01;
    optimizer.MaximumIterations = 300;

    % Align the moving image with the fixed image
    Breg = imregister (B,A,'affine', optimizer, metric); 

    % View registered images
    figure
    imshowpair(A,Breg,'Scaling','joint');