Image registration not aligning images correctly

I am trying to align two images to be able to extract data from them and compare before and after.

I have tried intensity-based image registration and control point image registration but it doesn't seem to be aligning them up correctly.

I have attached the images and the code is below. When I use:

imshowpair(fixed_filtered,movingRegistered,'Scaling','joint');

They are not aligned up. Not sure what I'm doing wrong, I've tried playing around with the settings but it doesn't appear to make much of a difference, just makes the computing time longer.

Intensity code:

fixed = imread('Fixed.JPG');
fixed =  imcrop(fixed,[1700 1200 2000 1500]);
fixed_gray = rgb2gray(fixed);

thresh1 = graythresh (fixed_gray);
fixed_bw = im2bw(fixed_gray, thresh);
fixed_filtered = bwareafilt(fixed_bw,[10 500]);
fixed_filtered = double(fixed_filtered);

moving = imread('Moving.JPG');
moving =  imcrop(moving,[1700 1200 2000 1500]);
moving_gray = rgb2gray(moving);

thresh2 = graythresh (moving_gray);
moving_bw = im2bw(moving_gray, thresh);
moving_filtered = bwareafilt(moving_bw,[10 500]);
moving_filtered = double(moving_filtered);

imshowpair(fixed,moving,'Scaling','joint');
[optimizer, metric] = imregconfig('monomodal');
optimizer.MaximumIterations = 1000;
optimizer.MaximumStepLength = 0.001
movingRegistered = imregister(moving_filtered, fixed_filtered, 'rigid', optimizer, metric);

figure(1);
imshowpair(fixed_filtered,moving_filtered,'Scaling','joint');
figure(2);
imshowpair(fixed_filtered,movingRegistered,'Scaling','joint');

For control point, I use this instead of the optimizer metric part of the code:

cpselect(moving,fixed);
mytform = fitgeotrans(movingPoints, fixedPoints, 'similarity');
movingRegistered = imwarp(moving, mytform);

All help is greatly appreciated. Thank you!!

[msij]

Ok so I've kind of found a solution for this.

By changing modifying the code from:

movingRegistered = imwarp(moving, mytform);

to:

movingRegistered = imwarp(moving, mytform,'OutputView', imref2d(size(fixed)));

the image actually aligns up. I am not sure why, so if someone could explain that I'd be grateful.

However, I would still like to figure out a way to have this done automatically so any ideas on how to fix the intensity-based image registration?

Thanks!

[Vandana Rajan]

Hi,

When you use the 'OutputView' parameter, it preserves the world limits and resolution of the fixed image when forming the transformed image.