How can I load and plot the difference of a set of images to a reference image?

Try this:

% Demo by Image Analyst.
clc;    % Clear the command window.
fprintf('Beginning to run %s.m ...\n', mfilename);
close all;  % Close all figures (except those of imtool.)
clearvars;
workspace;  % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 16;

folder = 'C:\Users\lea\documents\Matlab\work\Images'; % Change to wherever your images are.
baseFileName = 'rock01b_noback.webp';
fullFileName = fullfile(folder, baseFileName);
reference_img = imread(fullFileName); % read reference img
subplot(2, 2, 1);
imshow(reference_img);
title(baseFileName);
morphimages = dir(fullfile(folder,'*.PNG'));  %specify pattern of files in folder
numImages = length(morphimages)
ssimval = zeros(1, numImages);
for k = 1 : length(morphimages)
	baseImageName = morphimages(k).name;
	fullImageName = fullfile(folder,baseImageName);
	fprintf(1, 'Reading %d of %d : %s.\n', k, numImages, fullImageName);
	subplot(2, 2, 2);
	imageArray = imread(fullImageName);
	if ~isequal(size(imageArray), size(imageArray))
		fprintf('Skipping %d because it is not the same size as the reference image\n', baseImageName);
		continue;
	end
	imshow(imageArray, []);
	title(baseImageName);
	ssimval(k) = ssim(imageArray, reference_img) %find ssim index for each img in folder
	subplot(2, 2, 3:4);
	plot(ssimval(1:k), 'b.-', 'LineWidth', 2, 'MarkerSize', 18);
	drawnow;
	grid on;
end
fprintf('Done running %s.m\n', mfilename);