Each image size where different. Therefore, I had to modify the code to resize the images. However, not able to display the second image as the loop continue.

clc; clear all; close all;
BaseFolder = 'C:\Users\Marilyn Urrea\Desktop\Machine Perception & Cognition\MarilynDataForDIP'; % Main Folder where folders of each Rats are saved
Rat = 'Rat1_all'; % Rat1 Folder
Types = {'BigDenStimulation','Control','SmallDenStimulation','Denervated'}; % Subfolders of Expiration and Inspiration
Inspiration =   '\Inspiration\InspBigDenStimulation'; % folder in which your Inspiration images exists
Expiration =    '\Expiration\ExpBigDenStimulation'; % folder in which your Expiration images exists
Subtraction =   '\Subtraction\SubBigDenStimulation'; % folder in which your Subtraction images exists
file_ext = ".bmp"; 
InspMP = strcat(BaseFolder,'\',Rat,Inspiration,'\*',file_ext);
ExpMP = strcat(BaseFolder,'\',Rat,Expiration,'\*',file_ext);
SubOut = strcat(BaseFolder,'\',Rat,Subtraction);
Insp_ds = imageDatastore(InspMP);
Exp_ds = imageDatastore(ExpMP);
firstImage = true; 
minRows = Inf;
minCols = Inf;
while hasdata(Insp_ds)
    [img,info] = read(Insp_ds); % we made need to use readimage if the sort (default) order mismatch
    Rows = size(img,1);
    Cols = size(img,2);
    if (firstImage)
        minRows = Rows;
        minCols = Cols;
        firstImage = false;
    else
        minRows = min([minRows,Rows]);
        minCols = min([minCols,Cols]);
        %         if isempty(minRows) 
        %             temp = 0
        %         end
    end
    
end

while hasdata(Exp_ds)
    [img,~] = read(Exp_ds);
    Rows = size(img,1);
    Cols = size(img,2);
    minRows = min([minRows,Rows]);
    minCols = min([minCols,Cols]);
end
reset(Insp_ds);
reset(Exp_ds);
firstImage = true; 
while hasdata(Insp_ds)
    [imgI,info] = read(Insp_ds);
    
    inspFileName = extractFileName(info.Filename);
    imgI = getMiddle(imgI,minRows,minCols);
    [imgE,info] = read(Exp_ds);
    expFileName = extractFileName(info.Filename);
    imgE = getMiddle(imgE,minRows,minCols);
    imgS = imgI - imgE;
    output_image_folder = SubOut;
    output_image_fileName = strcat(inspFileName, "_sub_", expFileName);
    output_histeq_fileName = strcat(output_image_fileName, "_histeq");
    file_ext = ".bmp";
    output_image_path = strcat(output_image_folder,'\',output_image_fileName, file_ext);
    output_histeq_path = strcat(output_image_folder,'\',output_histeq_fileName, file_ext);
    
    img_gray = rgb2gray(imgS);
    I = imrotate(img_gray,270);
    
    
    if firstImage 
        figure(1), imshow(I); % creates a new window for each image
        title("Original X-ray Image")
        xlabel("Select first top left and then secondly the bottom right corner")
        disp('Click first the top left and then secondly the bottom right corner')
        [x,y] = ginput(2);
        x = uint16(x);
        y = uint16(y);
        
        x_rec = [x(1) x(1) x(2) x(2)];
        y_rec = [y(1) y(2) y(2) y(1)];
        BW = roipoly(I,x_rec,y_rec);
        firstImage = false;
        
        J = I.*uint8(BW);
        
        figure(2),imshow(J);
        K = I(y(1): y(2), x(1): x(2));
        title("Region of Interest to be Analyzed")
        
        % Be able to cut in half and keep both sides since the goal is to
        % subtract both sides and has a ratio
        
        
        
        figure(3),imshow(K);
        title("Select the vertical slice point to cut the image in half and click the side you want to keep.")
        disp('Select the vertical slice point to cut the image in half')
        [x_slice,~] = ginput(1);
        x_slice = uint16(x_slice);
        disp('Click which side you want to keep')
        [x_select,~] = ginput(1);
        x_select = uint16(x_select);
        
    else
        J = I.*uint8(BW);
        K = I(y(1): y(2), x(1): x(2));
        
    end
    if x_select < x_slice 
        L = K(:,1:x_slice);%keeping the left side
    else
        L = K(:,x_slice:end);%keepin the right side
    end
    pout = L;
    pout_imadjust = imadjust(pout);
    pout_histeq = histeq(pout);
    pout_adapthisteq = adapthisteq(pout);
    figure(4)
    montage({pout,pout_imadjust,pout_histeq,pout_adapthisteq},"Size",[1 4])
    title("Original Image and Enhanced Images using imadjust, histeq, and adapthisteq")
    figure(5)
    subplot(1,4,1)
    histogram(pout)
    y_L = ylim();
    xlim([0, 255])
    subplot(1,4,2)
    histogram(pout_imadjust)
    xlim([0, 255])
    ylim(y_L)
    subplot(1,4,3)
    histogram(pout_histeq)
    xlim([0, 255])
    ylim(y_L)
    subplot(1,4,4)
    histogram(pout_adapthisteq)
    xlim([0, 255])
    ylim(y_L)
    sgtitle("Histograms of Original Image and Enhanced Images using imadjust, histeq, and adapthisteq")
end
function imgCenter = getMiddle(img,minRows,minCols)
Rows = size(img,1);
Cols = size(img,2);
firstRow = floor((Rows - minRows)/2);
firstCol = floor((Cols - minCols)/2);
lastRow = firstRow + minRows-1;
lastCol = firstCol + minCols-1;
imgCenter = img(firstRow:lastRow,firstCol:lastCol,:);
end
function [fileName, folder] = extractFileName(path)
slashLocations = strfind(path,'\');
lastSlash = max(slashLocations);
folder = path(1:lastSlash-1);
fileName = path(lastSlash + 1:end-4);

end

[Image Analyst]

Uh, ok. Thanks for the announcement, I guess.

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