How do I save the coordinates that I find freehand

Hi there, i'm almost new in Matlab and I have a really big question:

I have 21 images. Taking the last of these images as a reference: I have to find 7 freehand square roi on the image (maybe with impixel or imcrop function). Save the coordinates and use the same coordinates to crop the ROIs in the same positions as the reference image.

For now I have only been able to start a loop that read the 21 images. The format of the images is dicom, but It changes just the imread function with dicomread

srcFile = dir('DIR\*.dcm');

%change with DIR the file destination

pathname = ('DIR\');

for i=1:21

filename=(num2str(i));

%the files are named to the corresponding number. For example the first image is named as "1"

I=dicomread(strcat(pathname,filename));

info=dicominfo(strcat(pathname,filename));

figure; imshow(I);

end

Answer 1

[DGM]

An example:

% generate some example test images
% you don't need to do any of this
inpict = repmat(double(imread('cameraman.tif')),[1 1 3]); % grayscale reference image
% colored example images in a cell array
A = uint8(inpict.*permute([1 0.3 0.8],[1 3 2]));
B = uint8(inpict.*permute([0.85 0.51 0],[1 3 2]));
C = uint8(inpict.*permute([0 0.68 0.45],[1 3 2]));
D = uint8(inpict.*permute([0 0.63 0.86],[1 3 2]));
pileofimages = {A B C D};
inpict = uint8(inpict);

% define these somehow
numberofimages = numel(pileofimages); % you'll have to know how many images you have
numberofroi = 2;

% show the reference image
imshow(inpict)

% use imcrop to get rectangle coordinates
R = zeros(numberofroi,4);
for nr = 1:numberofroi
    [~,R(nr,:)] = imcrop(gca);
end

% crop corresponding ROIs from each non-reference image
roibasket = cell(numberofroi,numberofimages);
for ni = 1:numberofimages
    for nr = 1:numberofroi
        thisimage = pileofimages{ni}; % you'll read from disk instead
        roibasket{nr,ni} = imcrop(thisimage,R(nr,:));
    end
end

% show the cropped image regions for demonstration
montage(roibasket.','size',[numberofroi numberofimages])

Your usage will be different. I simply put the images in a cell array. You'll be reading them from disk instead.

[HelpAStudent]

With your code I was able to crop just the first two ROIs out of seven. Then MATLAB find an error that I will show you:

I=dicomread('21')
imshow(I)
% use imcrop to get rectangle coordinates
R = zeros(numberofroi,4);
for nr = 1:numberofroi
    [~,R(nr,:)] = imcrop(gca);
end
% crop corresponding ROIs from each non-reference image
roibasket = cell(numberofroi,numberofimages);

for ni = 1:20
    for nr = 1:7
        
        thisimage = pileofimages{ni}; % you'll read from disk instead
        roibasket{nr,ni} = imcrop(thisimage,R(nr,:));

Here, there is an error

Index in position 1 exceeds array bounds (must not exceed 2).

Error in YOURFILE (line 15)

roibasket{nr,ni} = imcrop(thisimage,R(nr,:));

    end
end
% show the cropped image regions for demonstration
montage(roibasket.','size',[numberofroi numberofimages])

As you can see I have 21 images and 7 ROIs to analyze. After the second ROI the program stop to compile. Can you help me with that?

[HelpAStudent]

Sorry Now the program goes, but how can I be sure that It does the same 7 crop to the other images? Because after the crop, whit the ROIs I have to perform the mean (with the function mean2, I guess) and create a matrix with 21 rows and 7 columns: each element of the matrix is the mean of the grey in the image.

[DGM]

In the example, I set numberofroi = 2. Set it to 7, and set numberofimages to 21.

In order to verify that the same ROI location is the same in each image, do something similar to the example. Test the routine on copies of the same image so that colocation is visually and quantitatively identifiable (e.g. using immse()).

If you want the mean for the extracted images,

% transposed to match description
roimeans = cell2mat(cellfun(@mean2,roibasket,'uniform',false)).'

That basically gives the global mean for each image.

[HelpAStudent]

Thank you very much