MATLAB: Cropping DICOM image to exact size

dicomimage analysisimage processingImage Processing Toolboximage segmentation

I have a large batch of DICOM images that I'm pre-processing for use in a convolutional neural network (for classification). Part of this pre-processing involves segmentating the images to a smaller exact size around the area of interest in the scan, keeping all of these segmentations the same size. Essentially, I want to just crop a 128×128 square out of each image, manually selecting where this square is each time.
It seems like a simple enough thing to do but I'll be working with a lot of images so I'm really just looking for suggestions and pointers to help me develop a method to do this efficiently.
Thanks in advance for your help!

Best Answer

OK, try this:
clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
clear;  % Erase all existing variables. Or clearvars if you want.
workspace;  % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 25;
%===============================================================================

% Get the name of the image the user wants to use.
% Have user browse for a file, from a specified "starting folder."
% For convenience in browsing, set a starting folder from which to browse.
startingFolder = pwd;
if ~exist(startingFolder, 'dir')
  % If that folder doesn't exist, just start in the current folder.
  startingFolder = pwd;
end
% Get the name of the file that the user wants to use.
defaultFileName = fullfile(startingFolder, '*.*');
[baseFileName, folder] = uigetfile(defaultFileName, 'Select a file');
if baseFileName == 0
  % User clicked the Cancel button.
  return;
end
% Get the full filename, with path prepended.
fullFileName = fullfile(folder, baseFileName);
%===============================================================================
% Read in a demo image.
grayImage = imread(fullFileName);
% Get the dimensions of the image.
% numberOfColorChannels should be = 1 for a gray scale image, and 3 for an RGB color image.
[rows, columns, numberOfColorChannels] = size(grayImage)
if numberOfColorChannels > 1
  % It's not really gray scale like we expected - it's color.
  % Use weighted sum of ALL channels to create a gray scale image.
  grayImage = rgb2gray(grayImage);
  % ALTERNATE METHOD: Convert it to gray scale by taking only the green channel,
  % which in a typical snapshot will be the least noisy channel.
  % grayImage = grayImage(:, :, 2); % Take green channel.
end
% Display the image.

subplot(1, 2, 1);
imshow(grayImage, []);
axis on;
axis image;
caption = sprintf('Original Gray Scale Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;
hp = impixelinfo();
% Set up figure properties:
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
% Get rid of tool bar and pulldown menus that are along top of figure.
% set(gcf, 'Toolbar', 'none', 'Menu', 'none');
% Give a name to the title bar.
set(gcf, 'Name', 'Demo by Mark Hayworth', 'NumberTitle', 'Off')
drawnow;
uiwait(msgbox('Drag out a 128x128 box'));
% Let user draw the box.
k = waitforbuttonpress;
point1 = get(gca,'CurrentPoint');    % button down detected
finalRect = rbbox;                   % return figure units
point2 = get(gca,'CurrentPoint');    % button up detected
point1 = point1(1,1:2);              % extract x and y
point2 = point2(1,1:2);
x1 = point1(1);
y1 = point1(2);
x2 = point2(1);
y2 = point2(2);
% Find the coordinates of the box.

xUserBox = [x1, x2, x2, x1, x1];
yUserBox = [y1, y1, y2, y2, y1];
% The box from rbbox() disappears after drawing.
% Redraw what they drew.
hold on
axis manual
plot(xUserBox, yUserBox, 'r-', 'LineWidth', 2); % Draw box.
% Now we need to get a 128x128 box centered at that location.
% Compute the center
xCenter = (x1 + x2)/2; % Get average.

yCenter = (y1 + y2)/2; % Get average.
plot(xCenter, yCenter, 'r+', 'MarkerSize', 30, 'LineWidth', 2); % Plot cross at center.
% Get box edges for a 128x128 box centered at the center of the box that they drew.
x1 = round(xCenter - 64)
y1 = round(yCenter - 64)
x2 = x1 + 127
y2 = y1 + 127
% Find the coordinates of the box.
xBox128 = [x1, x2, x2, x1, x1];
yBox128 = [y1, y1, y2, y2, y1];
% Draw the 128x128 box
plot(xBox128, yBox128, 'b-', 'LineWidth', 2);
% Display the image.
croppedImage = grayImage(y1:y2, x1:x2);
[rows, columns, numColors] = size(croppedImage) % Show values just to make sure.
subplot(1, 2, 2);
imshow(croppedImage, []);
axis on;
title('Cropped 128x128 Image', 'FontSize', fontSize, 'Interpreter', 'None');
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