MATLAB: Problem with image brain tumor image processing

brain segmentationimage analysisimage enhancementimage processingImage Processing Toolboximage segmentationMATLABtumor

Hi everyone, I have to do tumor brain segmentation for this picture. The lesion is located at the upper right of the brain. I'm currently having difficulties in removing the background as the colour of the background is similar to the other parts of the brain too. Can someone help me with the coding? thank you so much

the final outcome should be like this:

Best Answer

See my skull stripping demo. It does that.

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MATLAB: Crop dark area and display the face only

Convert to grayscale and then threshold and find the bounding box

clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
imtool close all;  % Close all imtool figures.
clear;  % Erase all existing variables. Or clearvars if you want.
workspace;  % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 20;
% Read in the color image.
folder = pwd;
baseFileName = 'm2.bmp';
% Get the full filename, with path prepended.
fullFileName = fullfile(folder, baseFileName);
if ~exist(fullFileName, 'file')
  % Didn't find it there.  Check the search path for it.
  fullFileName = baseFileName; % No path this time.
  if ~exist(fullFileName, 'file')
    % Still didn't find it.  Alert user.
    errorMessage = sprintf('Error: %s does not exist.', fullFileName);
    uiwait(warndlg(errorMessage));
    return;
  end
end
rgbImage = imread(fullFileName);
% Get the dimensions of the image.  numberOfColorBands should be = 3.
[rows, columns, numberOfColorBands] = size(rgbImage);
% Display the original color image.
subplot(2, 3, 1);
imshow(rgbImage, []);
axis on;
title('Original Color Image', 'FontSize', fontSize);
drawnow;
% Enlarge figure to full screen.
set(gcf, 'units','normalized','outerposition',[0 0 1 1]);
% Histogram the red channel, but there is a huge spike at 255 so let's not count those.
subplot(2, 3, 2);
grayImage = rgb2gray(rgbImage);
imshow(grayImage, []);
title('Gray Scale version', 'FontSize', fontSize);
subplot(2, 3, 3);
histogram(grayImage(grayImage<255))
grid on;
title('Histogram of Gray Scale Image', 'FontSize', fontSize);
someThresholdValue = 150;
binaryImage = grayImage > someThresholdValue;
% Take largest blob
binaryImage = bwareafilt(binaryImage, 1);
subplot(2, 3, 4);
imshow(binaryImage);
grid on;
title('Binary Image', 'FontSize', fontSize);
% Label the binary image.
labeledImage = bwlabel(binaryImage);
props = regionprops(labeledImage, 'BoundingBox');
bbox = props.BoundingBox
croppedImageRGB = imcrop(rgbImage, bbox);
subplot(2, 3, 5);
imshow(croppedImageRGB);
grid on;
title('Cropped RGB Image', 'FontSize', fontSize);
% Gray scale version of cropped image
croppedImageGray = imcrop(grayImage, bbox);
subplot(2, 3, 6);
imshow(croppedImageGray);
grid on;
title('Cropped Gray Scale Image', 'FontSize', fontSize);

MATLAB: How to get those object and turn background color into white of the binary image

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 = 20;
% Check that user has the Image Processing Toolbox installed.
hasIPT = license('test', 'image_toolbox');
if ~hasIPT
  % User does not have the toolbox installed.
  message = sprintf('Sorry, but you do not seem to have the Image Processing Toolbox.\nDo you want to try to continue anyway?');
  reply = questdlg(message, 'Toolbox missing', 'Yes', 'No', 'Yes');
  if strcmpi(reply, 'No')
    % User said No, so exit.
    return;
  end
end
% Read in a demo image.
folder = pwd % or wherever the image lives
baseFileName = 'batik22.PNG';
%===============================================================================
% Read in a color reference image.
% Get the full filename, with path prepended.
fullFileName = fullfile(folder, baseFileName);
if ~exist(fullFileName, 'file')
  % Didn't find it there.  Check the search path for it.
  fullFileName = baseFileName; % No path this time.
  if ~exist(fullFileName, 'file')
    % Still didn't find it.  Alert user.
    errorMessage = sprintf('Error: %s does not exist.', fullFileName);
    uiwait(warndlg(errorMessage));
    return;
  end
end
rgbImage = imread(fullFileName);
% Get the dimensions of the image.  numberOfColorBands should be = 3.
[rows, columns, numberOfColorBands] = size(rgbImage);
% Display the original color image.
subplot(2, 2, 1);
imshow(rgbImage);
title('Original Color Image', 'FontSize', fontSize, 'Interpreter', 'None');
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'Outerposition', [0, 0, 1, 1]);
% Take the red channel
grayImage = rgbImage(:,:, 1);
subplot(2, 2, 2);
imshow(grayImage);
axis on;
title('Red Channel Image', 'FontSize', fontSize, 'Interpreter', 'None');
% Threshold the image
binaryImage = grayImage < 127;
subplot(2, 2, 3);
imshow(binaryImage, []);
title('Binary Image', 'FontSize', fontSize, 'Interpreter', 'None');
% Take the 8 largest blobs, then invert the image
binaryImage = ~bwareafilt(binaryImage, 8);
subplot(2, 2, 4);
imshow(binaryImage, []);
caption = sprintf('Final Binary Image with 8 largest blobs');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');

Best Answer

Related Solutions

MATLAB: Crop dark area and display the face only

MATLAB: How to get those object and turn background color into white of the binary image

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