Help me with the code? I am doing project in brain tumor segmentation! Skull stripping is the first step !!
MATLAB: How to perform skull stripping using anisotropic diffusion filter??
brain tumor segmentationfilterskull stripping
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Try this code:
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 = 24;% 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; endend%===============================================================================
% Read in a standard MATLAB gray scale demo image.
folder = 'D:\Temporary stuff';baseFileName = 'Jones-54-1-jan10-f3.jpg';% Get the full filename, with path prepended.
fullFileName = fullfile(folder, baseFileName);% Check if file exists.
if ~exist(fullFileName, 'file') % File doesn't exist -- didn't find it there. Check the search path for it.
fullFileNameOnSearchPath = baseFileName; % No path this time.
if ~exist(fullFileNameOnSearchPath, 'file') % Still didn't find it. Alert user.
errorMessage = sprintf('Error: %s does not exist in the search path folders.', fullFileName); uiwait(warndlg(errorMessage)); return; endendgrayImage = imread(fullFileName);% Get the dimensions of the image.
% numberOfColorBands should be = 1.
[rows, columns, numberOfColorBands] = size(grayImage);if numberOfColorBands > 1 % It's not really gray scale like we expected - it's color.
% Convert it to gray scale by taking only the green channel.
grayImage = grayImage(:, :, 2); % Take green channel.
end% Display the original gray scale image.
subplot(2, 3, 1);imshow(grayImage, []);axis on;title('Original Grayscale Image', 'FontSize', fontSize);% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);% Give a name to the title bar.
set(gcf, 'Name', 'Demo by ImageAnalyst', 'NumberTitle', 'Off')% Let's compute and display the histogram.
[pixelCount, grayLevels] = imhist(grayImage);subplot(2, 3, 2);bar(grayLevels, pixelCount);grid on;title('Histogram of original image', 'FontSize', fontSize);xlim([0 grayLevels(end)]); % Scale x axis manually.
% Crop image to get rid of light box surrounding the image
grayImage = grayImage(3:end-3, 4:end-4);% Threshold to create a binary image
binaryImage = grayImage > 20;% Get rid of small specks of noise
binaryImage = bwareaopen(binaryImage, 10);% Display the original gray scale image.subplot(2, 3, 3);imshow(binaryImage, []);axis on;title('Binary Image', 'FontSize', fontSize);% Seal off the bottom of the head - make the last row white.
binaryImage(end,:) = true;% Fill the image
binaryImage = imfill(binaryImage, 'holes');subplot(2, 3, 4);imshow(binaryImage, []);axis on;title('Cleaned Binary Image', 'FontSize', fontSize);% Erode away 15 layers of pixels.
se = strel('disk', 15, 0);binaryImage = imerode(binaryImage, se);subplot(2, 3, 5);imshow(binaryImage, []);axis on;title('Eroded Binary Image', 'FontSize', fontSize);% Mask the gray image
finalImage = grayImage; % Initialize.
finalImage(~binaryImage) = 0;subplot(2, 3, 6);imshow(finalImage, []);axis on;title('Skull stripped Image', 'FontSize', fontSize);msgbox('Done with demo');
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