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Skull Stripping Matlab

This document summarizes the steps taken to read in a grayscale image, perform preprocessing like cropping and thresholding to create a binary image, erode the binary image, and use it as a mask on the original grayscale image to perform skull stripping. Key steps include loading an image, displaying its histogram, thresholding to create a binary image, morphological operations like erosion to clean it, and masking the original with the binary to remove background.

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adjie kazama
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46 views4 pages

Skull Stripping Matlab

This document summarizes the steps taken to read in a grayscale image, perform preprocessing like cropping and thresholding to create a binary image, erode the binary image, and use it as a mask on the original grayscale image to perform skull stripping. Key steps include loading an image, displaying its histogram, thresholding to create a binary image, morphological operations like erosion to clean it, and masking the original with the binary to remove background.

Uploaded by

adjie kazama
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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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;

end

end

%===============================================================================

% 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;

end

end

grayImage = 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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