I have tried this link to do skull striping. For .jpeg images, the answer is giving good solution. But when I tried that to .dcm image, I'm getting black image only.How can I do the skull striping to .dcm images without affecting it's internal parts. Please help me to do this
MATLAB: How to do Skull striping to a .dcm image in MATLAB
dicom imagesdigital image processingImage Processing Toolboximage segmentationskull stripping
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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; endendrgbImage = 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.BoundingBoxcroppedImageRGB = 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);
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; endend% 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; endendrgbImage = 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');
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