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How to do Skull striping to a .dcm image in MATLAB

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Suba Suba
Suba Suba 2016-11-4
评论： Image Analyst 2016-11-5
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

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Image Analyst
Image Analyst 2016-11-4
That link looks like it finds a tumor. Why don't you try searching for the tag skull stripping. I know I've given code for precisely that in prior posts. http://www.mathworks.com/matlabcentral/answers/?term=tag%3A%22skull+stripping%22
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Image Analyst
Image Analyst 2016-11-4
The only image you attached was in your.zip file and it was already binarized. The skull was broken into tiny bits. Your code already removed it, though, like I said, it's not too robust. If you were talking about a different image, then let me know exactly (what exact comment, question, or answer) where you attached it to, because it's not in the .zip file you attached - that has only the binary image.
Suba Suba
Suba Suba 2016-11-5
@Image Analyst Sorry for the late reply,here with this comment I'm again attaching my .dcm image. I just download the image from this link. Please help me to do this.

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更多回答（2 个）

Walter Roberson
Walter Roberson 2016-11-4
The code there assumes that the data is uint8 ,in the range 0 to 255. Data from dicom files is usually quite different ranges than that, with the range depending on the modality and instrument.
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Suba Suba
Suba Suba 2016-11-4
Is there any other method to do skull striping in .dcm images? Please help me to sort out this problem.

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Image Analyst
Image Analyst 2016-11-5
编辑：Image Analyst 2016-11-5
Actually you're not attaching it again. This is the first time you've attached the gray scale image. Here is my 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 = 15;
%===============================================================================
% Get the name of the image the user wants to use.
baseFileName = 'IM-0001-0009.dcm';
% Get the full filename, with path prepended.
folder = pwd
fullFileName = fullfile(folder, baseFileName);
%===============================================================================
% Read in a demo image.
grayImage = dicomread(fullFileName);
% Get the dimensions of the image.
% numberOfColorBands should be = 1.
[rows, columns, numberOfColorChannels] = size(grayImage);
if numberOfColorChannels > 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 image.
subplot(2, 3, 1);
imshow(grayImage, []);
axis on;
caption = sprintf('Original Grayscale Image, %s', baseFileName);
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 ImageAnalyst', 'NumberTitle', 'Off')
% Display the histogram so we can see what gray level we need to threshold it at.
subplot(2, 3, 2:3);
histogram(grayImage);
grid on;
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
% Threshold the image to make a binary image.
binaryImage = grayImage > 250;
% Display the image.
subplot(2, 3, 4);
imshow(binaryImage, []);
axis on;
caption = sprintf('Initial Binary Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
% Extract the outer blob, which is the skull
labeledImage = bwlabel(binaryImage);
binaryImage = ismember(labeledImage, 1);
% Thicken it a little
binaryImage = imdilate(binaryImage, true(5));
% Display the final binary image.
subplot(2, 3, 5);
imshow(binaryImage, []);
axis on;
caption = sprintf('Final Binary Image of Skull Alone');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
% Mask out the skull from the original gray scale image.
outputImage = grayImage; % Initialize
outputImage(binaryImage) = 0; % Mask out.
% Display the image.
subplot(2, 3, 6);
imshow(outputImage, []);
axis on;
caption = sprintf('Skull-Stripped Gray Scale Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
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Image Analyst
Image Analyst 2016-11-5
You're welcome. Thanks for accepting. I'm attaching a fancier demo where I find the tumor and then indicate it in the overlay in two ways, by a red outline and by a red solid patch in the overlay.

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