How to perform skull stripping using matlab?
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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;
fontSize = 24;
% Check that user has the Image Processing Toolbox installed.
hasIPT = license('test', 'image_toolbox');
% 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.
% 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);
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.
% Display the original gray scale image.
subplot(2, 3, 1);
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);
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);
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);
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);
title('Eroded Binary Image', 'FontSize', fontSize);
% Mask the gray image
finalImage = grayImage; % Initialize.
finalImage(~binaryImage) = 0;
subplot(2, 3, 6);
title('Skull stripped Image', 'FontSize', fontSize);
msgbox('Done with demo');
More Answers (4)
Alfonso Nieto-Castanon on 28 Jan 2015
Assuming that you do not have simply that slice but the entire MRI scan (e.g. a filename.nii or filename.img file) I would suggest using SPM (this is Matlab software). Applying segmentation to your structural volume will generate a number of masks (files named c#filename.nii) indicating the different tissues of interest.
To perform skull-stripping you typically want to keep the grey-matter, white-matter, and CSF masks (masks c1filename.nii to c3filename.nii, respectively) and remove everything else. You can do this after segmentation simply using SPM 'imcalc' option and multiplying your original structural volume by the sum of these masks (c1- to c3).
You may try searching through or posting to SPM email list for more info
To strip/remove the skull, look for my code and search for things like skull and brain in this Answers forum. I know I gave a demo for this some time back. A quick check didn't find my demo but I didn't look at a lot of questions on this, and there are a lot of them. I did find one answer I gave and it seems valid for your case.
To strip the skull you threshold it so that you get the skull separated - not connected to the brain. Then you label it with bwlabel() and then use ismember() to isolate the region with label 1, which should be the skull assuming it's the outermost object (no letters or annotation present in the image). Or you can use ismember to extract out everything with labels 2 and up to get everything except the skull.
Attach your image and attempt at coding that up for more help.
Magdalena Gierczynska on 7 Oct 2020
Hi, I have a question. I understand everything to "%Erode away 15 layers of pixels.". You used erosion to reduce border pixels, but what exactly happen in "% Mask the gray image"? On the next image you show "skull stripped image", how? I don't understand this part of code. Can you explain me? I will be greatful.