How to generate skull striped image for all slices ?

Hello

I'm working on masking out the skull from original gray scale MR image for just one slice using the following code :

outputImage = grayImage; % Initialize
outputImage(binaryImage) = 0; % Mask out.

Now, I want to calculate it for all slices(slice 1 to slice 14 ), I've maked a loop for that but this doesn't work:

for j=1:14
outputImage(:,:,j) = grayImage(:,:,j); % Initialize
outputImage(binaryImage(:,:,j)) = 0; % Mask out
end

Could anyone help me please ?

Answer 1

[Image Analyst]

You need to do something like

[rows, columns, numSlices] = size(grayImage);
for k = 1 : numSlices
    thisSlice = grayImage(:, :, k); % Extract one slice
    skullStrippedImage = StripSkull(thisSlice);  % Call function that strips skull off just one slice.
    outputImage(:,:,k) = skullStrippedImage ;
end

[MMSAAH]

Thank You for your response.

Actually, I've tried your code posted in this question.

https://www.mathworks.com/matlabcentral/answers/172701-how-to-perform-skull-stripping-using-matlab

This code works well for just one slice, now I want to run it for all MR slices using a loop. So I've not a function to call it that strips skull. Hope that you understand me ?

[Image Analyst]

Then turn that code into a function called StripSkull

function skullStrippedImage = StripSkull(thisSlice)
% Code goes here....