How extract skull ?

how to extract the skull from the brain (other than the thresholding method) ?

[ash fairy]

how did you segment the skull??

[Image Analyst]

Ash, I don't know if marwa ever did. However, if you're interested in a thresholding method (which marwa is NOT ) then you can see my attached demo.

Answer 1

[Image Analyst]

You can use manual tracing. See attach demos for imfreehand().

[marwa za]

thank you but I need an automatic way ?

[Image Analyst]

Then look at deep learning. It's the only other way I know of without thresholding in it explicitly. However you know that deep learning has thresholding internal to the algorithm, though it's hidden from you.

Why do you need a way without thresholding?

[marwa za]

I see your thresholding method for skull extraction ( https://www.mathworks.com/matlabcentral/answers/uploaded_files/70212/test3.m) But if we change the image we must change the threshold value each time)

[Image Analyst]

Yes, though you could come up with an automatic threshold selection algorithm that could perhaps pick what you'd pick yourself.

See my interactive, visual thresholding application: https://www.mathworks.com/matlabcentral/fileexchange/29372-thresholding-an-image

[marwa za]

please can you help me in this task : how to segment brain lesions using intra class variation and morphological operation as in this figure and thanks in advance

[Image Analyst]

Sorry, no.

http://matlab.wikia.com/wiki/FAQ#Can_you_program_up_the_algorithm_in_this_article_for_me_and_explain_it_to_me.3F

Perhaps I can help if you give something much, much smaller to ask about rather than programming up a whole algorithm, which could take hours to months to do.

[marwa za]

ok thanks

Answer 2

[Robert Welsh]

Lots of preexisting packages out there that are free for acadmic use:

SPM (which runs on matlab)

FSL (compiled c++ runs on LINUX and MAC OS X)

ANTs (runs on LINUX and MAC OS X)

Googling will get you the links.