Skull Removal of brain using matlab

Hi,

I want to remove the skull from brain Image, one link I found useful in mathworks is http://www.mathworks.cn/matlabcentral/answers/42820-skull-striping-without-affecting-tumor-region, Please tell me What are useful methods for this task is there is any efficient way in matlab to do it without any medical softwares, if there is very good medical software then which one is easy to useful for this purpose. Like this is The http://www.flickr.com/photos/95383933@N08/9339172769/ for which I would strip the skull,

thanks in advance for comments and solutions

Answer 1

[Image Analyst]

First, get rid of the text, if it's in the image. Then threshold the image to binarize it. Then label the image with bwlabel(). Then use ismember to get rid of blob #1 and keep all other blobs. This assumes that there is no strand of brightness that connects the skull to anything inside that you want to keep. So, it's like 2 or 3 lines of code. See if you can do it yourself first, but let us know if you can't.

[Muhammad Ali Qadar]

Following Code as you told me is working for me but I ask this question because this code dont work for every Image, I have to change the parameter 'insideSkull' and 'bw' to adjust for each image, I am looking for some more accurate one

 img=imread('img1.jpg');img=img(:,:,1);
insideSkull = (img > 0.2*255);   %isolate all dense material
insideSkull = imfill(insideSkull, 'holes'); 
bw = (img > 0.25*255); 
lbl = bwlabel(bw);
props = regionprops(lbl, 'Solidity', 'Area');
% solidity is the percentage "filled" of an area. For the skull, 
%the solidity will be really low.
solidity = [props.Solidity];
skull = find(solidity < 0.2);
skull = ismember(lbl, skull);
skullOrBorder = skull | ~insideSkull;
noSkull = img;
noSkull(skullOrBorder)=0;
imshow(noSkull);  %this only contains gray matter and tumor

[Image Analyst]

I can't try it since flickr is making it impossible to download your image. Try http://snag.gy

I didn't say anything about solidity. I was thinking something like

[labeledImage, numberOfBlobs] = bwlabel(binaryImage);
binaryImage2 = ismember(labeledImage, 2:numberOfBlobs);

It will get rid of blob #1 which will be the skull because that is the left most blob as the labeling proceeds from upper left, going down columns until it gets to the lower right corner.

[Muhammad Ali Qadar]

http://snag.gy/8pL44.jpg is the image, Thank you image Analyst can you please try this image with you coding in matlab.

[Muhammad Ali Qadar]

@Image Analyst, can you please Try the Image with your code

Answer 2

[Thomas]

Muhammad,

I use a program known as AFNI for such skull stripping. AFNI has been developed by the National Institute of Health (NIH) AFNI can be found here for download (it's free- http://afni.nimh.nih.gov/afni)

and the part used for skull stripping is called 3dSkullStrip http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dSkullStrip.html

[Muhammad Ali Qadar]

@Thomas, Thank for information Can you guide me more in it , please Tell me I am on windows 7 Platform, which one I need to download and how to use is it need to use with matlab or like simple softwares, Please inform me More about it. Looking forward

[Thomas]

Muhammad, AFNI works only only a UNIX/Linux based system (Ubuntu, Debian, CentOS, MAC-OSX) You just run your nifiti images throught he 3dSkullStripper and in my experience it does an excellent job around 98% of the time. All the documentation on how to use it is available on the website in my original answer.

[Muhammad Ali Qadar]

so It do not work for Windows then is there is no Way to use it for Windows