Skull Stripping using EMSegmenter

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Skull Stripping using EMSegmenter

willadu
Hello all, 

I've been trying to use slicer for skull stripping as an effort to unify my workflow. I previously was using FSL to perform skull stripping. It seems as if there is a consensus that the skull stripping module does not currently work. Correct? Thus, it seems as if EM segmenter is the best bet. However, when using EM segmenter, is there a way to mask the original MRI so that only brain material is shown. It would seem that mask scalar volume would work, but that only allows the masking of 1 label. Are there any solutions to this issue? Or any other ways to perform skull stripping? Many thanks in advance. 

William


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Re: Skull Stripping using EMSegmenter

Kilian Pohl
On 01/22/2013 12:03 AM, William Du wrote:
Hello all, 

I've been trying to use slicer for skull stripping as an effort to unify my workflow. I previously was using FSL to perform skull stripping. It seems as if there is a consensus that the skull stripping module does not currently work. Correct? Thus, it seems as if EM segmenter is the best bet. However, when using EM segmenter, is there a way to mask the original MRI so that only brain material is shown. It would seem that mask scalar volume would work, but that only allows the masking of 1 label. Are there any solutions to this issue? Or any other ways to perform skull stripping? Many thanks in advance.
Hi William,

There are two solutions :
a)  you simply apply the output of the EMSegmenter to Threshold Scalar Volume: Select option above, set Threshold Value and outside value to 1 . This will result in a binary mask which you then apply to the original image via Multiply Scalar Volume
b) You or I  can create a task "Brain Mask" in EMSegmenter which provides you with the binary mask. Simply setting all the labels in of CSF, GM , WM in MRI Humdan Brain to 1 will do the trick

Does that answer your question

Kilian

 


William



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