[Mristudio-users] about effect of masking

[Jim Li]

Hi Susumu,

Thanks a lot for your detailed instruction. I'll try them.


Jim

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There are three ways for skull stripping in RoiEditor.



1) Simple thresholding: This produce the same results as the DtiStudio's
masking function.

2) Region growing: if you use this function together with b0 or average(all
DWIs), you should be able to achieve very decent skull stripping. We use
this routinely. We use average(DWIs) often.

3) Skull-stripping button: The region growing may leak out to some tissues
outside the brain if high-intensity areas of the brain and outside tissues
are connected. This skull-stripping function poses some restrictions in the
shape of the object. Namely, the brain surface should be smooth without
anything budding out in an extreme manner. If the region growing function
consistently leaks out and defines tissues outside the brain, you can try
this function. This function also allows you to load "second image", such as
an anatomical T2. The brain contour defined by b0 or average(DWIs) will be
superimposed on the second image (please note, the brain contour will not
align perfectly because of subject motion and DTI (EPI)-related brain
distortion). This b0-defined contour then will be used as an initial guess
of the brain contour of the second image and do the skull strip. We use this
function for skull-strip of co-registered T2 (and T1). It works decently,
but not perfect (I've never seen any perfect automated skull-strip that
works for all images anyway).



susumu
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