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Automatic brain masking is too inclusive, add new method #6

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styner opened this issue Jan 2, 2015 · 0 comments
Open

Automatic brain masking is too inclusive, add new method #6

styner opened this issue Jan 2, 2015 · 0 comments

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@styner
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styner commented Jan 2, 2015

The current automatic brain masking is too inclusive for the purpose of entropy computation. Enable a new method that computes a restricted brain mask only comprising WM and GM excluding CSF for the purpose of entropy computation:
1- Compute IDWI as with FSL Bet on IDWI
2 - ImageMath -otsu
3 - ImageMath -conComp 1

This mask should be used ONLY for entropy computation.
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@styner