View source for Documentation/4.5/Modules/SwissSkullStripper

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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Extension: [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]]<br>
Acknowledgments:
This work is based the Skull-Stripper Filter for ITK, Stefan Bauer, Thomas Fejes and Mauricio Reyes, Institute for Surgical Technology and Biomechanics, University of Bern, Switzerland<br>
Author: Bill Lorensen (Noware)<br>
Contributor1: Stefan Bauer (Institute for Surgical Technology and Biomechanics, University of Bern)<br>
Contributor2: Thomas Fejes (Institute for Surgical Technology and Biomechanics, University of Bern)<br>
Contributor3: Mauricio Reyes (University of Bern)<br>
Contributor4: Arnaud Gelas (Crisalix)<br>
Contact: Bill Lorensen, <email>bill.lorensen@gmail.com</email><br>

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{{documentation/{{documentation/version}}/module-section|Module Description}}
A skull-stripping module that registers an atlas image to the patient
data. An atlas brain mask is propagated to the patient data. This
brain mask is eroded and then serves as initialization for a refined
brain extraction based on level-sets. The level-set is evolved towards
the edge of the brain-skull border with dedicated expansion, curvature
and advection terms.<br>
The module produces a brain mask for the patient data as well as the patient data with the masj applied.<br>
For the atlas, a customized isotropic T1-weighted MR image and a
manually generated brain mask are available for download.
* [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasImage.mha Download the atlas image]
* [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasMask.mha Download the atlas brain mask] '''NOTE: After you load the atlas brain mask, go to ''Volumes'', set the ''Active Volume'' to atlasMask. Then open ''Volume Information'' and check ''LabelMap''.'''
Users can also provide their own atlas image and brain mask. Be sure that the brain mask is loaded as a ''LabelMap''.
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{|
|[[Image:SwissSkullStripperAtlasImage.png|thumb|340px|Atlas Image]]
|[[Image:SwissSkullStripperAtlasMask.png|thumb|340px|Atlas Mask]]
|[[Image:SwissSkullStripperResults1.png|thumb|340px|Mask overlay on patient volume]]
|}

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|[[Image:SwissSkullStripperPanel.png|thumb|280px|Module UI]]
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The user provides three input volumes:
# An atlas image volume. Use your own, or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasImage.mha download one].
# An atlas brain mask volume, Use your own, or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasMask.mha download one].
# A patient volume. Use your own, or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/RegLib_C01_MRMeningioma_1.nrrd download one].
The module produces:
# A patient volume that resides within the patient mask
# A patient brain mask volume
The process takes about 2 minutes for most datasets.
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}
[[Documentation/Nightly/Modules/SkullStripper|SkullStripper]]
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{{documentation/{{documentation/version}}/module-section|References}}
* Bauer S., Fejes T., Reyes M., "A Skull-Stripping Filter for ITK", [http://hdl.handle.net/10380/3353 Insight Journal, January-December, 2012]

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{{documentation/{{documentation/version}}/module-section|Information for Developers}}
Source code for the extension is located [https://github.com/lorensen/SwissSkullStripperExtension here].<br>
A version of the module that can be used outside Slicer4 as an ITK remote module is located [http://github.com/lorensen/skullStrip here].

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[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]
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