https://www.slicer.org/w/index.php?title=Documentation/4.10/Modules/SwissSkullStripper&feed=atom&action=historyDocumentation/4.10/Modules/SwissSkullStripper - Revision history2024-03-29T07:07:03ZRevision history for this page on the wikiMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=Documentation/4.10/Modules/SwissSkullStripper&diff=60308&oldid=prevUpdateBot: Nightly -> 4.102018-10-19T00:47:39Z<p>Nightly -> 4.10</p>
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
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Extension: [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]]<br><br />
Acknowledgments:<br />
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><br />
Author: Bill Lorensen (Noware)<br><br />
Contributor1: Stefan Bauer (Institute for Surgical Technology and Biomechanics, University of Bern)<br><br />
Contributor2: Thomas Fejes (Institute for Surgical Technology and Biomechanics, University of Bern)<br><br />
Contributor3: Mauricio Reyes (University of Bern)<br><br />
Contributor4: Arnaud Gelas (Crisalix)<br><br />
Contact: Bill Lorensen, <email>bill.lorensen@gmail.com</email><br><br />
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{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
A skull-stripping module that registers an atlas image to the patient<br />
data. An atlas brain mask is propagated to the patient data. This<br />
brain mask is eroded and then serves as initialization for a refined<br />
brain extraction based on level-sets. The level-set is evolved towards<br />
the edge of the brain-skull border with dedicated expansion, curvature<br />
and advection terms.<br><br />
The module produces a brain mask for the patient data as well as the patient data with the masj applied.<br><br />
For the atlas, a customized isotropic T1-weighted MR image and a<br />
manually generated brain mask are available for download.<br />
* [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasImage.mha Download the atlas image]<br />
* [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''.'''<br />
Users can also provide their own atlas image and brain mask. Be sure that the brain mask is loaded as a ''LabelMap''.<br />
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{|<br />
|[[Image:SwissSkullStripperAtlasImage.png|thumb|340px|Atlas Image]]<br />
|[[Image:SwissSkullStripperAtlasMask.png|thumb|340px|Atlas Mask]]<br />
|[[Image:SwissSkullStripperResults1.png|thumb|340px|Mask overlay on patient volume]]<br />
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The user provides three input volumes:<br />
# An atlas image volume. Use your own, or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasImage.mha download one].<br />
# An atlas brain mask volume, Use your own, or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasMask.mha download one].<br />
# A patient volume. Use your own, or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/RegLib_C01_MRMeningioma_1.nrrd download one].<br />
The module produces:<br />
# A patient volume that resides within the patient mask<br />
# A patient brain mask volume<br />
The process takes about 2 minutes for most datasets.<br />
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
[[Documentation/Nightly/Modules/SkullStripper|SkullStripper]]<br />
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{{documentation/{{documentation/version}}/module-section|References}}<br />
* Bauer S., Fejes T., Reyes M., "A Skull-Stripping Filter for ITK", [http://hdl.handle.net/10380/3353 Insight Journal, January-December, 2012]<br />
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
Source code for the extension is located [https://github.com/lorensen/SwissSkullStripperExtension here].<br><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].<br />
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