Difference between revisions of "Documentation/Nightly/Modules/SwissSkullStripper"
Line 14: | Line 14: | ||
Contributor1: Stefan Bauer (Institute for Surgical Technology and Biomechanics, University of Bern)<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> | Contributor2: Thomas Fejes (Institute for Surgical Technology and Biomechanics, University of Bern)<br> | ||
− | Contributor3: | + | Contributor3: Mauricio Reyes (University of Bern)<br> |
Contributor4: Arnaud Gelas (Crisalix)<br> | Contributor4: Arnaud Gelas (Crisalix)<br> | ||
Contact: Bill Lorensen, <email>bill.lorensen@gmail.com</email><br> | Contact: Bill Lorensen, <email>bill.lorensen@gmail.com</email><br> | ||
Line 53: | Line 53: | ||
|} | |} | ||
The user provides three input volumes: | The user provides three input volumes: | ||
− | # An atlas image volume | + | # 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 | + | # 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 | + | # 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: | The module produces: | ||
# A patient volume that resides within the patient mask | # A patient volume that resides within the patient mask |
Revision as of 17:34, 16 June 2013
Home < Documentation < Nightly < Modules < SwissSkullStripper
For the latest Slicer documentation, visit the read-the-docs. |
Introduction and Acknowledgements
Extension: SwissSkullStripper |
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.
The module produces a brain mask for the patient data as well as the patient data with the masj applied.
For the atlas, a customized isotropic T1-weighted MR image and a
manually generated brain mask are available for download.
Users can also provide their own atlas image and brain mask.
Use Cases
Tutorials
Panels and their use
The user provides three input volumes:
- An atlas image volume. Use your own, or download one.
- An atlas brain mask volume, Use your own, or download one.
- A patient volume. Use your own, or 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.
Similar Modules
References
- Bauer S., Fejes T., Reyes M., "A Skull-Stripping Filter for ITK", Insight Journal, January-December, 2012
Information for Developers
Source code for the extension is located here.
A version of the module that can be used outside Slicer4 as an ITK remote module is located here.
Section under construction. |