For the latest Slicer documentation, visit the 4.10 page.
Introduction and Acknowledgements
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.
- Download the atlas image
- 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.
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.
- Bauer S., Fejes T., Reyes M., "A Skull-Stripping Filter for ITK", Insight Journal, January-December, 2012
Information for Developers
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