Documentation/Nightly/Modules/SwissSkullStripper

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Introduction and Acknowledgements

Extension: SwissSkullStripper 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 Author: Bill Lorensen (Noware) Contributor1: Stefan Bauer (Institute for Surgical Technology and Biomechanics, University of Bern) Contributor2: Thomas Fejes (Institute for Surgical Technology and Biomechanics, University of Bern) Contributor3: Mauricio Reyes (University of Bern) Contributor4: Arnaud Gelas (Crisalix) Contact: Bill Lorensen, <email>bill.lorensen@gmail.com</email>

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 mask 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
• Load the two image and mask files into Slicer using menu File / Add data or by drag-and-dropping the files to the application window.
  • Important: in Add data dialog, click Show options and make sure Labelmap checkbox is checked for the mask (if this step is missed then the mask volume will not appear in the atlas mask volume selector)

Users can also provide their own atlas image and brain mask.

Use Cases

Atlas Image

Atlas Mask

Mask overlay on patient volume

Panels and their use

Module UI

The user provides three input volumes:

1. An atlas image volume. Use your own, or download one.
2. An atlas brain mask volume, Use your own, or download one.
   • Important: in Add data dialog, click Show options and make sure Labelmap checkbox is checked for the mask (if this step is missed then the mask volume will not appear in the atlas mask volume selector)
3. A patient volume. Use your own, or download one.

The module produces:

1. A patient volume that resides within the patient mask
2. A patient brain mask volume

The process takes about 2 minutes for most datasets.

Similar Modules

SkullStripper

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.