Difference between revisions of "Documentation/Nightly/Modules/SwissSkullStripper"
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For the atlas, a customized isotropic T1-weighted MR image and a | For the atlas, a customized isotropic T1-weighted MR image and a | ||
manually generated brain mask are available for download. | 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] | * [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasMask.mha Download the atlas brain mask] | ||
Users can also provide their own atlas image and brain mask. | Users can also provide their own atlas image and brain mask. | ||
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|[[Image:SwissSkullStripperPanel.png|thumb|280px|Module UI]] | |[[Image:SwissSkullStripperPanel.png|thumb|280px|Module UI]] | ||
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| − | + | The user provides three input volumes: | |
| + | # An atlas image volume | ||
| + | # An atlas brain mask volume | ||
| + | # A patient volume | ||
| + | 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/{{documentation/version}}/module-section|Similar Modules}} | ||
| − | [[ | + | [[Documentation/Nightly/Modules/SkullStripper|SkullStripper]] |
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{{documentation/{{documentation/version}}/module-section|References}} | {{documentation/{{documentation/version}}/module-section|References}} | ||
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{{documentation/{{documentation/version}}/module-section|Information for Developers}} | {{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]. | ||
| + | |||
{{documentation/{{documentation/version}}/module-developerinfo}} | {{documentation/{{documentation/version}}/module-developerinfo}} | ||
Revision as of 13:14, 16 June 2013
Home < Documentation < Nightly < Modules < SwissSkullStripper
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For the latest Slicer documentation, visit the read-the-docs. |
Introduction and Acknowledgements
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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
- An atlas brain mask volume
- A patient volume
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.
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Section under construction. |
