Slicer Wiki - User contributions [en]

Documentation/4.3/Modules/SwissSkullStripper

2013-09-13T19:40:26Z

Lorensen:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|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> 

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|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.
* [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]
'''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.

{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:SwissSkullStripperAtlasImage.png|thumb|340px|Atlas Image]]
|[[Image:SwissSkullStripperAtlasMask.png|thumb|340px|Atlas Mask]]
|[[Image:SwissSkullStripperResults1.png|thumb|340px|Mask overlay on patient volume]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|
|[[Image:SwissSkullStripperPanel.png|thumb|280px|Module UI]]
|}
The user provides three input volumes:
# 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, Use your own, or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasMask.mha download one].
# 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:
# A patient volume that resides within the patient mask
# A patient brain mask volume
The process takes about 2 minutes for most datasets.

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
[[Documentation/Nightly/Modules/SkullStripper|SkullStripper]]

{{documentation/{{documentation/version}}/module-section|References}}
* Bauer S., Fejes T., Reyes M., "A Skull-Stripping Filter for ITK", [http://hdl.handle.net/10380/3353 Insight Journal, January-December, 2012]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
Source code for the extension is located [https://github.com/lorensen/SwissSkullStripperExtension here]. 
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-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Modules/SwissSkullStripper

2013-09-13T19:33:43Z

Lorensen:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|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> 

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|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.
* [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] '''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''.

{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:SwissSkullStripperAtlasImage.png|thumb|340px|Atlas Image]]
|[[Image:SwissSkullStripperAtlasMask.png|thumb|340px|Atlas Mask]]
|[[Image:SwissSkullStripperResults1.png|thumb|340px|Mask overlay on patient volume]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|
|[[Image:SwissSkullStripperPanel.png|thumb|280px|Module UI]]
|}
The user provides three input volumes:
# 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, Use your own, or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasMask.mha download one].
# 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:
# A patient volume that resides within the patient mask
# A patient brain mask volume
The process takes about 2 minutes for most datasets.

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
[[Documentation/Nightly/Modules/SkullStripper|SkullStripper]]

{{documentation/{{documentation/version}}/module-section|References}}
* Bauer S., Fejes T., Reyes M., "A Skull-Stripping Filter for ITK", [http://hdl.handle.net/10380/3353 Insight Journal, January-December, 2012]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
Source code for the extension is located [https://github.com/lorensen/SwissSkullStripperExtension here]. 
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-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions

2013-09-13T12:44:42Z

Lorensen: Added Swiss Skull Stripper

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>
__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]
** [[Documentation/{{documentation/version}}/Modules/PatientHierarchy|Patient hierarchy]]
** [[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Transform visualizer (moved to separate extension)]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] [[image:UnderConstruction.png|tumb|10px]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)
* [[Documentation/{{documentation/version}}/Extensions/PathPlanner|PathPlanner]] (Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/VisuaLine|VisuaLine]] (Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)
* [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)
* [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)
**[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Andinet Enquobahrie, Luis G. Torres)
* [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)
* [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]
** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]
** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)
* [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)
<noinclude>
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}
</noinclude>

Documentation/4.3/Extensions

2013-09-13T12:42:16Z

Lorensen: Added Swiss Skull Stripper

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>
__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]
** [[Documentation/{{documentation/version}}/Modules/PatientHierarchy|Patient hierarchy]]
** [[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Transform visualizer (moved to separate extension)]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] [[image:UnderConstruction.png|tumb|10px]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)
* [[Documentation/{{documentation/version}}/Extensions/PathPlanner|PathPlanner]] (Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/VisuaLine|VisuaLine]] (Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)
* [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)
* [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)
**[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Andinet Enquobahrie, Luis G. Torres)
* [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)
* [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)
<noinclude>
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}
</noinclude>

Modules:GrayscaleModelMaker-Documentation-3.6

2013-07-23T03:43:58Z

Lorensen: Updated links

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Grayscale Model Maker

{|
|[[Image:GMMSkin.png|thumb|280px|CT Study, Skin. Threshold=-300 [http://en.wikipedia.org/wiki/Hounsfield_scale Hounsfield Units]]]
|[[Image:GMMBone.png|thumb|280px|CT Study, Bone. Threshold=200 [http://en.wikipedia.org/wiki/Hounsfield_scale Hounsfield Units]]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Surface Models

===Authors, Collaborators & Contact===
* Authors: Bill Lorensen, Nicole Aucoin
* Contact: bill.lorensen at gmail.com

===Module Description===

{| style="color:green" border="1"

|Program title || Grayscale Model Maker

|-
|Program description ||
Create 3D surface models from grayscale data. This module uses Marching Cubes to create an isosurface at a given threshold. The resulting surface consists of triangles that separate a volume into regions below and above the threshold. The resulting surface can be smoothed and decimated. This module works on continuous data while the module Model Maker works on labeled (or discrete) data.

|-
|Program version || 3.0

|-
|Program documentation-url || http://www.slicer.org/slicerWiki/index.php/Modules:GrayscaleModelMaker-Documentation-3.6

|-
|}

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1: when have a continuous data set as input (ie grey scale volume)

Examples of the module in use:

* Example 1: to create a model of the skin or bone from a volume
* Example 2

===Tutorials===

* Tutorial 1
** Data Set 1

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them.

{|
|
* '''''IO''''' 
** '''Input Volume''' : Volume containing the input grayscale data.
** '''Output Geometry''' : Output that contains geometry model.

* '''''Grayscale Model Maker Parameters''''' 
** '''Threshold''' [----threshold] [--t]: Grayscale threshold of isosurface. The resulting surface of triangles separates the volume into voxels that lie above (inside) and below (outside) the threshold. ''Default value: 100.0''
** '''Model Name''' [----name] [--n]: Name to use for this model. ''Default value: Model''
** '''Smooth''' [----smooth] : Number of smoothing iterations. If 0, no smoothing will be done. ''Default value: 15''
** '''Decimate''' [----decimate] : Target reduction during decimation, as a decimal percentage reduction in the number of polygons. If 0, no decimation will be done. ''Default value: 0.25''
** '''Split Normals?''' [----splitnormals] : Splitting normals is useful for visualizing sharp features. However it creates holes in surfaces which affect measurements ''Default value: true''
** '''Compute Point Normals?''' [----pointnormals] : Calculate the point normals? Calculated point normals make the surface appear smooth. Without point normals, the surface will appear faceted. ''Default value: true''

|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Source code & documentation===
Source Code: [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleModelMaker/GrayscaleModelMaker.cxx?view=co GrayscaleModelMaker.cxx]

XML Description: [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleModelMaker/GrayscaleModelMaker.xml?view=co GrayscaleModelMaker.xml]

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===
Model smoothing is done using the windowed sinc algorithm:
http://www.vtk.org/doc/nightly/html/classvtkWindowedSincPolyDataFilter.html#details

Documentation/Nightly/ElevatorStory

2013-07-22T19:35:53Z

Lorensen: /* Email template */

<noinclude>{{documentation/versioncheck}}</noinclude>
= What is it ?=
<pre>An elevator story is a summary you can provide to someone you
meet in an elevator, traveling a few floors. The same holds for an
e-mail you can present in a few lines (~10).</pre>

See http://slicer-devel.65872.n3.nabble.com/Slicer-Elevator-Story-tt4026759.html

= Email template =
Please cut and paste the following into an e-mail if you think Slicer can solve a user's problem.

<pre>
3D Slicer is:
* A software platform for the analysis and visualization of medical images and for research in image guided therapy.
* A free, open source software available on multiple operating systems (Windows, MAC, Linux).
* Extensible, with powerful plug-in capabilities for adding algorithms and applications.
http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Developers

Features include:
* Available for windows, linux and Mac OS X
* Support for many modalities, including, MRI, CT, US, nuclear medicine, and microscopy
* Robust support for DICOM
* Flexible display capabilities with a variety of predefined layouts for slice reformats and 3d views
* Annotations
* Accelerated volume rendering
* Powerful data fusion and registration capabilities
* Automated and interactive segmentation tools
* Surface reconstruction from image data (Marching Cubes, Isosurface modelling)
* Bidirectional interface for devices (OpenIGTLink)
* Plugin architecture for IO formats and algorithms
* Extensible & scriptable development platform (C++/Python)

Please visit http://www.slicer.org/pages/Introduction for a more
complete description
</pre>

3D Slicer is:
* A software platform for the analysis and visualization of medical images and for research in image guided therapy.
* A free, open source software available on multiple operating systems (Windows, MAC, Linux).
* Extensible, with powerful [[Documentation/{{documentation/currentversion}}/Developers| plug-in capabilities]] for adding algorithms and applications.

Features include:
* Available for windows, linux and Mac OS X
* Support for many modalities, including, MRI, CT, US, nuclear medicine, and microscopy
* Robust support for DICOM
* Flexible display capabilities with a variety of predefined layouts for slice reformats and 3d views
* Annotations
* Accelerated volume rendering
* Powerful data fusion and registration capabilities
* Automated and interactive segmentation tools
* Surface reconstruction from image data (Marching Cubes, Isosurface modelling)
* Bidirectional interface for devices (OpenIGTLink)
* Plugin architecture for IO formats and algorithms
* Extensible & scriptable development platform (C++/Python)

Please visit http://www.slicer.org/pages/Introduction for a more
complete description

There is no restriction on use, but permissions and compliance with rules
are responsibility of users. See http://www.slicer.org/pages/LicenseText.

See http://download.slicer.org/ to download Slicer4 for your platform.

Documentation/Nightly/Developers/Tutorials/BuildTestPackageDistributeExtensions

2013-06-22T19:56:38Z

Lorensen:

<noinclude>{{documentation/versioncheck}}</noinclude>
== Step-by-step: How to create, publish and distribute an extension ? ==

<ol start="1" style="list-style-type: decimal;">

<li>Scan through the [[Documentation/{{documentation/version}}/FAQ/Extensions|user]] and [[Documentation/{{documentation/version}}/Developers/FAQ/Extensions|developer]] extension FAQs</li>

<li>(Optionally) Present your extension(s) on the [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel slicer developers list] to check if other developer are working on a similar project, to seek for advice or to reach out for potential collaborator.</li>

<li>[[Documentation/{{documentation/version}}/Developers/Build_Instructions|Build Slicer application]] in <code>Release</code></li>

<li>Use the Wizard to create an extension bundling one Command line module:

{|width = "100%"
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Linux or MacOSX
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Windows
|-
| valign="top" |
Start a terminal.
{{pre2|<nowiki>
$ cd Slicer

$ ../Slicer-SuperBuild/python-build/bin/python ./Utilities/Scripts/ModuleWizard.py --template ./Extensions/Testing/CLIExtensionTemplate/ --target ~/MyExtension MyExtension

$ rm -rf ~/MyExtension/CLIModuleTemplate/

$ ../Slicer-SuperBuild/python-build/bin/python ./Utilities/Scripts/ModuleWizard.py --template ./Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplate/ --target ~/MyExtension/MyCLI MyCLI

$ sed -i.bak 's/add_subdirectory(CLIModuleTemplate)/add_subdirectory(MyCLI)/g' ~/MyExtension/CMakeLists.txt && rm ~/MyExtension/CMakeLists.txt.bak
</nowiki>}}

To learn more about:
: the Wizard, click [[Documentation/{{documentation/version}}/Developers/ModuleWizard|here]].
: the different type of modules, click [[Documentation/{{documentation/version}}/Developers/Modules|here]].
| valign="top" |

Start Git Bash (not the Windows command line). [https://help.github.com/articles/set-up-git#platform-windows Need help ?]
{{pre2|<nowiki>
$ cd Slicer

$ ../Slicer-SuperBuild/python-build/bin/Release/python.exe ./Utilities/Scripts/ModuleWizard.py --template ./Extensions/Testing/CLIExtensionTemplate/ --target ~/MyExtension MyExtension

$ rm -rf ~/MyExtension/CLIModuleTemplate/

$ ../Slicer-SuperBuild/python-build/bin/Release/python.exe ./Utilities/Scripts/ModuleWizard.py --template ./Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplate/ --target ~/MyExtension/MyCLI MyCLI

$ sed.exe -i.bak 's/add_subdirectory(CLIModuleTemplate)/add_subdirectory(MyCLI)/g' ~/MyExtension/CMakeLists.txt && rm ~/MyExtension/CMakeLists.txt.bak
</nowiki>}}
|}

</li>

<li>Create a repository to save your extension located in <code>~/MyExtension</code> directory. We recommend [https://github.com/ GitHub]. [https://help.github.com/articles/create-a-repo Need help ?]</li>

<li>Implement your extension. <code>Hack, hack, hack :)</code>. Make sure to commit often using meaningful commit message.</li>

<li>[[Documentation/{{documentation/version}}/Developers/Tutorials/DocumentExtension#Extension_page|Create a documentation page for your extension]].</li>

<li>[[Documentation/{{documentation/version}}/Developers/Tutorials/ObtainExtensionServerApiKey|Create an account on the extension server and obtain an API Key]]. You will then use your midas login and api key to substitute <code><YOUR-MIDAS-LOGIN></code> and <code><YOUR-MIDAS-APIKEY></code> in the examples.</li>

<li>If not already done, go to [http://slicer.kitware.com/midas3/community/23 NA-MIC community] and click on <code>Join community</code></li>

<li>If not already done, send an email on the [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel slicer developers list] asking to be granted write permission on the [http://slicer.kitware.com/midas3/folder/253 experimental folder].
<pre>
To: slicer-devel@bwh.harvard.edu
Subject: Extension NAME-OF-YOUR-EXTENSION - Asking permission to write to the Experimental folder
Hi,

This extension will allows to [...]

Could you grant user YourUserName write access to the Experimental folder ?

</pre></li>

<li>Assuming the source code of your extension is located in folder <code>MyExtension</code>, you could upload your extension doing:

{|width = "100%"
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Linux or MacOSX (Makefile)
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Windows (Visual Studio)
|-
| valign="top" |
{{pre2|<nowiki>
$ mkdir MyExtension-build

$ cd MyExtension-build

$ cmake -DCMAKE_BUILD_TYPE:STRING=Release -DMIDAS_PACKAGE_EMAIL:STRING=<YOUR-MIDAS-LOGIN> -DMIDAS_PACKAGE_API_KEY:STRING=<YOUR-MIDAS-APIKEY> -DSlicer_DIR:PATH=/path/to/Slicer-Superbuild/Slicer-build ../MyExtension

$ make ExperimentalUpload
</nowiki>}}
| valign="top" |
<ol start="1" style="list-style-type: decimal;">
<li>Start CMake, select source and build directory</li>
<li>Add <code>Slicer_DIR</code>, <code>MIDAS_PACKAGE_EMAIL</code> and <code>MIDAS_PACKAGE_API_KEY</code> entries to the cache</li>
[[File:Slicer Extensions Configure Windows.png|600px]]
<li>Click on <code>Configure</code>, select Generator, then click on <code>Generate</code> button.</li>
<li>Open <code>MyExtension.sln</code> (1), select <code>Release</code> configuration (2), select <code>ExperimentalUpload</code> (3) and <code>Build</code> (4).</li>
[[File:Slicer_Extension_ExperimentalUpload_Windows_VS2008.png|400px]]
</ol>
|}
</li>

<li>Check submission results on the dashboard: http://slicer.cdash.org/index.php?project=Slicer4#Extensions-Experimental
<ol style="list-style-type:none; border-left:thick solid red; padding-left:1em;">
<li>You should expect the test <code>MyCLITest</code> to fail with error of the form:
{{pre2|scroll|[nrrd] nrrdIoStateDataFileIterNext: couldn't open "~/MyExtension-build/MyCLI/Data/Baseline/CLIModuleTemplateTest.raw"}}
This is explained by the fact the <code>*.nhdr</code> file available on midas and downloaded locally still reference <code>CLIModuleTemplateTest.raw</code></li>
</ol>
</li>

<li>Check that the extension can be installed by starting the Slicer executable from <code>/path/to/Slicer-Superbuild/Slicer-build</code> and installing your extension as explained [[Documentation/{{documentation/version}}/SlicerApplication/ExtensionsManager|here]].'''NOTE:''' MacOSX users cannot install experimental extensions.</li>

<li>If you consider your extension ready for distribution, follow [[Documentation/{{documentation/version}}/Developers/Tutorials/Contribute_Extension_Description_File|these instructions.]] to contribute the already generated description file.</li>

</ol>

Documentation/Nightly/Extensions/SkullStripper

2013-06-20T15:58:11Z

Lorensen: #REDIRECT must be the first text line on the page

#REDIRECT [[Documentation/Nightly/Modules/SkullStripper]]

Documentation/Nightly/Extensions/SwissSkullStripper

2013-06-20T15:52:50Z

Lorensen: Redirected page to Documentation/Nightly/Modules/SwissSkullStripper

#REDIRECT [[Documentation/Nightly/Modules/SwissSkullStripper]]
<noinclude>{{documentation/versioncheck}}</noinclude>

Documentation/Nightly/Modules/SwissSkullStripper

2013-06-16T17:34:12Z

Lorensen:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|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> 

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|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.
* [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]
Users can also provide their own atlas image and brain mask.

{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:SwissSkullStripperAtlasImage.png|thumb|340px|Atlas Image]]
|[[Image:SwissSkullStripperAtlasMask.png|thumb|340px|Atlas Mask]]
|[[Image:SwissSkullStripperResults1.png|thumb|340px|Mask overlay on patient volume]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|
|[[Image:SwissSkullStripperPanel.png|thumb|280px|Module UI]]
|}
The user provides three input volumes:
# 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, Use your own, or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasMask.mha download one].
# 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:
# A patient volume that resides within the patient mask
# A patient brain mask volume
The process takes about 2 minutes for most datasets.

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
[[Documentation/Nightly/Modules/SkullStripper|SkullStripper]]

{{documentation/{{documentation/version}}/module-section|References}}
* Bauer S., Fejes T., Reyes M., "A Skull-Stripping Filter for ITK", [http://hdl.handle.net/10380/3353 Insight Journal, January-December, 2012]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
Source code for the extension is located [https://github.com/lorensen/SwissSkullStripperExtension here]. 
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-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

{{documentation/{{documentation/version}}/extension-footer}}

File:SwissSkullStripper.png

2013-06-16T15:20:53Z

Lorensen:

Documentation/Nightly/Modules/SwissSkullStripper

2013-06-16T13:14:17Z

Lorensen:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|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: Mauriicio Reyes (University of Bern) 
Contributor4: Arnaud Gelas (Crisalix) 
Contact: Bill Lorensen, <email>bill.lorensen@gmail.com</email> 

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|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.
* [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]
Users can also provide their own atlas image and brain mask.

{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:SwissSkullStripperAtlasImage.png|thumb|340px|Atlas Image]]
|[[Image:SwissSkullStripperAtlasMask.png|thumb|340px|Atlas Mask]]
|[[Image:SwissSkullStripperResults1.png|thumb|340px|Mask overlay on patient volume]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|
|[[Image:SwissSkullStripperPanel.png|thumb|280px|Module UI]]
|}
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.

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
[[Documentation/Nightly/Modules/SkullStripper|SkullStripper]]

{{documentation/{{documentation/version}}/module-section|References}}
* Bauer S., Fejes T., Reyes M., "A Skull-Stripping Filter for ITK", [http://hdl.handle.net/10380/3353 Insight Journal, January-December, 2012]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
Source code for the extension is located [https://github.com/lorensen/SwissSkullStripperExtension here]. 
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-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/SwissSkullStripper

2013-06-16T13:04:53Z

Lorensen: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> #REDIRECT Documentation/Nightly/Modules/SwissSkullStripper'

<noinclude>{{documentation/versioncheck}}</noinclude>
#REDIRECT [[Documentation/Nightly/Modules/SwissSkullStripper]]

Documentation/Nightly/Modules/SwissSkullStripper

2013-06-16T12:56:06Z

Lorensen: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude>  {{documentation/{{documentation/version}}/module-header}} <!-- -----------------------…'

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|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: Mauriicio Reyes (University of Bern) 
Contributor4: Arnaud Gelas (Crisalix) 
Contact: Bill Lorensen, <email>bill.lorensen@gmail.com</email> 

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|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.
* [[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]
Users can also provide their own atlas image and brain mask.

{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:SwissSkullStripperAtlasImage.png|thumb|340px|Atlas Image]]
|[[Image:SwissSkullStripperAtlasMask.png|thumb|340px|Atlas Mask]]
|[[Image:SwissSkullStripperResults1.png|thumb|340px|Mask overlay on patient volume]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|
|[[Image:SwissSkullStripperPanel.png|thumb|280px|Module UI]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
[[

{{documentation/{{documentation/version}}/module-section|References}}
* Bauer S., Fejes T., Reyes M., "A Skull-Stripping Filter for ITK", [http://hdl.handle.net/10380/3353 Insight Journal, January-December, 2012]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

{{documentation/{{documentation/version}}/extension-footer}}

File:SwissSkullStripperPanel.png

2013-06-16T12:55:26Z

Lorensen:

File:SwissSkullStripperResults1.png

2013-06-16T12:54:45Z

Lorensen:

File:SwissSkullStripperAtlasMask.png

2013-06-16T12:54:15Z

Lorensen:

File:SwissSkullStripperAtlasImage.png

2013-06-16T12:53:35Z

Lorensen:

Documentation/Nightly/ElevatorStory

2012-11-09T21:25:56Z

Lorensen: /* Email template */

= What is it ?=
<pre>An elevator story is a summary you can provide to someone you
meet in an elevator, traveling a few floors. The same holds for an
e-mail you can present in a few lines (~10).</pre>

See http://slicer-devel.65872.n3.nabble.com/Slicer-Elevator-Story-tt4026759.html

= Email template =
Please cut and paste the following into an e-mail if you think Slicer can solve a user's problem.

<pre>
Slicer is a free, open source software package for visualization and
image analysis. 3D Slicer is natively designed to be available on
multiple platforms, including Windows, Linux and Mac Os X. Leverages VTK and ITK.

Features include:
* Multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy
* DICOM support
* Volume Rendering
* 2D Image Display
* Multi Modality Registration
* Segmentation Algorithms
* Marching Cubes, Isosurface modelling
* Bidirectional interface for devices (OpenIGTLink)
* Plugin architecture for IO formats and algorithms

Please visit http://www.slicer.org/pages/Introduction for a more
complete description

There is no restriction on use, but permissions and compliance with rules
are responsibility of users. See http://www.slicer.org/pages/LicenseText.

See http://download.slicer.org/ to download Slicer4 for your platform.
</pre>

Documentation/Nightly/ElevatorStory

2012-11-09T21:23:38Z

Lorensen:

= What is it ?=
<pre>An elevator story is a summary you can provide to someone you
meet in an elevator, traveling a few floors. The same holds for an
e-mail you can present in a few lines (~10).</pre>

See http://slicer-devel.65872.n3.nabble.com/Slicer-Elevator-Story-tt4026759.html

= Email template =
Please cut and paste the following into an e-mail if you think Slicer can solve a user's problem.

<pre>
Slicer is a free, open source software package for visualization and
image analysis. 3D Slicer is natively designed to be available on
multiple platforms, including Windows, Linux and Mac Os X. Leverages VTK and ITK.

Features include:
* Multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy
* DICOM support
* Volume Rendering
* 2D Image Display
* Multi Modality Registration
* Segmentation Algorithms
* Marching Cubes, Isosurface modelling
* Bidirectional interface for devices (OpenIGTLink)
* Installation of extensions providing domain-specific functionality
* Plugin architecture for IO formats and algorithms

Please visit http://www.slicer.org/pages/Introduction for a more
complete description

There is no restriction on use, but permissions and compliance with rules
are responsibility of users. See http://www.slicer.org/pages/LicenseText.

See http://download.slicer.org/ to download Slicer4 for your platform.
</pre>

Documentation/Nightly/ElevatorStory

2012-11-09T21:21:26Z

Lorensen: /* Email template */

= What is it ?=
<pre>An elevator story is a summary you can provide to someone you
meet in an elevator, traveling a few floors. The same holds for an
e-mail you can present in a few lines (~10).</pre>

See http://slicer-devel.65872.n3.nabble.com/Slicer-Elevator-Story-tt4026759.html

= Email template =
<pre>
Slicer is a free, open source software package for visualization and
image analysis. 3D Slicer is natively designed to be available on
multiple platforms, including Windows, Linux and Mac Os X. Leverages VTK and ITK.

Features include:
* Multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy
* DICOM support
* Volume Rendering
* 2D Image Display
* Multi Modality Registration
* Segmentation Algorithms
* Marching Cubes, Isosurface modelling
* Bidirectional interface for devices (OpenIGTLink)
* Installation of extensions providing domain-specific functionality
* Plugin architecture for IO formats and algorithms

Please visit http://www.slicer.org/pages/Introduction for a more
complete description

There is no restriction on use, but permissions and compliance with rules
are responsibility of users. See http://www.slicer.org/pages/LicenseText.

See http://download.slicer.org/ to download Slicer4 for your platform.
</pre>

Documentation/Nightly/ElevatorStory

2012-11-09T20:52:45Z

Lorensen: /* Email template */

Documentation/Nightly/ElevatorStory

2012-11-09T20:47:41Z

Lorensen:

Documentation/Nightly/ElevatorStory

2012-11-09T20:32:47Z

Lorensen:

Documentation/4.0/SlicerApplication/ExtensionCatalogPolicies

2012-02-23T21:18:24Z

Lorensen: /* Introduction */

=Introduction=
Ron: In the near future we will have a download site for extensions to Slicer
4. In terms of functionality this is like the Apple App Store or the
Android Market.
I would like to use a name for that capability that will
resonate with the end users.

*Slicer Solution Catalog
*app exchange
*Tool Set
*Toolbox
*Tool Cabinet
*Tool Drawer
*Extension Tools
*Tool Room
*Tool Store
*Tool Line
*Tool Depot
*Tool Set
*Tool Box
*Tool Hub
*Tool Cabinet
*Tool Drawer
*Extension Tools
*Tool Room
*Tool Store
*Tool Selector
*Tool Line
*Tool Chest
*Tool Shed
*Slicer Extension Catalog
*Bargin Bin
*Slicer Exchange
*ToolPlace
*Slicer Mart
*Slicer Bazaar (recall the "Cathedral and the Bazaar")
*Slicer Mall

Documentation/4.0/SlicerApplication/ExtensionCatalogPolicies

2012-02-23T21:18:11Z

Lorensen: /* Introduction */

Documentation/4.0/SlicerApplication/ExtensionCatalogPolicies

2012-02-23T21:04:37Z

Lorensen: /* Introduction */

Documentation/4.0/Developers/Build Instructions

2010-06-04T20:53:17Z

Lorensen: /* Step1 : Checkout slicer sources using subversion */

The build system for [[Slicer4]] is being developed during the second half of 2010. The goal is to provide a cross-platform build system that allows developers to quickly install and configure the multiple packages.

Where [[Slicer3:Build_Instructions|Slicer3's build system]] relied on a [[Slicer3:getbuildtest|custom build script called getbuildtest]], new features added to [http://www.cmake.org CMake], partly driven by slicer's requirements, allow porting of the scripts to rely on more on native CMake functionality with the benefit that build script is more modular and general purpose.

== Prerequisites ==

* Download (and if required compile) Qt - Use one of the link provided below:

{| border="1"
|- bgcolor="#FFFFCC"
!rowspan="3"|
!colspan="2" rowspan="2"|Linux
!colspan="4"|Mac
!colspan="2" rowspan="2"|Windows
|- bgcolor="#FFFFCC"
!colspan="2"|Tiger, Leopard
!colspan="2"|SnowLeopard
|- bgcolor="#FFFFCC"
!|32bits
!|64bits
!|32bits
!|64bits
!colspan="2"|64bits
!|32bits
!|64bits
|-
! bgcolor="#FFFFCC" | [http://get.qt.nokia.com/qt/source/ Qt source link]
|align="center" colspan="4"| [http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.6.2.tar.gz 4.6.2]
|align="center" colspan="2"| [http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.7.0-beta1.tar.gz 4.7 beta]
|align="center" colspan="2"| [http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.6.2.zip 4.6.2]
|-
! bgcolor="#FFFFCC" | [http://get.qt.nokia.com/qt/source/ Qt binary link]
|align="center" colspan="1"| [http://get.qt.nokia.com/qtsdk/qt-sdk-linux-x86-opensource-2010.02.bin 4.6.2]
|align="center" colspan="1"| [http://get.qt.nokia.com/qtsdk/qt-sdk-linux-x86_64-opensource-2010.02.bin 4.6.2]
|align="center" colspan="2"| [http://get.qt.nokia.com/qtsdk/qt-sdk-mac-opensource-2010.02.dmg 4.6.2]
|align="center" colspan="2"| [http://get.qt.nokia.com/qt/source/qt-mac-opensource-4.7.0-beta1.dmg 4.7 beta]
|align="center" colspan="1"| [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.6.2-vs2008.exe 4.6.2 (vs2008)]
|align="center" colspan="1"| -
|}

* How to build Qt ?

Configure options common to all platform:

Check our different tutorials:
* Build Qt on Windows
* Build Qt on Linux
* Build Qt on Mac

== Step1 : Checkout slicer sources using subversion ==
For example:
<pre>
cd MyProjects
svn co http://svn.slicer.org/Slicer3/trunk Slicer3
</pre>

== Step2 : Configure slicer project using either ccmake or cmake-gui ==

The grids displayed below summarized the available options.

''Using ccmake'':
<pre>
mkdir Slicer3-SuperBuild
cd Slicer3-SuperBuild
ccmake -DQT_QMAKE_EXECUTABLE:FILEPATH=/home/myself/qt-4.6.2/qt/bin/qmake ../Slicer3/SuperBuild
</pre>

''Using cmake-gui''
<pre>
Where is the source code: C:/MyProjects/Slicer3/SuperBuild
Where to build the binaries: C:/MyProjects/Slicer3-SuperBuild
</pre>

Set of options and supported plateforms:

{| border="1"
|- bgcolor="#FFFFCC"
! rowspan="2"| Description
! colspan="4"| Options
! colspan="3"| Platform
|- bgcolor="#FFFFCC"
!| Slicer3_USE_KWWIDGETS
!| Slicer3_USE_PYTHON
!| Slicer3_USE_QT
!| Slicer3_USE_PYTHONQT
!| Linux
!| Mac
!| windows
|-
|align="center"| Kww-Python '''DEFAULT'''
|align="center" bgcolor="lightgreen"| ON
|align="center" bgcolor="lightgreen"| ON
|align="center"| OFF
|align="center"| OFF
|align="center" bgcolor="lightgreen"| Y
|align="center" bgcolor="lightgreen"| Y
|align="center" bgcolor="lightgreen"| Y
|-
|align="center"| Kww-NoPython
|align="center" bgcolor="lightgreen"| ON
|align="center"| OFF
|align="center"| OFF
|align="center"| OFF
|align="center" bgcolor="lightgreen"| Y
|align="center" bgcolor="lightgreen"| Y
|align="center" bgcolor="lightgreen"| Y
|-
|align="center"| KwwAndQt-Python
|align="center" bgcolor="lightgreen"| ON
|align="center" bgcolor="lightgreen"| ON
|align="center" bgcolor="lightgreen"| ON
|align="center"| OFF
|align="center" bgcolor="lightgreen"| Y
|align="center" bgcolor="lightgray"| N
|align="center" bgcolor="lightgreen"| Y
|-
|align="center"| Qt-NoPythonQt
|align="center"| OFF
|align="center"| OFF
|align="center" bgcolor="lightgreen"| ON
|align="center"| OFF
|align="center" bgcolor="lightgreen"| Y
|align="center" bgcolor="lightgreen"| Y
|align="center" bgcolor="lightgreen"| Y
|-
|align="center"| Qt-PythonQt
|align="center"| OFF
|align="center"| OFF
|align="center" bgcolor="lightgreen"| ON
|align="center" bgcolor="lightgreen"| ON
|align="center" bgcolor="lightgreen"| Y
|align="center" bgcolor="lightgreen"| Y
|align="center" bgcolor="lightgreen"| Y
|}

''What is the difference between Python and PythonQt build ?''
Todo ...

== Step3: Configure, Generate the solution files and Build ==

==Platform Notes==

* On windows and mac python gets rebuilt every time you type make.
* You currently need to manually set the DYLD_LIBRARY_PATH (mac) and related paths to run the executable Slicer3-SuperBuild/Slicer3-build/bin/SlicerQT
export DYLD_LIBRARY_PATH=<path/to>/Slicer4-SuperBuild/CTK-build/CTK-build/bin:<path/to>/Slicer4-SuperBuild/CTK-build/CMakeExternals/Install/lib

Documentation/3.6

2010-04-29T11:43:01Z

Lorensen: /* Surface Models */

This is work in progress

=Main GUI=

*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Mesh Contour Segmentation (Peter Karasev)
* Crop Volume (Subvolume extraction with ROI widget) (Andriy Fedorov)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)
* PETCTFusion (Wendy Plesniak)
* N4 Bias Field Correction (Andriy Fedorov)

=List of Modules=
==Core==
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
*[[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) Not yet 3.6Not yet 3.6
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)

==Specialized Modules==

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

===Wizards===
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)

===Informatics Modules===
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QDECModule-Documentation-3.6| QDEC Module]] (Nicole Aucoin)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

===Registration===
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller)
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Expert Pipeline Rigid-Affine-Nonrigid Registration]]: automated registration with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
** [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu). Belongs to registration, robust
** [[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust
** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust

*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: align a single brain along AC-PC line , (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)
*Experimental and auxiliary
**[[Modules:RegistrationMetrics-Documentation-3.6 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) Updated to 3.6 but needs checking
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]]: obsolete: old version of the ''Fast Rigid Registration'' (Daniel Blezek)

===Segmentation===
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Modules:BRAINSROIAuto|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)

===Diffusion MRI===
*Diffusion MRI
** DWI filtering
***[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
***[[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
***[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
** Diffusion tensor utilities
***[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
***[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
***[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal)
***[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

===IGT===
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

===Time Series===
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

===Filtering===
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] '''In progress''' (Bill Lorensen, Xiaodong Tao)
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) Not yet 3.6Not yet 3.6
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] '''In progress''' (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

===Surface Models===
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)

===Batch processing===
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] '''(In progress)''' (Xiaodong Tao)
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)

==Experimental==
* [[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov)

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

'''Installation'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

===Listing of plug-ins===

'''Available Extensions'''

* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''. Belongs to segmentation

* [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools). Belongs to tractography

* [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)

* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to segmentation.

* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''. Belongs to Statistics.

* [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''. Belongs to wizards.

* [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''. Belongs to DWI

* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu). Belongs to wizards

* [[Image:Slicervmtk_logo.png|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

====Example Extensions====

* [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''

* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

=QA=
[[Slicer-3.6-QA|Slicer 3.6 QA table]]

Modules:GrayscaleModelMaker-Documentation-3.6

2010-04-29T11:39:50Z

Lorensen:

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Grayscale Model Maker

{|
|[[Image:GMMSkin.png|thumb|280px|CT Study, Skin. Threshold=-300 hounsfeld]]
|[[Image:GMMBone.png|thumb|280px|CT Study, Bone. Threshold=200 hounsfeld]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Surface Models

===Authors, Collaborators & Contact===
* Authors: Bill Lorensen, Nicole Aucoin
* Contact: bill.lorensen at gmail.com

===Module Description===
Create 3D surface models from grayscale data. This module
uses Marching Cubes to create an isosurface at a given threshold. The
resulting surface consists of triangles that separate a volume into
regions below and above the threshold. The resulting surface can be
smoothed and decimated. This model works on continuous data while the
module Model Maker works on labeled (or discrete) data.

== Usage ==
<pre>
GrayscaleModelMaker
[--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--pointnormals] [--splitnormals]
[--decimate <float>] [--smooth
<int>] [-n <std::string>] [-t
<float>] [--] [--version] [-h]
<std::string> <std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--pointnormals
Calculate the point normals? Calculated point normals make the surface
appear smooth. Without point normals, the surface will appear faceted.
(default: 0)

--splitnormals
Splitting normals is useful for visualizing sharp features. However it
creates holes in surfaces which affect measurements (default: 0)

--decimate <float>
Target reduction during decimation, as a decimal percentage reduction
in the number of polygons. If 0, no decimation will be done. (default:
0.25)

--smooth <int>
Number of smoothing iterations. If 0, no smoothing will be done.
(default: 15)

-n <std::string>, --name <std::string>
Name to use for this model. (default: Model)

-t <float>, --threshold <float>
Grayscale threshold of isosurface. The resulting surface of triangles
separates the volume into voxels that lie above (inside) and below
(outside) the threshold. (default: 100)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Volume containing the input grayscale data.

<std::string>
(required) Output that contains geometry model.
</pre>

== Development ==

===Source code & documentation===
Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/GrayscaleModelMaker.cxx?view=annotate GrayscaleModelMaker.cxx]

XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/GrayscaleModelMaker.xml?view=co GrayscaleModelMaker.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/GrayscaleModelMakerTest.cxx?rev=11537&view=log GrayscaleModelMakerTest.cxx]

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

File:GMMBone.png

2010-04-29T11:39:02Z

Lorensen:

File:GMMSkin.png

2010-04-29T11:38:43Z

Lorensen:

Modules:GrayscaleModelMaker-Documentation-3.6

2010-04-29T11:26:24Z

Lorensen: Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Module Name=== Grayscale Model Maker {| |Input Image |[[Image:Sample2.pn…'

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Grayscale Model Maker

{|
|[[Image:Sample1.png|thumb|280px|Input Image]]
|[[Image:Sample2.png|thumb|280px|Median Filtered Image]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Surface Models

===Authors, Collaborators & Contact===
* Authors: Bill Lorensen, Nicole Aucoin
* Contact: bill.lorensen at gmail.com

===Module Description===
Create 3D surface models from grayscale data. This module
uses Marching Cubes to create an isosurface at a given threshold. The
resulting surface consists of triangles that separate a volume into
regions below and above the threshold. The resulting surface can be
smoothed and decimated. This model works on continuous data while the
module Model Maker works on labeled (or discrete) data.

== Usage ==
<pre>
GrayscaleModelMaker
[--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--pointnormals] [--splitnormals]
[--decimate <float>] [--smooth
<int>] [-n <std::string>] [-t
<float>] [--] [--version] [-h]
<std::string> <std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--pointnormals
Calculate the point normals? Calculated point normals make the surface
appear smooth. Without point normals, the surface will appear faceted.
(default: 0)

--splitnormals
Splitting normals is useful for visualizing sharp features. However it
creates holes in surfaces which affect measurements (default: 0)

--decimate <float>
Target reduction during decimation, as a decimal percentage reduction
in the number of polygons. If 0, no decimation will be done. (default:
0.25)

--smooth <int>
Number of smoothing iterations. If 0, no smoothing will be done.
(default: 15)

-n <std::string>, --name <std::string>
Name to use for this model. (default: Model)

-t <float>, --threshold <float>
Grayscale threshold of isosurface. The resulting surface of triangles
separates the volume into voxels that lie above (inside) and below
(outside) the threshold. (default: 100)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Volume containing the input grayscale data.

<std::string>
(required) Output that contains geometry model.
</pre>

== Development ==

===Source code & documentation===
Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/GrayscaleModelMaker.cxx?view=annotate GrayscaleModelMaker.cxx]

XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/GrayscaleModelMaker.xml?view=co GrayscaleModelMaker.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/GrayscaleModelMakerTest.cxx?rev=11537&view=log GrayscaleModelMakerTest.cxx]

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

Modules:GradientAnisotropicFilter-Documentation-3.6

2010-04-28T19:54:08Z

Lorensen: /* Module Name */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Gradient Anisotropic Filter

{|
|[[Image:MRIUnfiltered.png|thumb|280px|Unfiltered MRI image]]
|[[Image:MRIGradientAnisotropicDiffusion.png|thumb|280px|Gradient filtered with conductance=1 and iterations=10]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Filtering/Denoising

===Authors, Collaborators & Contact===
* Author: Bill Lorensen
* Contact: bill.lorensen at gmail.com

===Module Description===
Runs gradient anisotropic diffusion on a volume.

Anisotropic diffusion methods reduce noise (or unwanted detail) in
images while preserving specific image features, like edges. For many
applications, there is an assumption that light-dark transitions
(edges) are interesting. Standard isotropic diffusion methods move
and blur light-dark boundaries. Anisotropic diffusion methods are
formulated to specifically preserve edges.
The conductance term for this implementation is a function
of the gradient magnitude of the image at each point, reducing the
strength of diffusion at edges.
The numerical implementation of this equation is similar to that
described in the Perona-Malik paper, but uses a more robust technique
for gradient magnitude estimation and has been generalized to
N-dimensions.

== Usage ==
<pre>
GradientAnisotropicDiffusion [--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--timeStep <double>] [--iterations
<int>] [--conductance <double>]
[--] [--version] [-h] <std::string>
<std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--timeStep <double>
The time step depends on the dimensionality of the image. In Slicer3
the images are 3D and the default (.0625) time step will provide a
stable solution. (default: 0.0625)

--iterations <int>
The more iterations, the more smoothing. Each iteration takes the same
amount of time. If it takes 10 seconds for one iteration, then it will
take 100 seconds for 10 iterations. Note that the conductance controls
how much each iteration smooths across edges. (default: 5)

--conductance <double>
Conductance controls the sensitivity of the conductance term. As a
general rule, the lower the value, the more strongly the filter
preserves edges. A high value will cause diffusion (smoothing) across
edges. Note that the number of iterations controls how much smoothing
is done within regions bounded by edges. (default: 1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume to be filtered

<std::string>
(required) Output filtered
</pre>

== Development ==

===Source code & documentation===

Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/GradientAnisotropicDiffusion.cxx?view=co GradientAnisotropicDiffusion.cxx]

XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/GradientAnisotropicDiffusion.xml?view=co GradientAnisotropicDiffusion.xml]

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

File:MRIGradientAnisotropicDiffusion.png

2010-04-28T19:53:24Z

Lorensen:

Modules:CurvatureAnisotropicDiffusion-Documentation-3.6

2010-04-28T19:51:40Z

Lorensen: /* Module Name */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Curvature Anisotropic Diffusion Filter

{|
|[[Image:MRIUnfiltered.png|thumb|280px|Unfiltered MRI image]]
|[[Image:MRICurvatureAnisotropicDiffusion.png|thumb|280px|Curvature filtered with conductance=1 and iterations=10]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Filtering/Denoising

===Authors, Collaborators & Contact===
* Author: Bill Lorensen
* Contact: bill.lorensen at gmail.com

===Module Description===
Performs anisotropic diffusion on an image using a modified curvature
diffusion equation (MCDE).

MCDE does not exhibit the edge enhancing properties of classic
anisotropic diffusion, which can under certain conditions undergo a
'negative' diffusion, which enhances the contrast of edges. Equations
of the form of MCDE always undergo positive diffusion, with the
conductance term only varying the strength of that diffusion.

Qualitatively, MCDE compares well with other non-linear diffusion
techniques. It is less sensitive to contrast than classic
Perona-Malik style diffusion, and preserves finer detailed structures
in images. There is a potential speed trade-off for using this
function in place of Gradient Anisotropic Diffusion. Each iteration
of the solution takes roughly twice as long. Fewer iterations,
however, may be required to reach an acceptable solution.

== Usage ==
<pre>
CurvatureAnisotropicDiffusion
[--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--timeStep <double>] [--iterations
<int>] [--conductance <double>]
[--] [--version] [-h] <std::string>
<std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--timeStep <double>
Time Step (default: 0.0625)

--iterations <int>
The more iterations, the more smoothing. Each iteration takes the same
amount of time. If it takes 10 seconds for one iteration, then it will
take 100 seconds for 10 iterations. Note that the conductance controls
how much each iteration smooths across edges. (default: 1)

--conductance <double>
Conductance (default: 1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume to be filtered

<std::string>
(required) Output filtered
</pre>

== Development ==

===Source code & documentation===

Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/CurvatureAnisotropicDiffusion.cxx?view=co CurvatureAnisotropicDiffusion.cxx]

XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/CurvatureAnisotropicDiffusion.xml?view=co CurvatureAnisotropicDiffusion.xml]

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

File:MRIUnfiltered.png

2010-04-28T19:50:29Z

Lorensen:

File:MRICurvatureAnisotropicDiffusion.png

2010-04-28T19:49:38Z

Lorensen:

Documentation/3.6

2010-04-28T19:15:07Z

Lorensen: /* Filtering */

This is work in progress

=Main GUI=

*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Mesh Contour Segmentation (Peter Karasev)
* Crop Volume (Subvolume extraction with ROI widget) (Andriy Fedorov)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)
* PETCTFusion (Wendy Plesniak)
* N4 Bias Field Correction (Andriy Fedorov)
* BRAINS Registration Tools (Hans Johnson)

=List of Modules=
==Core==
*[[Slicer3:Multiple_Cameras| Camera Module]] (Sebastian Barre)
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) Not yet 3.6Not yet 3.6
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)

==Specialized Modules==

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

===Wizards===
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)

===Informatics Modules===
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QDECModule-Documentation-3.6| QDEC Module]] (Nicole Aucoin)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

===Registration===
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller) Not yet 3.6Not yet 3.6'
**[[Modules:AffineRegistration-Documentation-3.4|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller) Not yet 3.6Not yet 3.6'
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Expert Pipeline Rigid-Affine-Nonrigid Registration]]: automated registration with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: align a single brain along AC-PC line , (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*Experimental and auxiliary
**[[Modules:RegistrationMetrics-Documentation-3.6 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) Updated to 3.6 but needs checking
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]]: obsolete: old version of the ''Fast Rigid Registration'' (Daniel Blezek) Not yet 3.6Not yet 3.6

===Segmentation===
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)

===Diffusion MRI===
*Diffusion MRI
** DWI filtering
***[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
***[[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
***[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
** Diffusion tensor utilities
***[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
***[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
***[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal)
***[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

===IGT===
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

===Time Series===
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

===Filtering===
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] '''In progress''' (Bill Lorensen, Xiaodong Tao)
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin, Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) Not yet 3.6Not yet 3.6
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] '''In progress''' (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Jim Miller) Not yet 3.6Not yet 3.6
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

===Surface Models===
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen) Not yet 3.6Not yet 3.6
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)

===Batch processing===
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] '''(In progress)''' (Xiaodong Tao)
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)

==Experimental==
* [[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] '''(in progress)''' (Andriy Fedorov)

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

'''Installation'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

===Listing of plug-ins===

'''Available Extensions'''

* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''. Belongs to segmentation

* [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration, robust

* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust

* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools). Belongs to tractography

* [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)

* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to segmentation.

* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''. Belongs to Statistics.

* [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''. Belongs to wizards.

* [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''. Belongs to DWI

* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu). Belongs to wizards

* [[Image:Slicervmtk_logo.png|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

====Example Extensions====

* [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''

* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

=QA=
[[Slicer-3.6-QA|Slicer 3.6 QA table]]

Modules:CurvatureAnisotropicDiffusion-Documentation-3.6

2010-04-28T19:13:05Z

Lorensen: moved Modules:CurvatureAnisotropicFilter-Documentation-3.6 to Modules:CurvatureAnisotropicDiffusion-Documentation-3.6

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Curvature Anisotropic Diffusion Filter

{|
|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Filtering/Denoising

===Authors, Collaborators & Contact===
* Author: Bill Lorensen
* Contact: bill.lorensen at gmail.com

===Module Description===
Performs anisotropic diffusion on an image using a modified curvature
diffusion equation (MCDE).

MCDE does not exhibit the edge enhancing properties of classic
anisotropic diffusion, which can under certain conditions undergo a
'negative' diffusion, which enhances the contrast of edges. Equations
of the form of MCDE always undergo positive diffusion, with the
conductance term only varying the strength of that diffusion.

Qualitatively, MCDE compares well with other non-linear diffusion
techniques. It is less sensitive to contrast than classic
Perona-Malik style diffusion, and preserves finer detailed structures
in images. There is a potential speed trade-off for using this
function in place of Gradient Anisotropic Diffusion. Each iteration
of the solution takes roughly twice as long. Fewer iterations,
however, may be required to reach an acceptable solution.

== Usage ==
<pre>
CurvatureAnisotropicDiffusion
[--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--timeStep <double>] [--iterations
<int>] [--conductance <double>]
[--] [--version] [-h] <std::string>
<std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--timeStep <double>
Time Step (default: 0.0625)

--iterations <int>
The more iterations, the more smoothing. Each iteration takes the same
amount of time. If it takes 10 seconds for one iteration, then it will
take 100 seconds for 10 iterations. Note that the conductance controls
how much each iteration smooths across edges. (default: 1)

--conductance <double>
Conductance (default: 1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume to be filtered

<std::string>
(required) Output filtered
</pre>

== Development ==

===Source code & documentation===

Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/CurvatureAnisotropicDiffusion.cxx?view=co CurvatureAnisotropicDiffusion.cxx]

XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/CurvatureAnisotropicDiffusion.xml?view=co CurvatureAnisotropicDiffusion.xml]

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

Modules:CurvatureAnisotropicFilter-Documentation-3.6

2010-04-28T19:13:05Z

Lorensen: moved Modules:CurvatureAnisotropicFilter-Documentation-3.6 to Modules:CurvatureAnisotropicDiffusion-Documentation-3.6

#REDIRECT [[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6]]

Modules:CurvatureAnisotropicDiffusion-Documentation-3.6

2010-04-28T19:09:04Z

Lorensen: Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Module Name=== Curvature Anisotropic Diffusion Filter {| |[[Image:screenshotBlank.png|thumb|280px|Caption …'

Modules:GradientAnisotropicFilter-Documentation-3.6

2010-04-28T18:53:50Z

Lorensen: Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Module Name=== Gradient Anisotropic Filter {| |Caption 1 |[[Imag…'

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Gradient Anisotropic Filter

{|
|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Filtering/Denoising

===Authors, Collaborators & Contact===
* Author: Bill Lorensen
* Contact: bill.lorensen at gmail.com

===Module Description===
Runs gradient anisotropic diffusion on a volume.

Anisotropic diffusion methods reduce noise (or unwanted detail) in
images while preserving specific image features, like edges. For many
applications, there is an assumption that light-dark transitions
(edges) are interesting. Standard isotropic diffusion methods move
and blur light-dark boundaries. Anisotropic diffusion methods are
formulated to specifically preserve edges.
The conductance term for this implementation is a function
of the gradient magnitude of the image at each point, reducing the
strength of diffusion at edges.
The numerical implementation of this equation is similar to that
described in the Perona-Malik paper, but uses a more robust technique
for gradient magnitude estimation and has been generalized to
N-dimensions.

== Usage ==
<pre>
GradientAnisotropicDiffusion [--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--timeStep <double>] [--iterations
<int>] [--conductance <double>]
[--] [--version] [-h] <std::string>
<std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--timeStep <double>
The time step depends on the dimensionality of the image. In Slicer3
the images are 3D and the default (.0625) time step will provide a
stable solution. (default: 0.0625)

--iterations <int>
The more iterations, the more smoothing. Each iteration takes the same
amount of time. If it takes 10 seconds for one iteration, then it will
take 100 seconds for 10 iterations. Note that the conductance controls
how much each iteration smooths across edges. (default: 5)

--conductance <double>
Conductance controls the sensitivity of the conductance term. As a
general rule, the lower the value, the more strongly the filter
preserves edges. A high value will cause diffusion (smoothing) across
edges. Note that the number of iterations controls how much smoothing
is done within regions bounded by edges. (default: 1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume to be filtered

<std::string>
(required) Output filtered
</pre>

== Development ==

===Source code & documentation===

Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/GradientAnisotropicDiffusion.cxx?view=co GradientAnisotropicDiffusion.cxx]

XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/GradientAnisotropicDiffusion.xml?view=co GradientAnisotropicDiffusion.xml]

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

Documentation/3.6

2010-04-23T19:21:02Z

Lorensen: /* Filtering */

This is work in progress

=Main GUI=

*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] '''(in progress)''' (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] '''(in progress)''' (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) '''(in progress)''' (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) '''(in progress)''' (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] '''(in progress)''' (Wendy Plesniak)
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Mesh Contour Segmentation (Peter Karasev)
* Subvolume extraction with ROI widget (Andriy Fedorov)
* Registration Metrics (HD and DSC) (Haytham Elhawary)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)

=List of Modules=
==Core==
*[[Slicer3:Multiple_Cameras| Camera Module]] (Sebastian Barre)
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) [[Modules:Slices-Documentation-3.6|'''3.6 in process''']]
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) Not yet 3.6Not yet 3.6
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)

==Specialized Modules==

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

===Wizards===
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta) Not yet 3.6Not yet 3.6

===Informatics Modules===
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QDECModule-Documentation-3.6| QDEC Module]] (Nicole Aucoin)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

===Registration===
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Modules:Transforms-Documentation-3.6|Transforms Module]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.4|Fast Affine Module]]: automated fast affine registration , (Daniel Blezek) Not yet 3.6Not yet 3.6'
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Non-rigid BSpline Module]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Robust Rigid-Affine-Nonrigid Module]]: registration with robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Module]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform Module]]: align a single brain along AC-PC line , (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration Module]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.4|Surface Registration Module]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek) Not yet 3.6Not yet 3.6
*Experimental and auxiliary
**[[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) Not yet 3.6Not yet 3.6
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration Module]]: (fast) rigid registration m (Daniel Blezek) Not yet 3.6Not yet 3.6

===Segmentation===
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) Not yet 3.6Not yet 3.6
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)

===Diffusion MRI===
*Diffusion MRI
** DWI filtering
***[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
***[[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
***[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
** Diffusion tensor utilities
***[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
***[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
***[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal)
***[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

===IGT===
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

===Time Series===
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

===Filtering===
*[[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen)
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen)
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Bill Lorensen)
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Bill Lorensen)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) Not yet 3.6Not yet 3.6
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) Not yet 3.6Not yet 3.6
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) Not yet 3.6Not yet 3.6
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) Not yet 3.6Not yet 3.6
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) Not yet 3.6Not yet 3.6
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

===Surface Models===
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen) Not yet 3.6Not yet 3.6
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) Not yet 3.6Not yet 3.6
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) Not yet 3.6Not yet 3.6
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) Not yet 3.6Not yet 3.6
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)

===Batch processing===
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) Not yet 3.6Not yet 3.6
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) Not yet 3.6Not yet 3.6
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) Not yet 3.6Not yet 3.6
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) Not yet 3.6Not yet 3.6
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

'''Installation'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

===Listing of plug-ins===

'''Available Extensions'''

* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''. Belongs to segmentation

* [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration, robust

* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust

* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) '''Not yet 3.6'''. Belongs to tractography

* [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)

* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to segmentation.

* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''. Belongs to IGT.

* [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''. Belongs to wizards.

* [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''. Belongs to DWI

* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu). Belongs to wizards

* [[Image:Slicervmtk_logo.png|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

====Example Extensions====

* [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''

* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

=QA=
[[Slicer-3.6-QA|Slicer 3.6 QA table]]

Modules:HistogramMatching-Documentation-3.6

2010-04-23T19:09:13Z

Lorensen: Created page with 'Return to Slicer 3.6 Documentation ===Module Name=== Histogram Matching {| |Reference image: MR Acquisition 1…'

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

===Module Name===
Histogram Matching

{|
|[[Image:HistogramMatching1.png|thumb|280px|Reference image: MR Acquisition 1]]
|[[Image:HistogramMatching2.png|thumb|280px|Source image: MR Acquisition 2 ]]
|[[Image:HistogramMatching3.png|thumb|280px|Output image: MR Acquisition 2 matched to MR Acquisition 1]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Filtering

===Authors, Collaborators & Contact===
* Author: Bill Lorensen
* Contact: bill.lorensen at gmail.com

===Module Description===
Normalizes the grayscale values of a source image based on
the grayscale values of a reference image. This filter uses a histogram
matching technique where the histograms of the two images are matched
only at a specified number of quantile values. The filter was orginally
designed to normalize MR images of the same MR protocol and same body
part. The algorithm works best if background pixels are excluded from
both the source and reference histograms. A simple background exclusion
method is to exclude all pixels whose grayscale values are smaller than
the mean grayscale value. ThresholdAtMeanIntensity switches on this
simple background exclusion method. Number of match points governs the
number of quantile values to be matched. The filter assumes that both
the source and reference are of the same type and that the input and
output image type have the same number of dimension and have scalar
pixel types.

== Usage ==
<pre>
./HistogramMatching [--processinformationaddress <std::string>] [--xml]
[--echo] [--threshold] [--numberOfMatchPoints
<int>] [--numberOfHistogramLevels <int>] [--]
[--version] [-h] <std::string> <std::string>
<std::string>

Where:

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--threshold
If on, only pixels above the mean in each volume are thresholded.
(default: 0)

--numberOfMatchPoints <int>
The number of match points to use (default: 10)

--numberOfHistogramLevels <int>
The number of hisogram levels to use (default: 128)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume to be filtered

<std::string>
(required) Input volume whose histogram will be matched

<std::string>
(required) Output volume. This is the input volume with intensities
matched to the reference volume.
</pre>

== Development ==

===Source code & documentation===

Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/HistogramMatching.cxx?view=co HistogramMatching.cxx]

XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/HistogramMatching.xml?view=co HistogramMatching.xml]

===References===

Documentation/3.6

2010-04-23T19:02:22Z

Lorensen:

This is work in progress

=Main GUI=

*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] '''(in progress)''' (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] '''(in progress)''' (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) '''(in progress)''' (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) '''(in progress)''' (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] '''(in progress)''' (Wendy Plesniak)
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Mesh Contour Segmentation (Peter Karasev)
* Subvolume extraction with ROI widget (Andriy Fedorov)
* Registration Metrics (HD and DSC) (Haytham Elhawary)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)

=List of Modules=
==Core==
*[[Slicer3:Multiple_Cameras| Camera Module]] (Sebastian Barre)
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) [[Modules:Slices-Documentation-3.6|'''3.6 in process''']]
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) Not yet 3.6Not yet 3.6
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)

==Specialized Modules==

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

===Wizards===
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta) Not yet 3.6Not yet 3.6

===Informatics Modules===
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QDECModule-Documentation-3.6| QDEC Module]] (Nicole Aucoin)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

===Registration===
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Modules:Transforms-Documentation-3.6|Transforms Module]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.4|Fast Affine Module]]: automated fast affine registration , (Daniel Blezek) Not yet 3.6Not yet 3.6'
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Non-rigid BSpline Module]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Robust Rigid-Affine-Nonrigid Module]]: registration with robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Module]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform Module]]: align a single brain along AC-PC line , (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration Module]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.4|Surface Registration Module]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek) Not yet 3.6Not yet 3.6
*Experimental and auxiliary
**[[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) Not yet 3.6Not yet 3.6
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration Module]]: (fast) rigid registration m (Daniel Blezek) Not yet 3.6Not yet 3.6

===Segmentation===
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) Not yet 3.6Not yet 3.6
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)

===Diffusion MRI===
*Diffusion MRI
** DWI filtering
***[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
***[[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
***[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
** Diffusion tensor utilities
***[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
***[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
***[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal)
***[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

===IGT===
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

===Time Series===
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

===Filtering===
*[[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen)
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) Not yet 3.6Not yet 3.6
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Bill Lorensen)
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Bill Lorensen)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) Not yet 3.6Not yet 3.6
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) Not yet 3.6Not yet 3.6
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) Not yet 3.6Not yet 3.6
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) Not yet 3.6Not yet 3.6
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) Not yet 3.6Not yet 3.6
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

===Surface Models===
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen) Not yet 3.6Not yet 3.6
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) Not yet 3.6Not yet 3.6
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) Not yet 3.6Not yet 3.6
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) Not yet 3.6Not yet 3.6
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)

===Batch processing===
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) Not yet 3.6Not yet 3.6
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) Not yet 3.6Not yet 3.6
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) Not yet 3.6Not yet 3.6
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) Not yet 3.6Not yet 3.6
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

'''Installation'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

===Listing of plug-ins===

'''Available Extensions'''

* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''. Belongs to segmentation

* [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration, robust

* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust

* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) '''Not yet 3.6'''. Belongs to tractography

* [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)

* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to segmentation.

* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''. Belongs to IGT.

* [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''. Belongs to wizards.

* [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''. Belongs to DWI

* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu). Belongs to wizards

* [[Image:Slicervmtk_logo.png|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

====Example Extensions====

* [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''

* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

=QA=
[[Slicer-3.6-QA|Slicer 3.6 QA table]]

Modules:OtsuThresholdSegmentation-Documentation-3.6

2010-04-23T17:01:55Z

Lorensen:

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Otsu Threshold Segmentation

== General Information ==
===Module Type & Category===

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Author: Bill Lorensen
* Contact: bill.lorensen at gmail.com

===Module Description===
This filter creates a labeled image from a grayscale image.
First, it calculates an optimal threshold that separates the image into
foreground and background. This threshold separates those two classes so
that their intra-class variance is minimal (see
http://en.wikipedia.org/wiki/Otsu%27s_method). Then the filter runs a
connected component algorithm to generate unique labels for each
connected region of the foreground. Finally, the resulting image is
relabeled to provide consecutive numbering.

The original reference is:
N.Otsu, ‘‘A threshold selection method from gray level histograms,’’
IEEE Trans.Syst.ManCybern.SMC-9,62–66 1979.

== Usage ==
<pre>
OtsuThresholdSegmentation [--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--minimumObjectSize <int>]
[--faceConnected] [--numberOfBins
<int>] [--brightObjects] [--]
[--version] [-h] <std::string>
<std::string>
Where:
--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).
--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)
--xml
Produce xml description of command line arguments (default: 0)
--echo
Echo the command line arguments (default: 0)
--minimumObjectSize <int>
Minimum size of object to retain. This parameter can be used to get
rid of small regions in noisy images. (default: 0)
--faceConnected
This is an advanced parameter. Adjacent voxels are face connected.
This affects the connected component algorithm. If this parameter is
false, more regions are likely to be identified. (default: 0)
--numberOfBins <int>
This is an advanced parameter. The number of bins in the histogram
used to model the probability mass function of the two intensity
distributions. Small numbers of bins may result in a more conservative
threshold. The default should suffice for most applications.
Experimentation is the only way to see the effect of varying this
parameter. (default: 128)
--brightObjects
Segmenting bright objects on a dark background or dark objects on a
bright background. (default: 0)
--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.
--version
Displays version information and exits.
-h, --help
Displays usage information and exits.
<std::string>
(required) Input volume to be segmented
<std::string>
(required) Output filtered
</pre>

===Source code & documentation===

Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/OtsuThresholdSegmentation.cxx?view=co OtsuThresholdSegmentation.cxx]

XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/OtsuThresholdSegmentation.xml?view=co OtsuThresholdSegmentation.xml]

== More Information ==

===Acknowledgement===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

* http://en.wikipedia.org/wiki/Otsu%27s_method
* http://www.labbookpages.co.uk/software/imgProc/otsuThreshold.html
* N.Otsu, [http://web.ics.purdue.edu/~kim497/ece661/OTSU_paper.pdf ‘‘A threshold selection method from gray level histograms,’’ IEEE Trans.Syst.ManCybern.SMC-9,62–66 1979.]

Modules:OtsuThresholdSegmentation-Documentation-3.6

2010-04-23T16:55:37Z

Lorensen: /* Usage */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Otsu Threshold Segmentation

== General Information ==
===Module Type & Category===

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Author: Bill Lorensen
* Contact: bill.lorensen at gmail.com

===Module Description===
This filter creates a labeled image from a grayscale image.
First, it calculates an optimal threshold that separates the image into
foreground and background. This threshold separates those two classes so
that their intra-class variance is minimal (see
http://en.wikipedia.org/wiki/Otsu%27s_method). Then the filter runs a
connected component algorithm to generate unique labels for each
connected region of the foreground. Finally, the resulting image is
relabeled to provide consequetive numbering.

The original reference is:
N.Otsu, ‘‘A threshold selection method from gray level histograms,’’
IEEE Trans.Syst.ManCybern.SMC-9,62–66 1979.

== Usage ==
<pre>
OtsuThresholdSegmentation [--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--minimumObjectSize <int>]
[--faceConnected] [--numberOfBins
<int>] [--brightObjects] [--]
[--version] [-h] <std::string>
<std::string>
Where:
--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).
--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)
--xml
Produce xml description of command line arguments (default: 0)
--echo
Echo the command line arguments (default: 0)
--minimumObjectSize <int>
Minimum size of object to retain. This parameter can be used to get
rid of small regions in noisy images. (default: 0)
--faceConnected
This is an advanced parameter. Adjacent voxels are face connected.
This affects the connected component algorithm. If this parameter is
false, more regions are likely to be identified. (default: 0)
--numberOfBins <int>
This is an advanced parameter. The number of bins in the histogram
used to model the probability mass function of the two intensity
distributions. Small numbers of bins may result in a more conservative
threshold. The default should suffice for most applications.
Experimentation is the only way to see the effect of varying this
parameter. (default: 128)
--brightObjects
Segmenting bright objects on a dark background or dark objects on a
bright background. (default: 0)
--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.
--version
Displays version information and exits.
-h, --help
Displays usage information and exits.
<std::string>
(required) Input volume to be segmented
<std::string>
(required) Output filtered
</pre>

===Source code & documentation===

Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/OtsuThresholdSegmentation.cxx?view=co OtsuThresholdSegmentation.cxx]

XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/OtsuThresholdSegmentation.xml?view=co OtsuThresholdSegmentation.xml]

== More Information ==

===Acknowledgement===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

* http://en.wikipedia.org/wiki/Otsu%27s_method
* http://www.labbookpages.co.uk/software/imgProc/otsuThreshold.html
* N.Otsu, [http://web.ics.purdue.edu/~kim497/ece661/OTSU_paper.pdf ‘‘A threshold selection method from gray level histograms,’’ IEEE Trans.Syst.ManCybern.SMC-9,62–66 1979.]

Modules:OtsuThresholdSegmentation-Documentation-3.6

2010-04-23T16:49:52Z

Lorensen: Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Module Name=== Otsu Threshold Segmentation == General Information == ===Module Type & Category=== Type: …'

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Otsu Threshold Segmentation

== General Information ==
===Module Type & Category===

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Author: Bill Lorensen
* Contact: bill.lorensen at gmail.com

===Module Description===
This filter creates a labeled image from a grayscale image.
First, it calculates an optimal threshold that separates the image into
foreground and background. This threshold separates those two classes so
that their intra-class variance is minimal (see
http://en.wikipedia.org/wiki/Otsu%27s_method). Then the filter runs a
connected component algorithm to generate unique labels for each
connected region of the foreground. Finally, the resulting image is
relabeled to provide consequetive numbering.

The original reference is:
N.Otsu, ‘‘A threshold selection method from gray level histograms,’’
IEEE Trans.Syst.ManCybern.SMC-9,62–66 1979.

== Usage ==
<pre>
OtsuThresholdSegmentation [--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--minimumObjectSize <int>]
[--faceConnected] [--numberOfBins
<int>] [--brightObjects] [--]
[--version] [-h] <std::string>
<std::string>
Where:
--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).
--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)
--xml
Produce xml description of command line arguments (default: 0)
--echo
Echo the command line arguments (default: 0)
--minimumObjectSize <int>
Minimum size of object to retain. This parameter can be used to get
rid of small regions in noisy images. (default: 0)
--faceConnected
This is an advanced parameter. Adjacent voxels are face connected.
This affects the connected component algorithm. If this parameter is
flase, more regions are likely to be identified. (default: 0)
--numberOfBins <int>
This is an advanced parameter. The number of bins in the histogram
used to model the probability mass function of the two intensity
distributions. Small numbers of bins may result in a more conservative
threshold. The default should suffice for most applications.
Experimentation is the only way to see the effect of varying this
parameter. (default: 128)
--brightObjects
Segmenting bright objects on a dark background or dark objects on a
bright background. (default: 0)
--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.
--version
Displays version information and exits.
-h, --help
Displays usage information and exits.
<std::string>
(required) Input volume to be segmented
<std::string>
(required) Output filtered
</pre>

===Source code & documentation===

Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/OtsuThresholdSegmentation.cxx?view=co OtsuThresholdSegmentation.cxx]

XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/OtsuThresholdSegmentation.xml?view=co OtsuThresholdSegmentation.xml]

== More Information ==

===Acknowledgement===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

* http://en.wikipedia.org/wiki/Otsu%27s_method
* http://www.labbookpages.co.uk/software/imgProc/otsuThreshold.html
* N.Otsu, [http://web.ics.purdue.edu/~kim497/ece661/OTSU_paper.pdf ‘‘A threshold selection method from gray level histograms,’’ IEEE Trans.Syst.ManCybern.SMC-9,62–66 1979.]

Modules:GrayscaleGrindPeak-Documentation-3.6

2010-04-21T14:34:00Z

Lorensen: Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Module Name=== GrayscaleGrindPeak {| |Caption 1 |[[Image:screens…'

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
GrayscaleGrindPeak

{|
|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Filtering/Morphology

===Authors, Collaborators & Contact===
* Author: Bill Lorensen
* Contact: bill.lorensen at gmail.com

===Module Description===
GrayscaleGrindPeakImageFilter removes peaks in a grayscale
image. Peaks are local maxima in the grayscale topography that are not
connected to boundaries of the image. Gray level values adjacent to a
peak are extrapolated through the peak. This filter is used to smooth
over local maxima without affecting the values of local minima. If you
take the difference between the output of this filter and the original
image (and perhaps threshold the difference above a small value), you'll
obtain a map of the local maxima. This filter uses the
GrayscaleGeodesicDilateImageFilter. It provides its own input as the
'mask' input to the geodesic erosion. The 'marker' image for the
geodesic erosion is constructed such that boundary pixels match the
boundary pixels of the input image and the interior pixels are set to
the minimum pixel value in the input image. This filter is the dual to
the GrayscaleFillholeImageFilter which implements the Fillhole
algorithm. Since it is a dual, it is somewhat superfluous but is
provided as a convenience. Geodesic morphology and the Fillhole
algorithm is described in Chapter 6 of Pierre Soille's book
'Morphological Image Analysis: Principles and Applications', Second
Edition, Springer, 2003. A companion filter, Grayscale Fill Hole, fills
holes in grayscale images.

== Usage ==
GrayscaleGrindPeakImageFilter.exe
[--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--] [--version] [-h] <std::string>
<std::string>
Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume to be filtered

<std::string>
(required) Output filtered

== Development ==

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/]

Documentation:

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===