Slicer Wiki - User contributions [en]

Modules:SPECTRE-Documentation-3.6

2011-04-19T02:13:29Z

Mchen55: /* Quick Tour of Features and Use */

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

'''UNDER CONSTRUCTION''' - [http://wiki.na-mic.org/Wiki/index.php/File:SPECTRE.s3ext.gz extension file] is not checked in to Slicer 3.6 branch nor trunk yet.

__NOTOC__
===SPECTRE===
SPECTRE

{|
|[[Image:SPECTREUserInterface_4_18_2011.png|thumb|280px|SPECTRE User Interface]]
|[[Image:SPECTRESplitResults_4_18_2011.png|thumb|280px|Output - Brain mask split at midsagittal plane overlaid on original image.]]
|[[Image:SPECTREStrippedResults_4_18_2011.png|thumb|280px|Output - Skullstripped results.]]
|}

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

Type: Extension

Category: Segmentation

===Authors, Collaborators & Contact===
* Nicole Aucoin, BWH
* Min Chen, JHU
* Aaron Carass, JHU
* Contact: Nicole Aucoin nicole@bwh.harvard.edu, Min Chen mchen55@jhu.edu

===Module Description===
Overview of what the module does goes here.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* 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. For instance:

{|
|
* '''Main Panel:'''
** '''Input volume'''
** '''Atlas List'''
** '''Initial Erosion distance'''
** '''Image Modality'''
** '''Output in Original Image Space'''
** '''Find Midsaggital Plane'''
* '''Advanced panel:'''
** '''Run Smooth Brain Mask'''
** '''Resample Data to Isotropic Voxels'''
** '''Initial Probability Threshold'''
** '''Minimum Probability threshold'''
** '''MMC Dilation Distance'''
** '''MMC Erosion Distance'''
* '''FANTASM panel:'''
** '''Inhomogeneity Correction'''
** '''Smoothing Parameter'''
** '''Background Threshold (%)'''
* '''MSP panel:'''
** '''Output Plane?'''
** '''Output Split-Halves?'''
** '''Output Segmentation on Plane?'''
* '''Optimized Automated Registration panel:'''
** '''Main Subpanel'''
*** '''Degres of freedom'''
*** '''Cost Function'''
*** '''Registration Interpolation'''
*** '''Output Interpolation'''
*** '''Apply Rotation'''
*** '''Minimum Angle'''
*** '''Maximum Angle '''
*** '''Coarse Angle Increment'''
*** '''Fine Angle Increment'''
** '''Advanced Subpanel'''
*** '''Multiple of Tolerance to Bracket the Minimum'''
*** '''Number of Iterations'''
*** '''Number of Minima From Level 8 to test at Level 4'''
*** '''Use the Max of the Min Resolutions of the Two Datasets when Resampling'''
*** '''Subsample Image for Speed'''
*** '''Skip Multilevel Search (Assume Images are Close to Alignment)'''
*** '''Multithreading for Registration'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:SPECTREUserInterfaceFull_4_18_2011.png|thumb|280px|SPECTRE User Interface (full)]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===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===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

*[http://www.na-mic.org/Wiki/index.php/NA-MIC_JHU_Skull_Stripping_Collaboration NA-MIC Collaboration]
*[http://www.na-mic.org/Wiki/index.php/2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration Winter 2010 Project Week ]
* [http://www.na-mic.org/Wiki/index.php/2010_Summer_Project_Week_SPECTRE Summer 2010 Project Week]

Modules:SPECTRE-Documentation-3.6

2011-04-19T02:13:00Z

Mchen55: /* SPECTRE */

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

'''UNDER CONSTRUCTION''' - [http://wiki.na-mic.org/Wiki/index.php/File:SPECTRE.s3ext.gz extension file] is not checked in to Slicer 3.6 branch nor trunk yet.

__NOTOC__
===SPECTRE===
SPECTRE

{|
|[[Image:SPECTREUserInterface_4_18_2011.png|thumb|280px|SPECTRE User Interface]]
|[[Image:SPECTRESplitResults_4_18_2011.png|thumb|280px|Output - Brain mask split at midsagittal plane overlaid on original image.]]
|[[Image:SPECTREStrippedResults_4_18_2011.png|thumb|280px|Output - Skullstripped results.]]
|}

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

Type: Extension

Category: Segmentation

===Authors, Collaborators & Contact===
* Nicole Aucoin, BWH
* Min Chen, JHU
* Aaron Carass, JHU
* Contact: Nicole Aucoin nicole@bwh.harvard.edu, Min Chen mchen55@jhu.edu

===Module Description===
Overview of what the module does goes here.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* 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. For instance:

{|
|
* '''Main Panel:'''
** '''Input volume'''
** '''Atlas List'''
** '''Initial Erosion distance'''
** '''Image Modality'''
** '''Output in Original Image Space'''
** '''Find Midsaggital Plane'''
* '''Advanced panel:'''
** '''Run Smooth Brain Mask'''
** '''Resample Data to Isotropic Voxels'''
** '''Initial Probability Threshold'''
** '''Minimum Probability threshold'''
** '''MMC Dilation Distance'''
** '''MMC Erosion Distance'''
* '''FANTASM panel:'''
** '''Inhomogeneity Correction'''
** '''Smoothing Parameter'''
** '''Background Threshold (%)'''
* '''MSP panel:'''
** '''Output Plane?'''
** '''Output Split-Halves?'''
** '''Output Segmentation on Plane?'''
* '''Optimized Automated Registration panel:'''
** '''Main Subpanel'''
*** '''Degres of freedom'''
*** '''Cost Function'''
*** '''Registration Interpolation'''
*** '''Output Interpolation'''
*** '''Apply Rotation'''
*** '''Minimum Angle'''
*** '''Maximum Angle '''
*** '''Coarse Angle Increment'''
*** '''Fine Angle Increment'''
** '''Advanced Subpanel'''
*** '''Multiple of Tolerance to Bracket the Minimum'''
*** '''Number of Iterations'''
*** '''Number of Minima From Level 8 to test at Level 4'''
*** '''Use the Max of the Min Resolutions of the Two Datasets when Resampling'''
*** '''Subsample Image for Speed'''
*** '''Skip Multilevel Search (Assume Images are Close to Alignment)'''
*** '''Multithreading for Registration'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:SPECTREUserInterfaceFull_4_18_2011.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===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===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

*[http://www.na-mic.org/Wiki/index.php/NA-MIC_JHU_Skull_Stripping_Collaboration NA-MIC Collaboration]
*[http://www.na-mic.org/Wiki/index.php/2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration Winter 2010 Project Week ]
* [http://www.na-mic.org/Wiki/index.php/2010_Summer_Project_Week_SPECTRE Summer 2010 Project Week]

File:SPECTREUserInterfaceFull 4 18 2011.png

2011-04-19T02:10:16Z

Mchen55:

Modules:SPECTRE-Documentation-3.6

2011-04-19T02:10:07Z

Mchen55: /* Quick Tour of Features and Use */

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

'''UNDER CONSTRUCTION''' - [http://wiki.na-mic.org/Wiki/index.php/File:SPECTRE.s3ext.gz extension file] is not checked in to Slicer 3.6 branch nor trunk yet.

__NOTOC__
===SPECTRE===
SPECTRE

{|
|[[Image:SPECTREUserInterface_4_18_2011.png|thumb|280px|User Interface]]
|[[Image:SPECTRESplitResults_4_18_2011.png|thumb|280px|Output]]
|[[Image:SPECTREStrippedResults_4_18_2011.png|thumb|280px|Caption]]
|}

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

Type: Extension

Category: Segmentation

===Authors, Collaborators & Contact===
* Nicole Aucoin, BWH
* Min Chen, JHU
* Aaron Carass, JHU
* Contact: Nicole Aucoin nicole@bwh.harvard.edu, Min Chen mchen55@jhu.edu

===Module Description===
Overview of what the module does goes here.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* 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. For instance:

{|
|
* '''Main Panel:'''
** '''Input volume'''
** '''Atlas List'''
** '''Initial Erosion distance'''
** '''Image Modality'''
** '''Output in Original Image Space'''
** '''Find Midsaggital Plane'''
* '''Advanced panel:'''
** '''Run Smooth Brain Mask'''
** '''Resample Data to Isotropic Voxels'''
** '''Initial Probability Threshold'''
** '''Minimum Probability threshold'''
** '''MMC Dilation Distance'''
** '''MMC Erosion Distance'''
* '''FANTASM panel:'''
** '''Inhomogeneity Correction'''
** '''Smoothing Parameter'''
** '''Background Threshold (%)'''
* '''MSP panel:'''
** '''Output Plane?'''
** '''Output Split-Halves?'''
** '''Output Segmentation on Plane?'''
* '''Optimized Automated Registration panel:'''
** '''Main Subpanel'''
*** '''Degres of freedom'''
*** '''Cost Function'''
*** '''Registration Interpolation'''
*** '''Output Interpolation'''
*** '''Apply Rotation'''
*** '''Minimum Angle'''
*** '''Maximum Angle '''
*** '''Coarse Angle Increment'''
*** '''Fine Angle Increment'''
** '''Advanced Subpanel'''
*** '''Multiple of Tolerance to Bracket the Minimum'''
*** '''Number of Iterations'''
*** '''Number of Minima From Level 8 to test at Level 4'''
*** '''Use the Max of the Min Resolutions of the Two Datasets when Resampling'''
*** '''Subsample Image for Speed'''
*** '''Skip Multilevel Search (Assume Images are Close to Alignment)'''
*** '''Multithreading for Registration'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:SPECTREUserInterfaceFull_4_18_2011.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===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===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

*[http://www.na-mic.org/Wiki/index.php/NA-MIC_JHU_Skull_Stripping_Collaboration NA-MIC Collaboration]
*[http://www.na-mic.org/Wiki/index.php/2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration Winter 2010 Project Week ]
* [http://www.na-mic.org/Wiki/index.php/2010_Summer_Project_Week_SPECTRE Summer 2010 Project Week]

File:SPECTREStrippedResults 4 18 2011.png

2011-04-19T01:53:57Z

Mchen55:

File:SPECTRESplitResults 4 18 2011.png

2011-04-19T01:53:43Z

Mchen55:

File:SPECTREUserInterface 4 18 2011.png

2011-04-19T01:53:27Z

Mchen55:

Modules:SPECTRE-Documentation-3.6

2011-04-19T01:53:17Z

Mchen55: /* SPECTRE */

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

'''UNDER CONSTRUCTION''' - [http://wiki.na-mic.org/Wiki/index.php/File:SPECTRE.s3ext.gz extension file] is not checked in to Slicer 3.6 branch nor trunk yet.

__NOTOC__
===SPECTRE===
SPECTRE

{|
|[[Image:SPECTREUserInterface_4_18_2011.png|thumb|280px|User Interface]]
|[[Image:SPECTRESplitResults_4_18_2011.png|thumb|280px|Output]]
|[[Image:SPECTREStrippedResults_4_18_2011.png|thumb|280px|Caption]]
|}

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

Type: Extension

Category: Segmentation

===Authors, Collaborators & Contact===
* Nicole Aucoin, BWH
* Min Chen, JHU
* Aaron Carass, JHU
* Contact: Nicole Aucoin nicole@bwh.harvard.edu, Min Chen mchen55@jhu.edu

===Module Description===
Overview of what the module does goes here.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* 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. For instance:

{|
|
* '''Main Panel:'''
** '''Input volume'''
** '''Atlas List'''
** '''Initial Erosion distance'''
** '''Image Modality'''
** '''Output in Original Image Space'''
** '''Find Midsaggital Plane'''
* '''Advanced panel:'''
** '''Run Smooth Brain Mask'''
** '''Resample Data to Isotropic Voxels'''
** '''Initial Probability Threshold'''
** '''Minimum Probability threshold'''
** '''MMC Dilation Distance'''
** '''MMC Erosion Distance'''
* '''FANTASM panel:'''
** '''Inhomogeneity Correction'''
** '''Smoothing Parameter'''
** '''Background Threshold (%)'''
* '''MSP panel:'''
** '''Output Plane?'''
** '''Output Split-Halves?'''
** '''Output Segmentation on Plane?'''
* '''Optimized Automated Registration panel:'''
** '''Main Subpanel'''
*** '''Degres of freedom'''
*** '''Cost Function'''
*** '''Registration Interpolation'''
*** '''Output Interpolation'''
*** '''Apply Rotation'''
*** '''Minimum Angle'''
*** '''Maximum Angle '''
*** '''Coarse Angle Increment'''
*** '''Fine Angle Increment'''
** '''Advanced Subpanel'''
*** '''Multiple of Tolerance to Bracket the Minimum'''
*** '''Number of Iterations'''
*** '''Number of Minima From Level 8 to test at Level 4'''
*** '''Use the Max of the Min Resolutions of the Two Datasets when Resampling'''
*** '''Subsample Image for Speed'''
*** '''Skip Multilevel Search (Assume Images are Close to Alignment)'''
*** '''Multithreading for Registration'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===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===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

*[http://www.na-mic.org/Wiki/index.php/NA-MIC_JHU_Skull_Stripping_Collaboration NA-MIC Collaboration]
*[http://www.na-mic.org/Wiki/index.php/2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration Winter 2010 Project Week ]
* [http://www.na-mic.org/Wiki/index.php/2010_Summer_Project_Week_SPECTRE Summer 2010 Project Week]

Modules:SPECTRE-Documentation-3.6

2011-04-19T01:52:25Z

Mchen55: /* SPECTRE */

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

'''UNDER CONSTRUCTION''' - [http://wiki.na-mic.org/Wiki/index.php/File:SPECTRE.s3ext.gz extension file] is not checked in to Slicer 3.6 branch nor trunk yet.

__NOTOC__
===SPECTRE===
SPECTRE

{|
|[[Image:SPECTREUserInterface_4_18_2011|thumb|280px|User Interface]]
|[[Image:SPECTRESplitResults_4_18_2011|thumb|280px|Output]]
|[[Image:SPECTREStrippedResults_4_18_2011|thumb|280px|Caption]]
|}

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

Type: Extension

Category: Segmentation

===Authors, Collaborators & Contact===
* Nicole Aucoin, BWH
* Min Chen, JHU
* Aaron Carass, JHU
* Contact: Nicole Aucoin nicole@bwh.harvard.edu, Min Chen mchen55@jhu.edu

===Module Description===
Overview of what the module does goes here.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* 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. For instance:

{|
|
* '''Main Panel:'''
** '''Input volume'''
** '''Atlas List'''
** '''Initial Erosion distance'''
** '''Image Modality'''
** '''Output in Original Image Space'''
** '''Find Midsaggital Plane'''
* '''Advanced panel:'''
** '''Run Smooth Brain Mask'''
** '''Resample Data to Isotropic Voxels'''
** '''Initial Probability Threshold'''
** '''Minimum Probability threshold'''
** '''MMC Dilation Distance'''
** '''MMC Erosion Distance'''
* '''FANTASM panel:'''
** '''Inhomogeneity Correction'''
** '''Smoothing Parameter'''
** '''Background Threshold (%)'''
* '''MSP panel:'''
** '''Output Plane?'''
** '''Output Split-Halves?'''
** '''Output Segmentation on Plane?'''
* '''Optimized Automated Registration panel:'''
** '''Main Subpanel'''
*** '''Degres of freedom'''
*** '''Cost Function'''
*** '''Registration Interpolation'''
*** '''Output Interpolation'''
*** '''Apply Rotation'''
*** '''Minimum Angle'''
*** '''Maximum Angle '''
*** '''Coarse Angle Increment'''
*** '''Fine Angle Increment'''
** '''Advanced Subpanel'''
*** '''Multiple of Tolerance to Bracket the Minimum'''
*** '''Number of Iterations'''
*** '''Number of Minima From Level 8 to test at Level 4'''
*** '''Use the Max of the Min Resolutions of the Two Datasets when Resampling'''
*** '''Subsample Image for Speed'''
*** '''Skip Multilevel Search (Assume Images are Close to Alignment)'''
*** '''Multithreading for Registration'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===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===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

*[http://www.na-mic.org/Wiki/index.php/NA-MIC_JHU_Skull_Stripping_Collaboration NA-MIC Collaboration]
*[http://www.na-mic.org/Wiki/index.php/2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration Winter 2010 Project Week ]
* [http://www.na-mic.org/Wiki/index.php/2010_Summer_Project_Week_SPECTRE Summer 2010 Project Week]

Modules:SPECTRE-Documentation-3.6

2011-04-04T20:16:40Z

Mchen55: /* Quick Tour of Features and Use */

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

'''UNDER CONSTRUCTION''' - [http://wiki.na-mic.org/Wiki/index.php/File:SPECTRE.s3ext.gz extension file] is not checked in to Slicer 3.6 branch nor trunk yet.

__NOTOC__
===SPECTRE===
SPECTRE

{|
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|[[Image:screenshotBlank.png|thumb|280px|Output]]
|[[Image:screenshotBlank.png|thumb|280px|Caption]]
|}

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

Type: Extension

Category: Segmentation

===Authors, Collaborators & Contact===
* Nicole Aucoin, BWH
* Min Chen, JHU
* Aaron Carass, JHU
* Contact: Nicole Aucoin nicole@bwh.harvard.edu, Min Chen mchen55@jhu.edu

===Module Description===
Overview of what the module does goes here.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* 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. For instance:

{|
|
* '''Main Panel:'''
** '''Input volume'''
** '''Atlas List'''
** '''Initial Erosion distance'''
** '''Image Modality'''
** '''Output in Original Image Space'''
** '''Find Midsaggital Plane'''
* '''Advanced panel:'''
** '''Run Smooth Brain Mask'''
** '''Resample Data to Isotropic Voxels'''
** '''Initial Probability Threshold'''
** '''Minimum Probability threshold'''
** '''MMC Dilation Distance'''
** '''MMC Erosion Distance'''
* '''FANTASM panel:'''
** '''Inhomogeneity Correction'''
** '''Smoothing Parameter'''
** '''Background Threshold (%)'''
* '''MSP panel:'''
** '''Output Plane?'''
** '''Output Split-Halves?'''
** '''Output Segmentation on Plane?'''
* '''Optimized Automated Registration panel:'''
** '''Main Subpanel'''
*** '''Degres of freedom'''
*** '''Cost Function'''
*** '''Registration Interpolation'''
*** '''Output Interpolation'''
*** '''Apply Rotation'''
*** '''Minimum Angle'''
*** '''Maximum Angle '''
*** '''Coarse Angle Increment'''
*** '''Fine Angle Increment'''
** '''Advanced Subpanel'''
*** '''Multiple of Tolerance to Bracket the Minimum'''
*** '''Number of Iterations'''
*** '''Number of Minima From Level 8 to test at Level 4'''
*** '''Use the Max of the Min Resolutions of the Two Datasets when Resampling'''
*** '''Subsample Image for Speed'''
*** '''Skip Multilevel Search (Assume Images are Close to Alignment)'''
*** '''Multithreading for Registration'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===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===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

*[http://www.na-mic.org/Wiki/index.php/NA-MIC_JHU_Skull_Stripping_Collaboration NA-MIC Collaboration]
*[http://www.na-mic.org/Wiki/index.php/2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration Winter 2010 Project Week ]
* [http://www.na-mic.org/Wiki/index.php/2010_Summer_Project_Week_SPECTRE Summer 2010 Project Week]

Modules:SPECTRE-Documentation-3.6

2011-04-04T20:14:58Z

Mchen55: /* Quick Tour of Features and Use */

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

'''UNDER CONSTRUCTION''' - [http://wiki.na-mic.org/Wiki/index.php/File:SPECTRE.s3ext.gz extension file] is not checked in to Slicer 3.6 branch nor trunk yet.

__NOTOC__
===SPECTRE===
SPECTRE

{|
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|[[Image:screenshotBlank.png|thumb|280px|Output]]
|[[Image:screenshotBlank.png|thumb|280px|Caption]]
|}

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

Type: Extension

Category: Segmentation

===Authors, Collaborators & Contact===
* Nicole Aucoin, BWH
* Min Chen, JHU
* Aaron Carass, JHU
* Contact: Nicole Aucoin nicole@bwh.harvard.edu, Min Chen mchen55@jhu.edu

===Module Description===
Overview of what the module does goes here.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* 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. For instance:

{|
|
* '''Main Panel:'''
** '''Input volume'''
** '''Atlas List'''
** '''Initial Erosion distance'''
** '''Image Modality'''
** '''Output in Original Image Space'''
** '''Find Midsaggital Plane'''
* '''Advanced panel:'''
** '''Run Smooth Brain Mask'''
** '''Resample Data to Isotropic Voxels'''
** '''Initial Probability Threshold'''
** '''Minimum Probability threshold'''
** '''MMC Dilation Distance'''
** '''MMC Erosion Distance'''
* '''FANTASM panel:'''
** '''Inhomogeneity Correction'''
** '''Smoothing Parameter'''
** '''Background Threshold (%)'''
* '''MSP panel:'''
** '''Output Plane?'''
** '''Output Split-Halves?'''
** '''Output Segmentation on Plane?'''
* '''Optimized Automated Registration panel:'''
** '''Main'''

Degres of freedom
Cost Function
REgistration Interpolation
Output Interpolation
apply roatation
Minimum angle
Maximum angle
Coarse Angle Increment
Fine Angle Increment
** '''Second parameter'''
Multiple of Tolerance to Bracket the Minimum
Number of Iterations
Number of Minima From Level 8 to test at Level 4
Use the Max of the Min Resolutions of the Two Datasets when REsampling
Subsample Image for Speed
Skip Multilevel Search (Assume Images are close to alignment)
Multithreading for Registration

* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===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===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

*[http://www.na-mic.org/Wiki/index.php/NA-MIC_JHU_Skull_Stripping_Collaboration NA-MIC Collaboration]
*[http://www.na-mic.org/Wiki/index.php/2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration Winter 2010 Project Week ]
* [http://www.na-mic.org/Wiki/index.php/2010_Summer_Project_Week_SPECTRE Summer 2010 Project Week]

Modules:SPECTRE-Documentation-3.6

2011-04-04T19:48:58Z

Mchen55: /* Quick Tour of Features and Use */

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

'''UNDER CONSTRUCTION''' - [http://wiki.na-mic.org/Wiki/index.php/File:SPECTRE.s3ext.gz extension file] is not checked in to Slicer 3.6 branch nor trunk yet.

__NOTOC__
===SPECTRE===
SPECTRE

{|
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|[[Image:screenshotBlank.png|thumb|280px|Output]]
|[[Image:screenshotBlank.png|thumb|280px|Caption]]
|}

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

Type: Extension

Category: Segmentation

===Authors, Collaborators & Contact===
* Nicole Aucoin, BWH
* Min Chen, JHU
* Aaron Carass, JHU
* Contact: Nicole Aucoin nicole@bwh.harvard.edu, Min Chen mchen55@jhu.edu

===Module Description===
Overview of what the module does goes here.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* 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. For instance:

{|
|
* '''Main Panel:'''
** '''Input volume'''
** '''Atlas List'''
** '''Initial Erosion distance'''
** '''Image Modality'''
** '''Output in Original Image Space'''
** '''Find Midsaggital Plane'''
* '''Advanced panel:'''
** '''Run Smooth Brain Mask'''
** '''Resample Data to Isotropic Voxels'''
** '''Initial Probability Threshold'''
** '''Minimum Probability threshold'''
** '''MMC Dilation Distance'''
** '''MMC Erosion Distance'''
* '''FANTASM panel:'''
** '''Inhomogeneity Correction'''
** '''Smoothing Parameter'''
** '''Background Threshold (%)'''
* '''MSP panel:'''
** '''Output Plane?'''
** '''Output Split-Halves?'''
** '''Output Segmentation on Plane?'''
* '''Optimized Automated Registration panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===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===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

*[http://www.na-mic.org/Wiki/index.php/NA-MIC_JHU_Skull_Stripping_Collaboration NA-MIC Collaboration]
*[http://www.na-mic.org/Wiki/index.php/2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration Winter 2010 Project Week ]
* [http://www.na-mic.org/Wiki/index.php/2010_Summer_Project_Week_SPECTRE Summer 2010 Project Week]

Modules:SPECTRE-Documentation-3.6

2011-04-04T19:41:57Z

Mchen55: /* Quick Tour of Features and Use */

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

'''UNDER CONSTRUCTION''' - [http://wiki.na-mic.org/Wiki/index.php/File:SPECTRE.s3ext.gz extension file] is not checked in to Slicer 3.6 branch nor trunk yet.

__NOTOC__
===SPECTRE===
SPECTRE

{|
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|[[Image:screenshotBlank.png|thumb|280px|Output]]
|[[Image:screenshotBlank.png|thumb|280px|Caption]]
|}

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

Type: Extension

Category: Segmentation

===Authors, Collaborators & Contact===
* Nicole Aucoin, BWH
* Min Chen, JHU
* Aaron Carass, JHU
* Contact: Nicole Aucoin nicole@bwh.harvard.edu, Min Chen mchen55@jhu.edu

===Module Description===
Overview of what the module does goes here.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* 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. For instance:

{|
|
* '''Main Panel:'''
** '''Input volume'''
** '''Atlas List'''
** '''Initial Erosion distance'''
** '''Image Modality'''
** '''Output in Original Image Space'''
** '''Find Midsaggital Plane'''
* '''Advanced panel:'''
** '''Run Smooth Brain Mask'''
** '''Resample Data to Isotropic Voxels'''
** '''Initial Probability Threshold'''
** '''Minimum Probability threshold'''
** '''MMC Dilation Distance'''
** '''MMC Erosion Distance'''
* '''MSP panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Optimized Automated Registration panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===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===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

*[http://www.na-mic.org/Wiki/index.php/NA-MIC_JHU_Skull_Stripping_Collaboration NA-MIC Collaboration]
*[http://www.na-mic.org/Wiki/index.php/2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration Winter 2010 Project Week ]
* [http://www.na-mic.org/Wiki/index.php/2010_Summer_Project_Week_SPECTRE Summer 2010 Project Week]

Modules:SPECTRE-Documentation-3.6

2011-04-04T19:20:37Z

Mchen55: /* Quick Tour of Features and Use */

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

'''UNDER CONSTRUCTION''' - [http://wiki.na-mic.org/Wiki/index.php/File:SPECTRE.s3ext.gz extension file] is not checked in to Slicer 3.6 branch nor trunk yet.

__NOTOC__
===SPECTRE===
SPECTRE

{|
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|[[Image:screenshotBlank.png|thumb|280px|Output]]
|[[Image:screenshotBlank.png|thumb|280px|Caption]]
|}

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

Type: Extension

Category: Segmentation

===Authors, Collaborators & Contact===
* Nicole Aucoin, BWH
* Min Chen, JHU
* Aaron Carass, JHU
* Contact: Nicole Aucoin nicole@bwh.harvard.edu, Min Chen mchen55@jhu.edu

===Module Description===
Overview of what the module does goes here.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* 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. For instance:

{|
|
* '''Main Panel:'''
** '''Input volume'''
** '''Atlas List'''
** '''Initial Erosion distance'''
** '''Image Modality'''
** '''Output in Original Image Space'''
* '''Advanced panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''MSP panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Optimized Automated Registration panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===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===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

*[http://www.na-mic.org/Wiki/index.php/NA-MIC_JHU_Skull_Stripping_Collaboration NA-MIC Collaboration]
*[http://www.na-mic.org/Wiki/index.php/2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration Winter 2010 Project Week ]
* [http://www.na-mic.org/Wiki/index.php/2010_Summer_Project_Week_SPECTRE Summer 2010 Project Week]

Modules:SPECTRE-Documentation-3.6

2011-04-04T18:10:46Z

Mchen55: /* Quick Tour of Features and Use */