Difference between revisions of "Modules:AtlasCreator"

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== coming soon ;) ==
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[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
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__NOTOC__
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===AtlasCreator===
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 +
{|
 +
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
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|[[Image:screenshotBlank.png|thumb|280px|Output]]
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|[[Image:screenshotBlank.png|thumb|280px|Caption]]
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|}
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== General Information ==
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===Module Type & Category===
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Type: Built-in Loadable Module
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 +
Category: Registration
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 +
===Authors, Collaborators & Contact===
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* Daniel Haehn, University of Pennsylvania
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* Kilian Pohl, University of Pennsylvania
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* Contact: Daniel Haehn (haehn@bwh.harvard.edu)
 +
 
 +
===Module Description===
 +
Overview of what the module does goes here.
 +
 
 +
== Usage ==
 +
 
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===Use Cases, Examples===
 +
 
 +
This module is especially appropriate for these use cases:
 +
 
 +
* Use Case 1:
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* 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
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** Data Set 1
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 +
===Quick Tour of Features and Use===
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 +
A list panels in the interface, their features, what they mean, and how to use them. For instance:
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 +
{|
 +
|
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* '''Main Panel:'''
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** '''Input volume'''
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** '''Atlas List'''
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** '''Initial Erosion distance'''
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** '''Image Modality'''
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** '''Output in Original Image Space'''
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** '''Find Midsaggital Plane'''
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* '''Advanced panel:'''
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** '''Run Smooth Brain Mask'''
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** '''Resample Data to Isotropic Voxels'''
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** '''Initial Probability Threshold'''
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** '''Minimum Probability threshold'''
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** '''MMC Dilation Distance'''
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** '''MMC Erosion Distance'''
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* '''FANTASM panel:'''
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** '''Inhomogeneity Correction'''
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** '''Smoothing Parameter'''
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** '''Background Threshold (%)'''
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* '''MSP panel:'''
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** '''Output Plane?'''
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** '''Output Split-Halves?'''
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** '''Output Segmentation on Plane?'''
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* '''Optimized Automated Registration panel:'''
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** '''Main Subpanel'''
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*** '''Degres of freedom'''
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*** '''Cost Function'''
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*** '''Registration Interpolation'''
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*** '''Output Interpolation'''
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*** '''Apply Rotation'''
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*** '''Minimum Angle'''
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*** '''Maximum Angle '''
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*** '''Coarse Angle Increment'''
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*** '''Fine Angle Increment'''
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** '''Advanced Subpanel'''
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*** '''Multiple of Tolerance to Bracket the Minimum'''
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*** '''Number of Iterations'''
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*** '''Number of Minima From Level 8 to test at Level 4'''
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*** '''Use the Max of the Min Resolutions of the Two Datasets when Resampling'''
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*** '''Subsample Image for Speed'''
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*** '''Skip Multilevel Search (Assume Images are Close to Alignment)'''
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*** '''Multithreading for Registration'''
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* '''Output panel:'''
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** '''First output'''
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** '''Second output'''
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* '''Viewing panel:'''
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|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
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|}
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 +
== Development ==
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 +
===Notes from the Developer(s)===
 +
 
 +
===Dependencies===
 +
 
 +
===Tests===
 +
 
 +
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:
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* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
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* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]
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 +
===Known bugs===
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 +
===Usability issues===
 +
 
 +
===Source code & documentation===
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 +
Links to the module's source code:
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Source code:
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*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
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*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]
 +
 +
Doxygen documentation:
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*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]
 +
 
 +
== More Information ==
 +
 
 +
===Acknowledgment===
 +
 
 +
===References===

Revision as of 19:04, 14 April 2011

Home < Modules:AtlasCreator

Return to Slicer 3.6 Documentation


AtlasCreator

User Interface
Output
Caption

General Information

Module Type & Category

Type: Built-in Loadable Module

Category: Registration

Authors, Collaborators & Contact

  • Daniel Haehn, University of Pennsylvania
  • Kilian Pohl, University of Pennsylvania
  • Contact: Daniel Haehn (haehn@bwh.harvard.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:
User Interface

Development

Notes from the Developer(s)

Dependencies

Tests

On the Dashboard, these tests verify that the module is working on various platforms:

Known bugs

Usability issues

Source code & documentation

Links to the module's source code:

Source code:

Doxygen documentation:

More Information

Acknowledgment

References

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