Difference between revisions of "Modules:ABC-Documentation-3.5"

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===Atlas Based Classification===
 
===Atlas Based Classification===
 
Atlas Based Classification
 
Atlas Based Classification
 +
  
 
{|
 
{|
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* Marcel Prastawa, Utah
 
* Marcel Prastawa, Utah
 
* Guido Gerig, Utah
 
* Guido Gerig, Utah
−
* Contact: Marcel Prastawa, prastawa@sci.utah.edu
+
* Contact: Marcel Prastawa, prastawa at sci.utah.edu
  
 
===Module Description===
 
===Module Description===
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===Examples, Use Cases & Tutorials===
 
===Examples, Use Cases & Tutorials===
  
−
* Note use cases for which this module is especially appropriate, and/or link to examples.
+
The software is designed and tested for healthy brain MRI (pediatric - adult).
−
* Link to examples of the module's use
+
 
−
* Link to any existing tutorials
+
The processing involved in the module is not designed for interactive use. It may take up to 30 minutes to 1 hour for processing a dataset. Speed-ups are possible by modifying the advanced parameters and disabling the bias correction and deformable registration of the atlas.
  
 
===Quick Tour of Features and Use===
 
===Quick Tour of Features and Use===
−
List all the panels in your interface, their features, what they mean, and how to use them. For instance:
 
  
−
[[Image:abc-slicer-inputs.png|thumb|250px|Input panel]]
+
{|
 +
|-
 +
|* '''Input Panel'''
 +
Specify the input images representing the different modalities of the same subject (up to five).  First image in the list is the reference image space. All other images are registered to first image. Intra-subject registration can be disabled in the advanced setting by choosing the identity transform type.
 +
|[[Image:abc-slicer-inputs.png|thumb|350px|Input panel]]
  
−
[[Image:abc-slicer-atlas.png|thumb|250px|Atlas information panel]]
+
|-
 +
|* '''Atlas Panel'''
 +
Specify the atlas information. The atlas is represented as a directory that contains the template file (template.mha), and the prior probabilities (1.mha, ..., 999.mha)
 +
The atlas orientation specifies the code for the different axes ([R]ight-[L]eft, [A]nterior-[P]osterior, [I]nferior-[S]uperior): RAI, ASR, LPS, etc. If the image orientation matrix is embedded in the image, you can simply specify "file" as the orientation code.
 +
The prior weight can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers. You must specify the same amount of numbers as the amount of priors in the atlas directory.
 +
|[[Image:abc-slicer-atlas.png|thumb|350px|Atlas information panel]]
  
−
[[Image:abc-slicer-outputs.png|thumb|250px|Output panel]]
+
|-
 +
|* '''Output Panel'''
 +
Specify where to store the output files (optional), this includes the segmentation label image, and bias corrected images.
 +
|[[Image:abc-slicer-outputs.png|thumb|350px|Output panel]]
  
−
[[Image:abc-slicer-advanced.png|thumb|250px|Advanced panel]]
+
|-
 +
|* '''Advanced Panel'''
 +
Advanced parameters for registration and bias correction. You can adjust the type of linear transformation for the alignment of the intra-subject modalities and the subject-template. Bias correction polynomial degree adjust the severity of the bias field in your images, and  this part can be disabled by setting it to zero. The amount of deformation of the atlas is controlled by the number of iterations in the fluid flow, and setting it to zero will disable the atlas deformation component.
 +
|[[Image:abc-slicer-advanced.png|thumb|350px|Advanced panel]]
 +
|}
  
−
* '''Input panel:'''
 
−
* '''Parameters panel:'''
 
−
* '''Output panel:'''
 
−
* '''Viewing panel:'''
 
  
 
== Development ==
 
== Development ==
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===Dependencies===
 
===Dependencies===
  
−
Other modules or packages that are required for this module's use.
+
[http://www.itk.org ITK]
  
 
===Known bugs===
 
===Known bugs===
  
−
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.  
+
Follow this [http://www.nitrc.org/tracker/?group_id=297 link] to the bug tracker at NITRC.  
  
−
 
−
===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 & documentation===
  
−
Customize following links for your module:
+
Available at [http://www.nitrc.org/projects/abc NITRC]
−
 
 
−
Source code:
 
−
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
 
−
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]
 
 
   
 
   
−
Doxygen documentation:
+
== More Information ==
−
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]
 
  
−
== More Information ==  
+
===Acknowledegment===
  
−
===Acknowledgment===
 
−
Include funding and other support here.
 
  
 
===References===
 
===References===
−
Publications related to this module go here. Links to pdfs would be useful.
 

Latest revision as of 19:47, 26 May 2010

Home < Modules:ABC-Documentation-3.5

Return to Slicer 3.5 Documentation

Gallery of New Features


Atlas Based Classification

Atlas Based Classification


Interface in Slicer 3
3D visualization of the result

General Information

Module Type & Category

Type: CLI

Category: Segmentation

Authors, Collaborators & Contact

  • Marcel Prastawa, Utah
  • Guido Gerig, Utah
  • Contact: Marcel Prastawa, prastawa at sci.utah.edu

Module Description

ABC (Atlas Based Classification) is a full segmentation pipeline developed and used at University of North Carolina and University of Utah for healthy brain MRIs. The processing pipeline includes image registration, filtering, and inhomogeneity correction.

Usage

Examples, Use Cases & Tutorials

The software is designed and tested for healthy brain MRI (pediatric - adult).

The processing involved in the module is not designed for interactive use. It may take up to 30 minutes to 1 hour for processing a dataset. Speed-ups are possible by modifying the advanced parameters and disabling the bias correction and deformable registration of the atlas.

Quick Tour of Features and Use

* Input Panel

Specify the input images representing the different modalities of the same subject (up to five). First image in the list is the reference image space. All other images are registered to first image. Intra-subject registration can be disabled in the advanced setting by choosing the identity transform type.

Input panel
* Atlas Panel

Specify the atlas information. The atlas is represented as a directory that contains the template file (template.mha), and the prior probabilities (1.mha, ..., 999.mha) The atlas orientation specifies the code for the different axes ([R]ight-[L]eft, [A]nterior-[P]osterior, [I]nferior-[S]uperior): RAI, ASR, LPS, etc. If the image orientation matrix is embedded in the image, you can simply specify "file" as the orientation code. The prior weight can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers. You must specify the same amount of numbers as the amount of priors in the atlas directory.

Atlas information panel
* Output Panel

Specify where to store the output files (optional), this includes the segmentation label image, and bias corrected images.

Output panel
* Advanced Panel

Advanced parameters for registration and bias correction. You can adjust the type of linear transformation for the alignment of the intra-subject modalities and the subject-template. Bias correction polynomial degree adjust the severity of the bias field in your images, and this part can be disabled by setting it to zero. The amount of deformation of the atlas is controlled by the number of iterations in the fluid flow, and setting it to zero will disable the atlas deformation component.

Advanced panel


Development

Dependencies

ITK

Known bugs

Follow this link to the bug tracker at NITRC.


Source code & documentation

Available at NITRC

More Information

Acknowledegment

References

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