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

From Slicer Wiki
Jump to: navigation, search
(New page: =Introduction= The 4D Analysis Module allows you to load, visualize and analyze a time-series of 3D images (4D image) on [http://www.slicer.org/ 3D Slicer]. Currently, the module offers th...)
 
Line 1: Line 1:
−
=Introduction=
+
[[Documentation-3.5|Return to Slicer 3.5 Documentation]]
−
The 4D Analysis Module allows you to load, visualize and analyze a time-series of 3D images (4D image) on [http://www.slicer.org/ 3D Slicer]. Currently, the module offers the following functions:
+
 
−
*'''4D image loader.''' The module can load up a series of 3D images from a specified directory. It analyzes DICOM header of the files in the directory and split them into time-frames, even if all frames have the same series number (some MRI scanners generates time-series images without incrementing series number, resulting a large number (typically several thousands) of 2D image files output in a single directory). The module can also read a directory, which contains NRRD files.
+
[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]
−
*'''Time scroll.''' The module provides a scroll-bar interface to scroll the frame in time-direction. It allows you to scroll the frame for foreground and background screens independently to compare two images at the different time points.
+
 
−
*'''Intensity plot.''' The module can draw intensity curve at the specified region of interest.
+
__NOTOC__
−
*'''Series registration.''' The module provides a user-interface to perform image registration for each frame with a key frame. This function is useful if you want to perform intensity curve analysis on a series of images of an organ moving through the frames.
+
===Module Name===
−
<center>
+
MyModule
 +
 
 
{|
 
{|
−
|[[Image:3DSlicerFourDAnalysis_Screenshot.png|thumb|540px|Screenshot of 4D Analysis Module for lung perfusion data. The module provides several functionality to analyze intensity variation in specified regions of interest, including plotting and curve fitting.]]
+
|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
 +
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
 +
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
 
|}
 
|}
−
</center>
 
  
−
=Installation=
+
== General Information ==
−
Currently, the module is only available in the NAMICSandBox repository. Before you start, you need to have the latest 3D Slicer built from the source code. Please follow [http://www.slicer.org/slicerWiki/index.php/Slicer3:Build_Instructions the instruction] to build 3D Slicer in you environment.
+
===Module Type & Category===
 +
 
 +
Type: Interactive or CLI
 +
 
 +
Category: Base or (Filtering, Registration, ''etc.'')
 +
 
 +
===Authors, Collaborators & Contact===
 +
* Author1: Affiliation & logo, if desired
 +
* Contributor1: Affiliation & logo, if desired
 +
* Contributor2: Affiliation & logo, if desired
 +
* Contact: name, email
 +
 
 +
===Module Description===
 +
Overview of what the module does goes here.
 +
 
 +
== Usage ==
 +
 
 +
===Examples, Use Cases & Tutorials===
 +
 
 +
* Note use cases for which this module is especially appropriate, and/or link to examples.
 +
* Link to examples of the module's use
 +
* Link to any existing tutorials
 +
 
 +
===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:
 +
 
 +
* '''Input panel:'''
 +
* '''Parameters panel:'''
 +
* '''Output panel:'''
 +
* '''Viewing panel:'''
 +
 
 +
== Development ==
 +
 
 +
===Dependencies===
 +
 
 +
Other modules or packages that are required for this module's use.
 +
 
 +
===Known bugs===
  
−
To install 4D Analysis Module in your 3D Slicer, first obtain the source code and put it into the modules' source directory:
+
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.
−
(Suppose you compile Slicer under <working directory>)
 
  
−
  cd <working directory>/Slicer3/Modules
 
−
  svn co http://svn.na-mic.org/NAMICSandBox/trunk/FourDAnalysis FourDAnalysis
 
  
−
Then edit CMakeFiles.txt in the Modules directory. Around line 69 (at the end of subdir()), insert the following code:
+
===Usability issues===
−
    ....
 
−
    ModelIntoLabelVolume
 
−
    FourDAnalysis                      <- this line!!
 
−
  )
 
  
−
Go to the module directory in the build directory, and run make to configure and build the module.
+
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.
−
  cd <working directory>/Slicer3-build/Modules
 
−
  make
 
  
−
If the module is successfully compiled, the module should be in the module menu of 3D Slicer.
+
===Source code & documentation===
  
−
=Usage=
+
Customize following [http://viewvc.slicer.org/viewcvs.cgi/ links] for your module.
  
 +
[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.
  
−
=Plans=
 
−
*Functions:
 
−
**Curve fitting
 
−
***Implemented as Python scripts (using SciPy)
 
−
***Users are allowed to edit the Python scripts
 
−
**Parameter map
 
−
***Perform curve fitting for each voxel
 
−
***Generate parameter map volume
 
  
−
=People=
+
== More Information ==
−
*[[User:Tokuda| Junichi Tokuda, PhD]] (BWH)
 
−
*Hiroto Hatabu, MD, PhD (BWH)
 
  
−
=Acknowledgements=
+
===Acknowledgment===
 +
Include funding and other support here.
  
−
This work is supported by NIH (5R21CA116271: Dynamic contrast-enhanced MRI of pulmonary nodule at 3T, PI: Hiroto Hatabu), NA-MIC, and NCIGT.
+
===References===
 +
Publications related to this module go here. Links to pdfs would be useful.

Revision as of 15:55, 16 June 2009

Home < Modules:FourDAnalysis-Documentation-3.5

Return to Slicer 3.5 Documentation

Gallery of New Features


Module Name

MyModule

Caption 1
Caption 2
Caption 3

General Information

Module Type & Category

Type: Interactive or CLI

Category: Base or (Filtering, Registration, etc.)

Authors, Collaborators & Contact

  • Author1: Affiliation & logo, if desired
  • Contributor1: Affiliation & logo, if desired
  • Contributor2: Affiliation & logo, if desired
  • Contact: name, email

Module Description

Overview of what the module does goes here.

Usage

Examples, Use Cases & Tutorials

  • Note use cases for which this module is especially appropriate, and/or link to examples.
  • Link to examples of the module's use
  • Link to any existing tutorials

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:

  • Input panel:
  • Parameters panel:
  • Output panel:
  • Viewing panel:

Development

Dependencies

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

Known bugs

Follow this link to the Slicer3 bug tracker.


Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

Customize following links for your module.

Links to documentation generated by doxygen.


More Information

Acknowledgment

Include funding and other support here.

References

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

Retrieved from "https://www.slicer.org/w/index.php?title=Modules:FourDAnalysis-Documentation-3.5&oldid=9791"