Modules:FourDAnalysis-Documentation-3.5

Return to Slicer 3.5 Documentation

Gallery of New Features

Module Name

4D Analysis Module

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.

General Information

Module Type & Category

Type: Interactive

Category: 4D

Authors, Collaborators & Contact

• Junichi Tokuda, Ph.D., Brigham and Women's Hospital
• Hiroto Hatabu, M.D., Ph.D., Brigham and Women's Hospital
• Contact: Junichi Tokuda, tokuda at bwh.harvard.edu

Module Description

The 4D Analysis Module allows you to load, visualize and analyze a time-series of 3D images (4D image) on 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.
• 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.
• 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.

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

Installation

Currently the module is available in the NA-MIC SandBox repository. (Will be integrated in 3D Slicer soon)

To install 4D Analysis Module in your 3D Slicer, first obtain the source code and put it into the modules' source directory: (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:

   ....
   ModelIntoLabelVolume
   FourDAnalysis                       <- this line!!
 )

Go to the module directory in the build directory, and run make to configure and build the module.

 cd <working directory>/Slicer3-build/Modules
 make

If the module is successfully compiled, the module should be in the module menu of 3D Slicer.

Dependencies

The intensity curve analysis functions depend on SciPy package. Please turn on SciPy option when you build your 3D Slicer.

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

This work is supported by NIH (5R21CA116271: Dynamic contrast-enhanced MRI of pulmonary nodule at 3T, PI: Hiroto Hatabu), NA-MIC, and NCIGT.