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 analyze a time-series of 3D images (4D image) on 3D Slicer. Currently, the module offers the following functions:

• Intensity plot. The module can draw intensity curves at the specified regions of interest.
• Pharmacokinetic model analysis. The users can perform pharmacokinetic model analysis based on the intensity curves. Models are defined in Python scripts so that the users can modify the existing models or create their own pharmacokinetic models.
• Parameter map. The module also allows generating a map of pharmacokinetic parameters.

Usage

Examples, Use Cases & Tutorials

• Plot intensity change at the specified region.
• Analyzing DCE MRI using pharmacokinetic models e.g. Tofts model etc.

Quick Tour of Features and Use

• Active 4D Bundle: Specify the active 4D image series.
• Frame Control: View the 4D image data. 4D images can be loaded from 4D Image Module
• Intensity Plot: Generate intensity curves and display them on this panel. The curves are measured for each labeled region in the specified label map. If the label map contains multiple labels, the module generates intensity curve for each label. The user can also load/save curves from/to CSV files.
• Model/Parameter: Select Python script and parameters for pharmacokinetic analysis.
• Curve Fitting: Perform a single curve fitting. It displays the result parameters.
• Parameter Map: Generate parameter map. The module performs curve fitting for each voxel in the specified region.

Development

Installation

Although the module's source directory is in the trunk repository, it is not included in the CMake configuration. To use 4D Analysis Module, you need edit Slicer3/Modules/CMakeLists.txt and build the module.

(Supposing you have your local copy of 3D SLicer under <working directory>, in the following instruction)

1. Edit Slicer3/Modules/CMakeLists.txt

In subdirs section, insert 'FourDAnalysis' as:

subdirs(
  MRIBiasFieldCorrection
  
  ...
  
  FastMarchingSegmentation
  FourDImage
  FourDAnalysis                                # <- Here!!
  ExtractSubvolumeROI
  
  ...
  )

2. Build the module

In Linux or Mac OS X,

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

In Windows, open the project file in <working directory>/Slicer3-build/Modules, and build all.

3. Check the module

If the module has been built successfully, it shows up in the '4D' section in the module selection list.

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

2D Graph

The module provides a set of classes to support 2D Graph for intensity curve plotting, which can potentially be used for other projects. Please refer Slicer3:2DPlotting for more detail.

Acknowledgment

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