View source for Slicer3:FourDAnalysis

=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 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.
<center>
{|
|[[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.]]
|}
</center>

=Installation=

<font color="red">NOTE: The 4D Analysis module will become '''4D Image''' and '''4D Analysis''' modules in Slicer 3.5 soon. Please refer [https://www.slicer.org/wiki/Modules:FourDImage-Documentation-3.5 4D Image Module Page] and [https://www.slicer.org/wiki/Modules:FourDAnalysis-Documentation-3.5 4D Analysis Module Page] for the latest information. </font>


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 [https://www.slicer.org/wiki/Slicer3:Build_Instructions the instruction] to build 3D Slicer in you environment.

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.

=Usage=


=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=
*[[User:Tokuda| Junichi Tokuda, PhD]] (BWH)
*Hiroto Hatabu, MD, PhD (BWH)

=Acknowledgements=

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