MultiTracer


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MultiTracer

Description

MultiTracer is a java-based tool that is useful for manual editing of MRI images in a variety of formats. Such editing is a prerequisite for most intersubject registration tools that can be used to create volume deformation parameters. In addition, the tool also allows manually delineated contours to be traced as used by the surface parameterization project. This tool is being used for landmark delineation in a variety of projects.

Features

  • The MultiTracer program is written in JAVA in order to have a portable interface to execute on any JAVA enabled platform. MultiTracer can save to UCF format.
  • MultiTracer includes tools for simple measurements (e.g., areas, volumes, lengths, widths, surface areas, etc.) as well as tools that resample the tracings into surface meshes that can be analyzed and displayed in three-dimensions.
  • Data can be viewed in any orthogonal plane and cursor positions are automatically tracked on all orthogonal views allowing easy identification of anatomic landmarks

Purpose

MultiTracer is a Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision. The traced structures can also be exported in the UCF format. These include tools for simple measurements (e.g., areas, volumes, lengths, width, surface areas, etc.) as well as tools that resample the tracings into surface meshes that can be analyzed and displayed.

Installation

The MultiTracer application is contained in a file called 'MultiTracer2.jar'. The application must be launched as an application (i.e., it cannot be used inside a web browser). The method for launching the application depends on the type of computer:

Normal launching
  • For PC's
    Find the icon for MultiTracer2.jar
    Double clicking the icon should launch the application
  • For Macintosh OS X
    Find the icon for MultiTracer2.jar
    Double clicking the icon should launch the application
    Alternatively, open the Terminal application (its usual location is in the Utilities folder inside the Applications folder) and change to the directory where MultiTracer2.jar is located
    On the command line, type: java -jar MultiTracer2.jar
    Alternatively, open the Terminal application as above and change to the directory where your data is located
    On the command line, type: java -jar /pathname/MultiTracer2.jar
    where /pathname/ is the Unix path to the directory containing MultiTracer2.jar
  • For Unix
    Change to the directory where MultiTracer2.jar is located
    On the command line, type: /usr/java/bin/java -jar MultiTracer2.jar
    Alternatively, change to the directory where your data is located
    On the command line, type: /usr/java/bin/java -jar /pathname/MultiTracer2.jar
    where /pathname/ is the Unix path to the directory containing MultiTracer2.jar

If successfully launched, the application will appear with a blank screen area, the next step is to load an image


 
Launching with extra memory

If you plan to load very large files or a large number of smaller files, the default maximum Java heap size that your system allocates to Java processes may be too small, in which case you will encounter "Out of Memory" errors. The method for altering the maximum heap size varies across platforms and implementations. Typing "java -X" or "/usr/java/bin/java -X" at the prompt will probably bring up a list of command line options that include an option for changing the maximum Java heap size.


 
Launching while specifying files to load on the command line

If you launch MultiTracer from the command line, you can enter up to sixteen file names to load into the sixteen available display slots. Simply append the file names, separated by spaces, at the end of the command.


 
Other command line options

The following options can be included on the command line:

-slot1 filename
loads file called 'filename' in display slot 1 of the main display
-slotN filename
loads file called 'filename' in display slot N of the main display (N can be 1 ... 16)
-flip_x
flips default x-axis in main display window
-flip_y
flips default y-axis in main display window
-coronal
changes initial display orientation in main window from transverse to coronal
-sagittal
changes initial display orientation in main window from transverse to sagittal
-swap
swaps display x- and y- axes in main display window
-ortho1_flip_x
flips default x-axis in first orthogonal display window
-ortho1_flip_y
flips default y-axis in first orthogonal display window
-ortho1_swap
swaps display x- and y- axes in first orthogonal display window
-ortho2_flip_x
flips default x-axis in second orthogonal display window
-ortho2_flip_y
flips default y-axis in second orthogonal display window
-ortho2_swap
swaps display x- and y- axes in second orthogonal display window

Grants & Acknowledgments

Beta testing and feature recommendations:
Katherine L. Narr, Ph.D., Sarah Stoltzner, and Maricela Alarcon, Ph.D.
 
Command line parsing uses the Apache Commons CLI package
(http://jakarta.apache.org/commons/cli/index.html)
 
Polygon mode tracing contributed by Juliane Gansert, Lars Hoemke, and Katrin Amunts of the Institute für Medizin, Forschungszentrum Jülich GmbH, Jülich, Germany
 
Supported by:
NCRR and NIBIB (RR13642 and RR12169)
The Human Brain Project (P20-MHDA52176 and P20-MH57180)
The NIA (AG 16750)
NIH P20MH65166
The Brain Mapping Medical Research Organization
The Brain Mapping Support Foundation
The Pierson-Lovelace Foundation
The Ahmanson Foundation
The Tamkin Foundation
The Jennifer Jones Simon Foundation
The Capital Group Companies Charitable Foundation
The Robson Family
The Northstar Fund