JIV2

JIV2 is a java-based applet that can be run locally or embedded into a webpage. It can display MINC volumes which are in their native space, and yet still synchronize viewing of all volumes by using an affine transform to transform the cursor coordinates. It can also display anatomical labels corresponding to the cursor’s position if a label atlas is included in the viewing window. JIV2 requires MINC files to be converted into raw images, and stores the image information in a header file. It also requires a configuration script (see .CONFIG file section below) which tells JIV2 a) which volumes should be displayed where, and b) what transform (see the .xfm transform) to use with each volume.

Demo

To view online the MNI Macaque atlas, the Paxinos Macaque labels, and a sample Cynomolgus macaque in its native space, click here.

Required Software

To run JIV2 as an applet on the web and view hosted volumes (as in the Demo above), nothing is required except a browser with Java enabled.
To run JIV2 as a standalone application (see How to Run below), nothing is required except Java, the shell script jiv2, and jiv2.jar (the actual JIV2 executable software) located somewhere on your computer, and in the folder containing the image volumes you wish to display:

  • a .CONFIG file (detailing the location of the volumes to view and their supporting files)
  • the following for each volume:
  • a .raw_byte.gz file (the raw image volume)
  • a .header file (describing properties of the volume like size, intensity range, start location)
  • a .xfm file (describing the affine transform needed to align the volume to your chosen MNI template)

To convert your MINC volumes into raw format (needed for JIV2), you will need to install the MINC2 library and tools which requires perl, among other things. Once you have done this, you need to run minc2jiv2 on each of your MINC volumes, then customize a copy of the .CONFIG file to reflect the location of your data, and run the jiv2 shell script as mentioned above.


How to Run

To Run JIV2 on your computer as a standalone:
To run JIV2 using the included sample data, simply download jiv2.tar.gz below, unpack it, and type:
> jiv2 demo/view_macaque_label_native.CONFIG

To run JIV2 using your own data, type:
> jiv2 path_to_your_data/your_view.CONFIG

To publish your JIV2 volumes online for viewing:
To publish your JIV2 data, type:
> jiv2 path_to_your_data/your_view.CONFIG path_to_webdir

To use the viewer:
The MNI stereotaxic coordinates (X,Y,Z) are displayed in the first row below the volumes. The second row is reserved for display of the native coordinates (Xnat,Ynat,Znat), and the third row for displaying the atlas coordinates (Breg,Lat,Sup or Fig,Lat,Sup). The fourth row is reserved for displaying the anatomic label (Anatomy) and the intensity (I) of the volume, wherever the cursor is currently located. For viewing, one can use the left most mouse button to click on any image, and the other cross-sectional images will be updated with the appropriate position. You can also hold the middle/rocker mouse button down while moving up or down, to pan through the image plane. Holding ‘Shift’ with the left or middle button will enable dragging and zooming. In the JIV window, you can “right-click” to get popup menus. One useful aspect is to turn on the ‘sync all cursors’ option so that all the column panels are updated with each left mouse click.
 

To generate the .xfm transform file:
The .xfm file can be created using manual tag points in register, or with the monkey script to automate minctracc registration.

To customize the .CONFIG file:
The .CONFIG file details the location of the volumes to view and their supporting files (see the monkey_example.CONFIG and the human_example.CONFIG). To use the .CONFIG file locally, first ensure that the MNI atlas paths are correct (line #6 “jiv.atlas_dir”). Then simply place a copy of this .CONFIG in the directory containing the data you wish to compare to the MNI atlas, and customize the “##Native Section##” (at least lines #31–34) of the .CONFIG to reflect the native volume you wish to view.

You can change the order that the columns/panels are displayed, the alias (name displayed) of the atlas, labels, or native volume, and other display properties. For more information, see Detailed Documentation below.


Detailed Documentation

Detailed documentation of JIV can be found here. It will be updated shortly to reflect changes made from JIV to JIV2.

License & Download

JIV2 is copyright © 2004, 2010 Chris Cocosco, Lara Bailey.
It is available under the GNU General Public License (GPL). Any bug reports, suggestions, improvements, or extensions are welcome.
To install, use tar -xvvzf to unzip the .tgz you want below, then see the included README
DOWNLOADS FOR JIV2beta. This release does not read RGB label volumes.

  • JIV2beta (with sample data, as well as human and monkey atlases): jiv_2.0b.tgz
  • JIV2beta (without any sample data or atlases): jiv_2.0b_novolumes.tgz
  • JIV2beta source code, for those who want it: jiv_2.0b_src.tgz

DOWNLOAD PATCHES TO UPGRADE FROM JIV2beta TO JIV2. They will be available soon.

  • JIV2 source code: jiv_2.0_src.tgz
  • JIV2 executable: jiv2.jar
  • Rhesus RGB Paxinos label volume: paxinos-MNI.tgz

DOWNLOAD FULL JIV2. Available soon.

  • JIV2 (with sample data, as well as human and monkey atlases): jiv_2.0.tgz
  • JIV2 (without any sample data or atlases): jiv_2.0_novolumes.tgz
  • JIV2 source code, for those who want it: jiv_2.0_src.tgz
     

Publications

The following publications should be referenced when using this software:

  • JIV Chris A. Cocosco and Alan C. Evans, “Java Internet Viewer: A WWW Tool for Remote 3D Medical Image Data Visualization and Comparison”, Fourth International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI 2001), Utrecht, The Netherlands, 14–17 October 2001
  • JIV2 L. Bailey, S. Frey, M.M. Chakravarty, C. Cocosco, and D.L. Collins, “Improved Java Internet Viewer: A Web-based tool for 3D medical image visualization and comparison”, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, 6–10 June 2010