jist:Prerequisites

If you are running Windows XP (32-bit), Windows Vista or Windows 7 (64-bit), please skip ahead to the "Install MIPAV" section.

If you are running a Mac OSX 10.5 and above: before installing any programs, you need to make sure that you've got the latest version of Java on your computer.

Install the latest Java Update for Mac OSX.
- You can do this by closing all of your programs and running only "Software Update."
- Alternatively, you can go online to the Apple website and download the .dmg files. You can find the latest Apple security updates here: [http://support.apple.com/kb/HT1222] For example, [Update 6 for Mac OSX 10.5.8] installs Java SE6, which is the equivalent of Java 1.6.0.
Change your Java Preferences:
- Go to: Macintosh HD/Applications/Utilities/Java Preferences

- Drag the "JavaSE6 (64-bit)" to the top of the list for Java Applet Plugin and Java Applications. Close the window to save.

cd /System/Library/Frameworks/JavaVM.framework/Versions

ls -al

Check the directories and what they link to.
- If the CurrentJDK does NOT link to "1.6", then type: sudo -ln -sfn 1.6 CurrentJDK
- At the "Password:" type in your Mac OSX password.

Next, still in the Terminal, type: java -version
- This should output something like:

java version "1.6.0_17"

Java(TM) SE Runtime Environment (build 1.6.0_17-b04-248-9M3125)

Java HotSpot(TM) 64-Bit Server VM (build 14.3-b01-101, mixed mode)

Check your Java Home: In the Finder window, go to: Macintosh HD/Library/Java/Home
- If it leads you to the directory for Java 1.6, then you're fine; i.e., "Macintosh HD/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home"
- If it leads you to the directory for Java 1.5, then restart your computer.

After you log back into your computer, check your Java Home. You can also type in the Terminal java -version to make sure that the version is at least 1.6.0.

The only currently supported version of MIPAV is indicated above. Newer releases may work, but we cannot assure full compatability until we have had a chance to test the code on all platforms.
Make sure that any previous versions are uninstalled.
The MIPAV website itself says that Mac OSX users can change their Java Preferences (BEFORE installing MIPAV) so that users can download the appropriate Java SE6 version.
You may download MIPAV from: http://mipav.cit.nih.gov/download.php
If the "current" version if newer than indicated, then you can access the old version at from the bottom of the download page:

We strongly recommend using using a 64 bit version of MIPAV
- 32 bit Java jvms (java virtual machines) are limited to approximately 1100 MB of memory.
After you've installed MIPAV, check the JVM information: Help->JVM Information to make sure that the Java Version is at least 1.6. To do this, see the "Troubleshooting: Verify MIPAV Install" section below.

The first time that you run MIPAV, you will have to set the preferences for "Check java-runtime Memory Allocation."
We suggest running MIPAV with about 2-4x more memory than a single complete DTI dataset occupies on the disk.
Typically, a 30 direction, whole head dataset at 2.2 mm isotropic resolution take about 250 MB of disk space when stored as uncompressed 16 bit integers. So, a little more than 1 GB of RAM works well.
- Example: MacBookPro with 2Gb of RAM: Maximum heap size (null): 1025megabytes
- Generally, the optimal amount is about twice the size of a DTI Dataset -- more than 500Mb, and less than the computer's total amount of RAM.
Other computations, such as cortical surface reconstruction, topology corrected volumetric parcellation, etc., may take substantially more RAM.
Note that JIST-CATNAP has been tuned to operate with 32 bit floating point data, so you may surprised to find out that your processed images occupy about twice the disk space as unprocessed ones. This "trick" greatly reduces potential confusion and errors due to scaling factors.