toads-cruise:Install

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1 Installing TOADS-CRUISE

Installing TOADS-CRUISE

System Requirements

TOADS-CRUISE plugins require an installation of the MIPAV software package (version 4.4.1), which is available on Windows, Mac, and Linux platforms. The memory requirements for the TOADS-CRUISE plugins are dependent on the size of the data being processed. To safely run all plugins except for cortical labeling for a standard magnetic resonance brain data set with 1mm cubic resolution, we recommend that MIPAV is run with a 8GB virtual machine. Cortical labeling requires a virtual machine with 12GB of memory.

Install MIPAV

Instructions for downloading and installing MIPAV are available here.

Install Plugins

Download the TOADS-CRUISE plugin jar package and save it to a directory of your choice. Launch MIPAV and select from the Plugins menu, "Install plugin".

This will open the Install Plugin window. Click on "Browse" to select the directory where you saved the jar file, and select Open. Then select the jar file, and click on the right arrow in the center of the window. Finally, click on "Install Plugins" at the bottom of the window. MIPAV will require some time to install the files. When installation is complete, a dialog will appear stating whether the plugins have been installed. Ignore any error message in this dialog box. Close any open MIPAV windows, then exit and relaunch MIPAV.

Initialize JIST Libraries

Before using the plugins, the JIST libraries must be initialized. JIST is a graphical image analysis pipeline development tool that is also available separately on NITRC. Because several of the TOADS-CRUISE algorithms are dependent on the JIST, it is included within the JAR. To initialize the JIST library, open the Plugins Menu, and under the "JIST" submenu, select the "JIST Layout Tool".

When running the Layout Tool for the first time, it will ask for a directory to store the module library. Choose any directory of your choice. If for some reason, you are not prompted to rebuild the library, in the Layout Manager go to Project->Global Preferences, select your library location, and then go to Project->Rebuild Library. When this step is completed, the layout tool should look like the window below. Close the layout tool window by clicking on the X in the top right corner.

Run Plug-ins

Any of the TOADS-CRUISE plugins can now be executed from the "TOADS-CRUISE" submenu under the "Plugins" menu. Some plugins may not be visible unless an image is already loaded. Most plugins should run properly with the most input images using default parameters. Additional information on individual plugins is available on this wiki.