Support for Batch Processing

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Objective:

To develop a command liner interface for the BRAINS3 project that will support batch processing with no graphical user interface. We have decided to use TCL because it integrates fully with our existing infrastructure. Present BRAINS3 consists of linking together three extensions of the TCL scripting language: ITK, VTK, and BRAINS2. For VTK, the TCL scripting is turned on using CMake. The VTK command line can be invoked from the BRAINS3 wish shell using the command

%package require VTK

ITK TCL command line is generated using WrapITK. This results in a very large package because all of the filters are created in both 2D and 3D for multiple data types. We will need to investigate how to reduce this memory footprint either by using fewer data types or loading and unloading various filters as they are used. This will require a better understanding of the dependency that filters have. This can be obtained from the Doxygen documentation generated for ITK.

Presently, the entire BRAINS2 command line interface is exposed in the TCL scripting layer. This is presently being used only for ROIs and Talairach parameters. This portion of the code should be updated and then all of the old infrastructure can be eliminated from this layer.

Progress:

• The BRAINS3 build system is being updated that will allow for integration of ITK, VTK, Slicer3, and BRAINS3 TCL command lines within a single executable. Adapters will then need to be written to pass data between these systems.
• ITK-VTK already exists with WrapITK wrapping.
• BRAINS3-ITK exists and needs to be wrapped with WrapITK.
• Need to determine how to get Data into slicer from VTK or ITK.

Key Investigators:

• University of Iowa: Vincent Magnotta, Hans Johnson, Nancy Andreasen
• The MIND Institute: Jeremy Bockholt

Links:

• University of Iowa Department of Psychiatry
• University of Iowa MRI Center
• The MIND Institute

Papers: