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Petiole is a set of experimental tools for computational neuroanatomy based on medical images. Petiole provides extensions and add-on's to ITK and ANTS.

Why Petiole [pet-ee-ohl] ?

1. Botany - The petiole is the stalk of a leaf and provides a connection between the stem and a leaf. Under this metaphor, the "stem" is ITK+ANTS and the "leaf" is a desired tool. Specific "leaves" may also require additional open-source packages such as VTK and Boost.

2. Entomology - The petiole provides a connection between segments of the ant. A common theme among the tools being developed here is using ITK+ANTS to implement measures of structural and functional connectivity. (i.e. providing connectivity to ants)

Tools

1. petioleFibers - A tool designed for working with fiber bundles which are stored as vtk polylines. The primary purpose of these tools is to use clusters of streamlines to create geometric models that provide a basis for statistical analysis. Typically, these streamlines are derived from diffusion tensor MRI tractography methods. A useful tool for generating the streamlines is the Camino toolkit.

2. petioleConnectivity - A tool for exploring methods for measuring connectivity. This includes an emphasis on graph-based methods for measuring structural connectivity.

Examples (coming soon)

• Example 1 - Creating a central-axis based geometric representation of a white matter fiber bundle (uncinate fasciculus).

Getting started

First you need to download and compile the following packages

1. ITK 4.0.0 with the following options set in CMake

   ITK_USE_REVIEW=ON

2. ANTS 2.0