User Guide

Release:0.2 Date:May 25, 2010, 21:08 PDT

• Download and install
  • Dependencies
  • Download
  • Install
  • Testing the install
• Available modules
  • SPM
  • FSL
  • FreeSurfer
  • Misc
• Tutorial : Interfaces
  • Specifying options
  • Getting Help
  • FSL interface example
  • SPM interface example
• Tutorial : Pipeline
  • Running a pipeline
  • Tutorials

Interfaces

Wrappers around existing software packages, through a uniform Python interface.

Pipeline

The pipeline consists of two main parts: nodewrappers, and the engine.

NodeWrappers

NodeWrappers are bridges between the Interface and the Pipeline. They provide added functionality to work with pipelines such as:

1. Adding iterable input values to be passed to interface.
2. Dealing with and generating directories that hold temporary processed data. This includes generating hash names that can be used to uniquely identify a specific process done to the data (with specific parameters), so the pipeline can avoid replicating redundant processes.
3. Validates inputs to each node of the Network exist.
4. Allows user to overwrite existing results.

Engine

This is the machinery that runs the pipeline. Controls the setup and execution of the pipeline. The current Engine uses NetworkX.