Day twenty eight: 25 October 2013

Scripting

Introduction

The importance of scripting for:

• recording and reproducibility
• reducing error

Introduction to scripting from the pna-utils repository at: https://github.com/practical-neuroimaging/pna-utils

• diagnostics script as an example of a python script using library code, with minimal code in the script.
• smoothing script as a worse example, where library code is still in the script, and should be refactored out
• Brief sketch of SPM scripting using spm batch script in python
• Python as a cross-language batch scripting language
• nipype - a sophisticated scripting framework for SPM, AFNI, FSL and other programs.