Day twenty eight: 25 October 2013



The importance of scripting for:

  • recording and reproducibility
  • reducing error

Introduction to scripting from the pna-utils repository at:

  • 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.