#################################
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 <https://github.com/practical-neuroimaging/pna-utils/blob/master/diagnostics_openfmri.py>`_
  as an example of a python script using library code, with minimal code in the
  script.
* `smoothing
  script <https://github.com/practical-neuroimaging/pna-utils/blob/master/smooth_openfmri.py>`_
  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 <https://github.com/practical-neuroimaging/pna-utils/blob/master/spm_batch_ds105.py>`_
* Python as a cross-language batch scripting language
* `nipype <http://nipy.org/nipype>`_ - a sophisticated scripting framework for
  SPM, AFNI, FSL and other programs.