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Day eleven : 10 May 2013
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************
Introduction
************

#. Workflow

   #. Organizing code and notebooks
   #. Using version control
   #. Building pipelines
   #. Reproducible analysis scripts

#. Registration

   #. Principles
   #. Motion correction

Notebooks for class
===================

* `workflow for class, raw
  <https://raw.github.com/practical-neuroimaging/pna-notebooks/master/workflow.ipynb>`_
  notebook file for downloading.
* `workflow for class, web
  <http://nbviewer.ipython.org/urls/raw.github.com/practical-neuroimaging/pna-notebooks/master/workflow.ipynb>`_
  notebook presented nicely as a web page.
* `Nipy registration intro for class, raw
  <https://raw.github.com/practical-neuroimaging/pna-notebooks/master/nipy_registration.ipynb>`_
  notebook file for downloading.
* `Nipy registration intro for class, web
  <http://nbviewer.ipython.org/urls/raw.github.com/practical-neuroimaging/pna-notebooks/master/nipy_registration.ipynb>`_
  notebook presented nicely as a web page.
* `Registration intro for class, raw
  <https://raw.github.com/practical-neuroimaging/pna-notebooks/master/Registration.ipynb>`_
  notebook file for downloading.
* `Registration intro for class, web
  <http://nbviewer.ipython.org/urls/raw.github.com/practical-neuroimaging/pna-notebooks/master/Registration.ipynb>`_
  notebook presented nicely as a web page.
* `git introduction intro for class, raw
  <https://raw.github.com/practical-neuroimaging/pna-notebooks/master/roll_your_own_cms.ipynb>`_
  notebook file for downloading.
* `git introduction intro for class, web
  <http://nbviewer.ipython.org/urls/raw.github.com/practical-neuroimaging/pna-notebooks/master/roll_your_own_cms.ipynb>`_
  notebook presented nicely as a web page.

Full notebooks with answers
===========================

* `Registration intro with answers, raw
  <https://raw.github.com/practical-neuroimaging/pna-notebooks/master/Registration_full.ipynb>`_
  notebook file for downloading.
* `Registration intro with answers, web
  <http://nbviewer.ipython.org/urls/raw.github.com/practical-neuroimaging/pna-notebooks/master/Registration_full.ipynb>`_
  notebook presented nicely as a web page.

**********
Background
**********

* A nice but technical `technical report
  <http://www.fmrib.ox.ac.uk/analysis/techrep/tr00mj2/tr00mj2/index.html>`_ on
  the components and issues in image registration.