Day 9: optimization, 2D interpolation and registration

4 / 24 / 2015


The reading for this weeks class is a notebook in the pna2015 repository:

cd pna2015
git pull
ipython notebook

The main notebook is day9/optimizing_space.ipynb - but you’ll see a couple of other notebooks there that the main notebook links to.

Here are the notebooks generated as non-interactive web pages, for reference:

You may also want to have a look at Formula for rotating a vector in 2D.


  • Convert optimization notebook to Python module;
  • Run;
  • Try different cost functions;
  • Try different optimization methods;
  • Local minima with a 180 degree rotation;
  • Investigate and run FSL motion correction.


The usual instructions:

  • cd pna/pna2015
  • git pull
  • ipython notebook

There is a web page listing of the exercise files at