Day 9: optimization, 2D interpolation and registration

4 / 24 / 2015

Reading

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:

• main notebook on spatial registration;
• background on Python functions;
• background on global variable scope.

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

Day

• 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.

Exercises

The usual instructions:

• cd pna/pna2015
• git pull
• ipython notebook

There is a web page listing of the exercise files at https://github.com/practical-neuroimaging/pna2015/tree/master/day9