Day 10

Lesson plan

We will go over the OpenFMRI notes.

We will then download and extract a dataset in class, and explain the directory structure and how to read the data.

Next we will do a couple of exercises with some introduction before each.

See Working with four dimensional images, with some revision:

  • BOLD images;
  • Revision of nibabel load, get_data;
  • Images with three and four dimensions;
  • Summary functions work on all dimensions unless you tell them otherwise; use axis= to tell them otherwise;
  • Negating booleans with ~bool_arr

Then we will do the Into four dimensions exercise.

  • Brain cartoons, and the frontal lobe;
  • Gray matter, white matter, CSF;
  • Block designs and event-related designs;
  • Repetition time (TR) is the time between the beginning of acquisition of one volume and the beginning of the next;
  • np.loadtxt loads text files into numpy arrays;

See Reading numerical data from text files

Now we do the A first go at finding brain activation exercise.