First & run-level analyses

First & run-level analyses

In this section (corresponding to week 5 of the course), we discuss two things: first- and run-level analyses and how to run them using the software package FSL. The presentation slides for this topic can be found below:

This section contains three notebooks:

The Linux and the command line notebook gives an introduction to Linux and how to use the command line to run programs (such as FSL). Most of this tutorial can also be done on a Mac computer, but not on Windows. If you’re not interested in running command-line programs such as FSL, this tutorial can safely be skipped.

The First-level analyses tutorial discusses how to implement and run first-level analyses (as discussed in the tutorials from this course thus far) in FSL. In additionally introduces you to the image viewer from FSl, FSLeyes, and introduces the dataset we will use in this tutorial and some of the following tutorials.

The Run-level analyses tutorial introduces the idea of the two-stage multilevel model approximation used in many univariate fMRI analyses and demonstrates how to run a run-level analysis in FSL.


The FSL-part of the first-level analyses notebooks requires about 350MB of data to be downloaded. The code to download the data is included in the notebook.