In order to analyze fMRI data, you will need to download an fMRI analysis package. The three most popular are:

  • SPM (Statistical Parametric Mapping, created by University College London)
  • FSL (FMRIB Software Library, created by the University of Oxford)
  • AFNI (Analysis of Functional Neuroimages, created by the National Institutes of Health, USA)

Most laboratories use one of these three packages to analyze fMRI data. Each package is maintained by a team of professionals, and each is updated at least every few years or so. This course will focus on analyzing an online dataset using FSL; in the future, tutorials will be added for SPM and AFNI.

Installing FSL

FSL can be installed on different operating systems, such as Windows, Macintosh, and Linux. The Windows version requires a virtual machine to run FSL. This course will assume that you have a Macintosh or Linux operating system, and the tutorials will be recorded using an iMac desktop.

The instructions for installing FSL on different operating systems can be found here. The instructions are detailed and will not be repeated here; but for those who are using a Macintosh computer, a screencast can be found here to walk you through the installation and setup: FSL Installation Video Walkthrough.


You may come across the following error when running fslinstaller.py: [FAILED] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661). In that case, try running the installer by specifying the absolute path to your python command, e.g.: /usr/bin/python fslinstaller.py.

Next Steps

If you have never used a command line before, click on the Next button to begin the Unix tutorials. If you do feel comfortable using Unix, then you can skip to the fMRI Short Course.