TBSS #1: Download and Install

Before you Begin

TBSS comes with the FSL software package, which is covered in a previous tutorial. If you haven’t used FSL before, I recommend reviewing that module to become familiar with it; the following chapters assume that you know how to use basic FSL commands, as well as the FSL viewer, FSLeyes.

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.


A demonstration of how to install FSL can be found `here https://youtu.be/E9FwDCYAto8?t=16>`__.

Next Steps

When you have installed FSL, you will need a sample dataset to analyze. To see how to download that data, click the Next button.