MRI tutorials

Freesurfer is a software package which allows analysing and extracting information (e.g., cortical thickness, area, volume) from MRI scans. Such information can be compared between groups (e.g., with vs without language impairment, or a particular condition like DLD), and can be correlated to behavioral measures to aid identify brain regions which may contribute to specific lanaguage or other cognitive processes. While Freesurfer can be used for analyses of both structural and functional MRI data of different types, these tutorials focus on the functionalities used for processing T1-weighted images.

This video series was prepared by Vânia de Aguiar (Associate Professor in Neurolinguistics at the University of Groningen, PI of CLaDis lab) for the students of the European Master's in clinical linguistic. Content is adapted from the tutorials available in the Freesurfer webpage. Directories require access to the RUG y drive, which is only available to students and staff of the University of Groningen. For people external to the University of Groningen, I recommend downloading Freesurfer and then the tutorial data from the Freesurfer page. You may then follow the tutorials below: all you'll need to do is adjust the directories so that Freesurfer can find the relevant files.

This first video gives a short introduction on where to find the materials and how to access the virtual workspace. See tutorial transcript and code here.

This second video shows on how to use the command line to run the most important Freesurfer commands.

See tutorial transcript and code here (this is the same same file as linked above for tutorial 1).

This third video gives an overview of the output obtained from recon-all, and the main functionality of Freeview, which is Freesurfer's main GUI.

See tutorial transcript and code here (this is the same same file as linked above for tutorials 1 and 2).

Tutorial 4 steps are available here, along with links to additional resources.