FreeSurfer Quality Control Guide


FreeSurfer is a neuroimaging tool for creating and manipulating surface-based representations of the brain. FreeSurfer has a highly-automated processing stream that is very accurate. However, sometimes the automatic reconstructions contain small errors. Before submitting data based on the FreeSurfer reconstruction to any subsequent analyses, it is important to verify that the FreeSurfer reconstructions are free from errors, and to correct any errors found. The typical FreeSurfer Quality Control process for brains in the CNRLab proceeds as follows:

  1. Step 1: Correct the Pial Surfaces to remove any non-brain tissue
  2. Step 2: Correct the White Matter Surfaces to include any missing white matter
  3. Step 3: Correct the White Matter Surfaces to remove any errant grey matter

Step 0: Connect to the computer where your data are stored

All brains live in the /home/cnrlab/brains directory on each terminal. Regardless of which terminal you’re sitting at, you can access the data on the other terminals using ssh.

To connect to your desired terminal, use a command like the following. (But be sure to replace sar-cnrlab3 with the name of the computer you actually want to connect to (e.g., sar-cnrlab2, sar-cnrlab3, etc)):

ssh -X

 Next: Go to Step 1