FreeSurfer is a software package used for brain imaging analysis. Amongst several other measures and analyses (diffusion analysis, fMRI analysis, etc.), FreeSurfer can be used to estimate cortical thickness, and volumes of cortical and subcortical structures.

FreeSurfer can be downloaded using the instructions detailed here: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall. Remember to obtain a license key from the FreeSurfer website.

More information on FreeSurfer can be found here: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki

Thickness and Volume Analysis

First, define your environment variable and source FreeSurfer. On Linux, it is as follows:

export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

Next, define your subject directory, which is where the subject data is. On Linux, you can do so with:

export SUBJECTS_DIR=<path to subject data>

Then, do recon-all (https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all). Note that input data needs to be in either DICOM (.dcm) or NIFTI (.nii) form. If your input data is in .dcm, you only need to specify one file from the series.

Examples of using recon-all with a .nii and a .dcm would be:

recon-all -i 001.nii.gz -s output -all
recon-all -i 0001.dcm -s output -all

This will create a folder named output in the directory that has been defined as the SUBJECTS_DIR above. In that output folder will be several other folders, such as "scripts" (contains log info), and "stats" (contains ROI-based thickness and volume results).

Visualization

Here is an introduction to FreeSurfer output: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview

Visualization can be done using freeview. To use freeview, you will need to have sourced FreeSurfer in your active terminal.

Considerations

Keep in mind that FreeSurfer results vary with different versions, operating systems, and workstations: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038234