[[https://surfer.nmr.mgh.harvard.edu/|FreeSurfer]] is a software suite for processing, analyzing, and visualizing human brain structural MRI images. It generates processed volumetric and surface data in subject native space.

The main workhorse of Freesurfer is [[https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all|recon-all]], which is discussed in [[https://andysbrainbook.readthedocs.io/en/latest/FreeSurfer/FS_ShortCourse/FS_03_ReconAll.html|Andy's Brain Book]]. There are modifications on recon-all for [[https://surfer.nmr.mgh.harvard.edu/fswiki/HighFieldRecon|high-field (7T) MRI]], [[https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon|high-resolution (submillimeter) MRI]], and [[https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing|longitudinal data]].

Freesurfer commands (recon-all and many, many more) can be run via the command line if you install the software and be sure to set up your terminal correctly with:

<code>
export FREESURFER_HOME=/path/to/fs/software
source $FREESURFER_HOME/SetUpFreesurfer.sh
export SUBJECTS_DIR=/path/to/fs/output
</code>

However for ease + reproducibility, you can also use the freesurfer BIDS app: https://github.com/bids-apps/freesurfer. Here is an [[https://github.com/LabNeuroCogDevel/corticalmyelin_maturation/blob/main/longitudinal_freesurfer/longitudinal_freesurfer_call.sh|example]]