FreeSurfer

FreeSurfer is a software package for processing and analyzing human brain MRI data. It focuses on automated reconstruction of the cerebral cortex and segmentation of subcortical structures, enabling researchers to measure cortical thickness, surface area, and volumetric statistics.

The core workflow is implemented in the recon-all pipeline, which integrates preprocessing steps such as motion correction, skull stripping, and bias field correction, followed by white matter/gray matter segmentation, generation of pial and white matter surface models, and alignment to a spherical atlas for cortical labeling. FreeSurfer provides cortical parcellations using atlases such as Desikan-Killiany and Destrieux, along with tools for computing surface-based metrics and surface maps.

Subcortical segmentation identifies structures including the caudate, putamen, thalamus, hippocampus, and amygdala, producing label maps and regional statistics. Outputs include surface models, label files, thickness maps, and statistical data suitable for group analyses or visualization. The package also includes utilities for visualization and data management and supports surface-based statistics through Qdec.

FreeSurfer is developed by researchers at the Martinos Center for Biomedical Imaging at Massachusetts General Hospital and Harvard Medical School. It runs on Linux and macOS and is distributed under a license that permits free use for non-commercial academic purposes; commercial use requires a separate license. The project is supported by comprehensive documentation and an active user community.