Published material describing the methods used in FreeSurfer (please cite our software!, see also boilerplate text):

surface reconstruction

inter-subject spherical averaging

thickness measurement

cortical parcellation

subcortical segmentation

longitudinal processing

related methodological papers



Published material citing Freesurfer:

(If you have a citation you would like to include in this list please e-mail your request to vinke[at]

cortical thickness

* Detection of focal changes in human cortical thickness: Spherical wavelets thresholding versus Gaussian smoothing. Bernal-Rusiel JL, Atienza M, Cantero JL (2008). Neuroimage, 41:1278-1292.

* Determining the optimal level of smoothing in cortical thickness analysis: a hierarchical approach based on sequential statistical thresholding. Bernal-Rusiel JL, Atienza M, Cantero JL (2010). Neuroimage, 52:158-171.

* Focal cortical damage parallels cognitive impairment in minimal hepatic encephalopathy. Montoliu C, Gonzalez-Escamilla G, Atienza M, Urios A, Gonzalez O, Wassel A, Aliaga R, Giner-Duran R, Serra MA, Rodrigo JM, Belloch V, Felipo V, Cantero JL (2012). Neuroimage, 61:1165-1175. * Sample size estimates for well-powered cross-sectional cortical thickness studies. Pardoe, H. R., Abbott, D. F., Jackson, G. D. and The Alzheimer's Disease Neuroimaging Initiative (2012), Hum. Brain Mapp.. doi: 10.1002/hbm.22120.

cortical surface area

local gyrification index (LGI)

clinical biomarkers


white matter


cortical region localization

cortical surface shape and folding analysis

surface-based analysis (SBA)

ROI-based analysis


diffusion analysis

CBF - cerebral blood flow

cortical flat-patches


validation / evaluation