Published material describing the techniques used in FreeSurfer ([http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/cite.php please cite our software!]):

• surface reconstruction:

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/dale99-recon1.pdf Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction], Dale, A.M., Fischl, B., Sereno, M.I., (1999). NeuroImage 9(2):179-194

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99b-recon2.pdf Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System], Fischl, B., Sereno, M.I., Dale, A.M., (1999). NeuroImage, 9(2):195-207.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl01-topology-fixing.pdf Automated Manifold Surgery: Constructing Geometrically Accurate and Topologically Correct Models of the Human Cerebral Cortex], Fischl, B., Liu, A. and Dale, A.M., (2001). IEEE Transactions on Medical Imaging, 20(1):70-80.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/dalesereno93-ms.pdf Improved localization of cortical activity by combining EEG and MEG with MRI cortical surface reconstruction: A linear approach], Dale, A.M., and Sereno, M.I. (1993). Journal of Cognitive Neuroscience 5:162-176.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/Neuroimage_Segonne_watershed.pdf A Hybrid Approach to the Skull-Stripping Problem in MRI], Ségonne, F., Dale, A.M., Busa, E., Glessner, M., Salvolini, U., Hahn, H.K., Fischl, B. (2004). NeuroImage, 22:1160-1075.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/segonne_ga_ipmi2005.pdf Genetic Algorithm for the Topology Correction of Cortical Surfaces], F. Segonne, E. Grimson, B. Fischl (2005). IPMI pp393--405.

• inter-subject spherical averaging:

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99-morphing.pdf High-resolution inter-subject averaging and a coordinate system for the cortical surface], Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). Human Brain Mapping, 8:272-284(1999).

• thickness measurement:

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl00-cortical-thickness.pdf Measuring the Thickness of the Human Cerebral Cortex from Magnetic Resonance Images], Fischl, B., and Dale, A.M., (2000). Proceedings of the National Academy of Sciences, 97:11044-11049.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/hd_neurology_reprint.pdf Regional and progressive thinning of the cortical ribbon in Huntington’s disease], Rosas et al., (2002). Neurology, 58:695-701.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/Kuperberg_and_Fischl_ArchGenPsy_03.pdf Regionally Localized Thinning of the Cerebral Cortex in Schizophrenia], Kuperberg et al., (2003). Archives of General Psychiatry, 60:878-888.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/salat04-thinning.pdf Thinning of the Cerebral Cortex in Aging], Salat et al., (2004). Cerebral Cortex, 14:721-730.

• cortical parcellation:

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf Automatically Parcellating the Human Cerebral Cortex], Fischl et al., (2004). Cerebral Cortex, 14:11-22.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest], Desikan et al., (2006). NeuroImage, in press.

• subcortical segmentation:

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain], Fischl et al., (2002). Neuron, 33:341-355.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf Sequence-Independent Segmentation of Magnetic Resonance Images], Fischl, B., Salat. D.H., van der Kouwe, A.J.W., Makris, N., Ségonne, F., and Dale, A.M. (2004) NeuroImage 23:S69-S84.

• related methodological papers

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/Golland_MICCAI2002.pdf Discriminative Analysis for Image-Based Studies], P. Golland, B. Fischl, M. Spiridon, N. Kanwisher, R.L. Buckner, M.E. Shenton, R. Kikinis, A. Dale, W.E.L. Grimson, (2002) In Proc. MICCAI'2002: Fifth International Conference on Medical Image Computing And Computer Assisted Intervention. LNCS 2488:508-515.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/golland-fischl-ipmi03.pdf Permutation Tests for Classification: Towards Statistical Significance in Image-Based Studies], P. Golland and B. Fischl, (2003) Proc. IPMI2003: 18th International Conference on Information Processing in Medical Imaging.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/segonne_subcortical_topology_miccai2003.pdf Topology Correction of Subcortical Segmentation], F. Segonne, E. Grimson and B. Fischl, (2003) MICCAI 2003.