Welcome
Welcome to the FreeSurferWiki. The FreeSurferWiki is the central documentation and download source for FreeSurfer, a software application developed at the Martinos Center for Biomedical Imaging.
NEW USERS: Please see the FreeSurferBeginnersGuide to get started. See also the FAQ page.
If you would like to contribute to the Wiki you will need a WikiUserName. Please see GettingAccess to obtain a WikiUserName.
See FreeSurferSupport for information on mailing lists relating to FreeSurfer. General questions about FreeSurfer should be directed to the freesurfer mailing list <freesurfer AT nmr DOT mgh DOT harvard DOT edu>. BugReporting should be directed to the analysis-bugs mailing list <analysis-bugs AT nmr DOT mgh DOT harvard DOT edu>.
Software
FreeSurfer download and install - New stable release v4.0.5 - See ReleaseNotes
Documentation
FreeSurferAnalysisPipelineOverview - Overview of the FreeSurfer analysis pipeline.
ArticlesSlidesAndPosters - Background describing the techniques used in the FreeSurfer tools, and their usage in research.
Tutorials - A walk-through of a FreeSurfer workflow, covering editing and troubleshooting techniques in-depth, as well as a group study example. There is also an FS-FAST tutorial.
ReconAllDevTable - An at-a-glance table showing the FreeSurfer files used & created during the recommended processing stream.
WorkFlows - Information on how the FreeSurfer tools are used in a processing stream.
ToolsAndCommands - GUI and command-line tool documentation.
FileFormats - Description of native FreeSurfer file formats, as well as external file formats used by FreeSurfer.
CoordinateSystems - Details on the voxel and RAS coordinate systems used in FreeSurfer.
DevelopersGuide - Information for developers of the FreeSurfer code-base (Martinos Center internal).
UserContributions - Scripts and techniques from users. This section is new, but if you have something you'd like to share, please do so. See also the FAQ page.
How to describe and cite Freesurfer - This document has a short description of Freesurfer methods to be used when citing Freesurfer. Alternatively, the text is available on the wiki at FreeSurferMethodsCitation
Acknowledgements
Support for this research was provided in part by the National Center for Research Resources (P41-RR14075, R01 RR16594-01A1 and the NCRR BIRN Morphometric Project BIRN002, U24 RR021382), the National Institute for Neurological Disorders and Stroke (R01 NS052585-01)), the National Institute of Biomedical Imaging and Bioengineering, as well as the Mental Illness and Neuroscience Discovery (MIND) Institute, and is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Thanks to Ron Kikinis, Steve Pieper and NA-MIC (NIH Roadmap for Medical Research Grant U54 EB005149) for providing engineering advice and support for testing and open-sourcing of FreeSurfer.
Thanks to Avi Snyder (Washington University School of Medicine) for porting his Talairach alignment implementation to FreeSurfer.
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References
Contents
Techniques
Published material describing the techniques used in FreeSurfer (please cite our software!):
surface reconstruction
Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction, Dale, A.M., Fischl, B., Sereno, M.I., (1999). NeuroImage 9(2):179-194
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.
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.
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.
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.
Genetic Algorithm for the Topology Correction of Cortical Surfaces, F. Segonne, E. Grimson, B. Fischl (2005). IPMI pp393--405.
inter-subject spherical averaging
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
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.
Reliability of MRI-derived measurements of human cerebral cortical thickness: The effects of field strength, scanner upgrade and manufacturer, X. Han, J. Jovichich, D. Salat, A. van der Kouwe, B. Quinn, S. Czanner, E. Busa, J. Pacheco, M. Albert, R. Killiany, P. Maguire, D. Rosas, N. Makris, A. Dale, B. Dickerson, and B. Fischl, (2006) NeuroImage, 32(1):180-194.
- see also below: Rosas et al. (histology) and Kuperberg et al. (MRI) were validation studies for the thickness measures
cortical parcellation
Automatically Parcellating the Human Cerebral Cortex, Fischl, B., A. van der Kouwe, C. Destrieux, E. Halgren, F. Segonne, D. Salat, E. Busa, L. Seidman, J. Goldstein, D. Kennedy, V. Caviness, N. Makris, B. Rosen, and A.M. Dale, (2004). Cerebral Cortex, 14:11-22.
An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest, Desikan, R.S., F. Segonne, B. Fischl, B.T. Quinn, B.C. Dickerson, D. Blacker, R.L. Buckner, A.M. Dale, R.P. Maguire, B.T. Hyman, M.S. Albert, and R.J. Killiany, (2006). NeuroImage 31(3):968-80.
Cortical Folding Patterns and Predicting Cytoarchitecture, Fischl, B., N. Rajendran, E. Busa, J. Augustinack, O. Hinds, B.T.T. Yeo, H. Mohlberg, K. Amunts, K. Zilles, (2007). Cerebral Cortex 2007, doi:10.1093/cercor/bhm225.
subcortical segmentation
Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain, Fischl, B., D.H. Salat, E. Busa, M. Albert, M. Dieterich, C. Haselgrove, A. van der Kouwe, R. Killiany, D. Kennedy, S. Klaveness, A. Montillo, N. Makris, B. Rosen, and A.M. Dale, (2002). Neuron, 33:341-355.
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.
Atlas Renormalization for Improved Brain MR Image Segmentation Across Scanner Platforms, Han, X. and B. Fischl, (2007). IEEE Transactions on Medical Imaging, 26(4):479-486.
related methodological papers
Discriminative Analysis for Image-Based Studies, Golland, P., 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.
Permutation Tests for Classification: Towards Statistical Significance in Image-Based Studies, Golland P., and B. Fischl, (2003) Proc. IPMI2003: 18th International Conference on Information Processing in Medical Imaging.
Topology Correction of Subcortical Segmentation, Segonne, F., E. Grimson and B. Fischl, (2003) MICCAI 2003.
Reliability in Multi-Site Structural MRI Studies: Effects of Gradient Non-linearity Correction on Phantom and Human Data, Jovicich J, Czanner S, Greve D, Haley E, Kouwe A, Gollub R, Kennedy D, Schmitt F, Brown G, MacFall J, Fischl B, Dale A., (2006) NeuroImage, 30(2): 436-443.
Geometrically Accurate Topology-Correction of Cortical Surfaces Using Nonseparating Loops, Segonne, F., J. Pacheco, B. Fischl, (2007) IEEE Transactions on Medical Imaging, 26(4):518-529.
Phase maps reveal cortical architecture, Bruce Fischl and Lawrence L. Wald, PNAS, July 10, 2007, vol. 104, no. 28.
Effects of Registration Regularization and Atlas Sharpness on Segmentation Accuracy, Yeo, B.T.T., M. Sabuncu, R. Desikan, B. Fischl, P. Golland (2007). Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2007).
What Data to Co-register for Computing Atlases, B.T.T. Yeo, M. Sabuncu, H. Mohlberg, K. Amunts, K. Zilles, P. Golland, B. Fischl (2007). Proceedings of the IEEE Computer Society Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA 2007).
A Technique for the Deidentification of Structural Brain MR Images, Bischoff-Grethe, A., I.B. Ozyurt, E. Busa, B.T. Quinn, C. Fennema-Notestine, C.P. Clark, S. Morris, M.W. Bondi, T.L. Jernigan, A.M. Dale, G.G. Brown, and B. Fischl (2007) Human Brain Mapping, volume 28, issue 9, pp 892-903.
An MRI-based method for measuring volume, thickness and surface area of entorhinal, perirhinal, and posterior parahippocampal cortex, Feczko, E., J.C. Augustinack, B. Fischl, B.C. Dickerson, (2007). Neurobiology of Aging, 2007 Sep 10.
Brain morphometry with multiecho MPRAGE, van der Kouwe, A.J.W., T. Benner, D.H. Salat, and B. Fischl (2008) NeuroImage 40 (2008) 559-569.
Citations
Published material citing Freesurfer:
cortical thickness
Regional and progressive thinning of the cortical ribbon in Huntington's disease, Rosas, H.D., A.K. Liu, S. Hersch, M. Glessner, R.J. Ferrante, D.H. Salat, A. van der Kouwe, B.G. Jenkins, A.M. Dale, and B. Fischl, (2002). Neurology, 58:695-701.
Regionally localized thinning of the cerebral cortex in schizophrenia, Kuperberg, G.R., M.R. Broome, P.K. McGure, A.S. David, M. Eddy, F. Ozawa, D. Goff, C. West, S.C.R. WIlliams, A.J.W. van der Kouwe, D.H. Salat, A.M. Dale, and B. Fischl, (2003). Archives of General Psychiatry, 60:878-888.
Focal thinning of the cerebral cortex in multiple sclerosis, Sailer, M., B. Fischl, D. Salat, C. Tempelmann, M. Schonfeld, E. Busa, N. Bodammer, H. Heinze, and A. Dale, (2003). Brain, 126(9):1734-1744. (See also: editorial)
Thinning of the Cerebral Cortex in Aging, D.H. Salat, R.L. Buckner, A.Z. Synder, R.S.R. Desikan, D.N. Greve, E. Busa, J.C. Morris, A.M. Dale, and B. Fischl, (2004). Cerebral Cortex, 14:721-730.
A magnetic resonance imaging study of cortical thickness in animal phobia, Rauch, S., C. Wright, B. Martis, E. Busa, K. McMullin, L. Shin, A. Dale, and B. Fischl, (2004). Biological Psychiatry, 55(9):946-952.
Differing neuropsychological and neuroanatomical correlates of abnormal reading in early-stage semantic dementia and dementia of the Alzheimer type, Gold, B.T., D.A. Balota, M.J. Cortes, S.D. Sergent-Marshall, A.Z. Snyder, D.H. Salat, B. Fischl, A.M. Dale, J.C. Morris, and R.L. Buckner, (2005). Neuropsychologia, 43: p. 833-846.
Thickness of ventromedial prefrontal cortex in humans is correlated with extinction memory, Milad, M.R., B.T. Quinn, R.K. Pitman, S.P. Orr, B. Fischl, and S.L. Rauch (2005). PNAS, 102(30):10706-10711.
Meditation experience is associated with increased cortical thickness, Lazar, S.W., C.E. Kerr, R.H. Wasserman, J.R. Gray, D.N. Greve, M.T. Treadway, M. McGarvey, B.T. Quinn, J.A. Dusek, H. Benson, S.L. Rauch, C.I. Moore, and B. Fischl, (2005). NeuroReport, 16(17): 1893-1897.
Selective increase of cortical thickness in high-performing elderly - structural indices of optimal cognitive aging, Fjell, A.M., K.B. Walhovd, I. Reinvang, A. Lundervold, D. Salat, B.T. Quinn, B. Fischl and A.M. Dale (2006). NeuroImage 29:984-994.
Regional cortical thickness matters in recall after months more than minutes, Walhovd, K.B., A.M. Fjell, A.M. Dale, B. Fischl, B.T. Quinn, N. Makris, D. Salat, and I. Reinvan (2006). NeuroImage 31:1343 - 1351.
Mapping an intrinsic MR property of gray matter in auditory cortex of living humans: A possible marker for primary cortex and hemispheric differences, Sigalovsky, I.S., B. Fischl, and J.R. Melchera (2006). NeuroImage 32:1524-1537.
Anatomical differences in the mirror neuron system and social cognition network in autism, Hadjikhani N., R.M. Joseph, J. Snyder, H. Tager-Flusberg (2006). Cerebral Cortex 16(9):1276-82.
Different regional patterns of cortical thinning in Alzheimer's disease and frontotemporal dementia, Du, AT, N. Schuff, J.H. Kramer, H.J. Rosen, M.L. Gorno-Tempini, K. Rankin, B.L. Miller and M.W. Weiner (2007). Brain 130:1159-1166.
Differential effects of aging and Alzheimer's disease on medial temporal lobe cortical thickness and surface area, Dickerson B.C, E. Feczko, J.C. Augustinack, J. Pacheco, J.C. Morris, B. Fischl, R.L. Buckner (2007). Neurobiology of Aging, 2007 Sep 13.
Thickening in the somatosensory cortex of patients with migraine, DaSilva, A.F.M., C. Granziera, J. Snyder and N. Hadjikhani (2007). Neurology 69:1990-1995.
Detection of cortical thickness correlates of cognitive performance: Reliability across MRI scan sessions, scanners, and field strengths, Dickerson, B.C., E. Fenstermacher, D.H. Salat, D.A. Wolk, R.P. Maguire, R. Desikan, J. Pacheco, B.T. Quinn, A. Van der Kouwe, D.N. Greve, D. Blacker, M.S. Albert, R.J. Killiany, and B. Fischl (2008). NeuroImage 39(1):10-8.
Regional neocortical thinning in mesial temporal lobe epilepsy, McDonald C.R., D.J. Hagler Jr., M.E. Ahmadi, E. Tecoma, V. Iragui, L. Gharapetian, A.M. Dale, E. Halgren (2008). Epilepsia. 2008 Feb 7.
Cerebral cortex and the clinical expression of Huntington's disease: complexity and heterogeneity, Rosas, D.H., D.H. Salat, S.Y. Lee, A.K. Zaleta, V. Pappu, B. Fischl, D. Greve, N. Hevelone and S.M. Hersch (2008). Brain doi:10.1093/brain/awn025.
Regional neocortical thinning in mesial temporal lobe epilepsy, McDonald, C.R., D.J. Hagler, Jr., M.E. Ahmadi, E. Tecoma, V. Iragui, L. Gharapetian, A.M. Dale, and E. Halgren (2008). Epilepsia 48 (2), 211-219.
Abnormal cerebral cortex structure in children with ADHD, Wolosin S.M., Richardson M.E., Hennessey J.G., Denckla M.B., Mostofsky S.H. Human Brain Mapping, 2007 Nov 5.
Morphometric Changes in the Episodic Memory Network and Tau Pathologic Features Correlate With Memory Performance in Patients With Mild Cognitive Impairment, A.M.Fjell, K.B.Walhovd, I.Amlien, A. Bjørnerud, I.Reinvang, L.Gjerstad, T.Cappelen, F.Willoch, P. Due-Tønnessen, R.Grambaite, A.Skinningsrud, V.Stenset, T.Fladby. AJNR Am J Neuroradiol, Jun-Jul 2008.
Accelerated age-related cortical thinning in healthy carriers of apolipoprotein E ε4, Thomas Espeseth , Lars T. Westlye, Anders M. Fjell, Kristine B. Walhovd, Helge Rootwelt, Ivar Reinvanga. Neurobiology of Aging 29 (2008) 329–340.
Cognitive Function, P3a/P3b Brain Potentials, and Cortical Thickness in Aging, Anders M. Fjell, Kristine B. Walhovd, Bruce Fischl and Ivar Reinvang. Human Brain Mapping 28:1098–1116 (2007).
Regional thinning of the cerebral cortex in schizophrenia: Effects of diagnosis, age and antipsychotic medication, Ragnar Nesvåg, Glenn Lawyer, Katarina Varnäs, Anders M. Fjell, Kristine B. Walhovd, Arnoldo Frigessi, Erik G. Jönsson, Ingrid Agartz. Schizophrenia Research 98 (2008) 16 – 28.
volumetric
Age does not increase rate of forgetting over weeks neuroanatomical volumes and visual memory across the adult life-span, Fjell, A.M., K.B. Walhovd, I. Reinvang, A. Lundervold, A.M. Dale, B.T. Quinn, N. Makris, and B. Fischl, (2005). Journal of the International Neuropsychological Society, 2-15(1):2-15.
Cortical volume and speed-of-processing are complementary in prediction of performance intelligence, Walhovd, K.B., A.M. Fjell, I. Reinvang, A. Lundervold, B. Fischl, B.T. Quinn, N. Makris, and A.M. Dale, (2005). Neuropsychologia, 43(5):704-713.
Effects of age on volumes of cortex, white matter and subcortical structures, Walhovd, K.B., A.M. Fjell, I. Reinvang, A. Lundervold, A.M. Dale, D.E. Eilertsen, B.T. Quinn, D. Salat, N. Makris, and B. Fischl (2005). Neurobiology of Aging 26:1261-1270. See also: Commentary: Neuroanatomical aging: Universal but not uniform.
The functional and structural significance of the frontal shift in the old/new ERP effect, Walhovd, K.B., A.M. Fjell, I. Reinvang, A. Lundervold, B. Fischl, B.T. Quinn, N. Makris, and A.M. Dale, (2006). Brain Research, 1081:156-170.
Detailed semiautomated MRI based morphometry of the neonatal brain: Preliminary results, Nishida, M., N. Makris, D.N. Kennedy, M. Vangel, B. Fischl, K.S. Krishnamoorthy, V.S. Caviness, and P.E. Grant (2007). NeuroImage 32:1041-1049.
Volumetric cerebral characteristics of children exposed to opiates and other substances in utero, Walhovd, K.B., V. Moe, K. Slinning, P. Due-Tønnessen, A. Bjørnerud, A.M. Dale, A. van der Kouwe, B.T. Quinn, B. Kosofsky, D. Greve, and B. Fischl, (2007). NeuroImage 36:1331-1344.
Feasibility of Multi-site Clinical Structural Neuroimaging Studies of Aging Using Legacy Data, Fennema-Notestine, C., A.C. Gamst, B.T. Quinn, J. Pacheco, T.L. Jernigan, L. Thal, R. Buckner, R. Killiany, D. Blacker, A.M. Dale, B. Fischl, B. Dickerson, R.L. Gollub, (2007). Neuroinformatics 5:235-245.
The Effect of Early Human Diet on Caudate Volumes and IQ, Isaacs, E.B., D.G. Gadian, S. Sabatini, W.K. Chong, B.T. Quinn, B.R. Fischl, and A. Lucas, (2008). Pediatric Research 63(3):308-314. (see also: commentary)
Subcortical and cerebellar atrophy in mesial temporal lobe epilepsy revealed by automatic segmentation, McDonald, C.R., D.J. Hagler, Jr., M.E. Ahmadi, E. Tecoma, V. Iragui, A.M. Dale, and E. Halgren (2008). Epilepsy Researc 2008 Mar 20.
White matter volume predicts reaction time instability, Kristine B. Walhovd , Anders M. Fjell. Neuropsychologia 45 (2007) 2277–2284.
Interactive effects of APOE and CHRNA4 on attention and white matter volume in healthy middle-aged and older adults, Thomas Espeseth, Pamela M. Greenwood, Ivar Reinvang, Anders M. Fjell, Kristine B. Walhovd, Lars T. Westlye, Eike Wehling, Astri Lundervold, Helge Rootwelt, Raja Parasuraman. Cognitive, Affective, & Behavioral Neuroscience 2006, 6(1), 31-43.
entorhinal cortex
Detection of entorhinal layer II using 7 Tesla magnetic resonance imaging, Augustinack, Jean C., Andre J. W. van der Kouwe, Megan L. Blackwell, David H. Salat, Christopher J. Wiggins, Matthew P. Frosch, Graham C. Wiggins, Andreas Potthast, Lawrence L. Wald, Bruce R. Fischl, (2005). Annals of Neurology, 57(4):489-494.
cortical surface shape and folding analysis
Cortical Surface Shape Analysis Based on Spherical Wavelets, Yu, P., P.E. Grant, Y. Qi, X. Han, F. Ségonne, R. Pienaar, E. Busa, J. Pacheco, N. Makris, R.L. Buckner, P. Golland, and B. Fischl (2007). IEEE Transactions on Medical Imaging, 26(4):582-597.
Cortical folding development study based on over-complete spherical wavelets Yu, P., B.T.T. Yeo, P.E. Grant, B. Fischl, P. Golland (2007). Proceedings of the IEEE International Conference on Computer Vision (MMBIA 2007).
Abnormal cortical folding patterns within Broca's area in schizophrenia: Evidence from structural MRI, Wisco, J.J., G. Kuperberg, D. Manoach, B.T. Quinn, E. Busa, B. Fischl, S. Heckers, A.G. Sorensen (2007). Schizophrenia Research, 94(1-3):317-327.
Accurate prediction of V1 location from cortical folds in a surface coordinate system, Hinds, O.P., N. Rajendran, J.R. Polimeni, J.C. Augustinack, G. Wiggins, L.L. Wald, H.D. Rosas, A. Potthast, E.L. Schwartz and B. Fischl (2007). NeuroImage 2007.10.033.
A Methodology for Analyzing Curvature in the Developing Brain from Preterm to Adult, R.Pienaar, B.Fischl, B.Caviness, N.Makris, P.E.Grant. (2008) International Journal of Imaging Systems and Technology Special Issue: Human Brain Imaging, 18(1): 42-68.
surface-based analysis
A human parietal face area contains aligned head-centered visual and tactile maps, Sereno, M.I. and RS Huang, (2006). Nature Neuroscience 9:1337-1343.
Enhanced Cortical Activation in the Contralesional Hemisphere of Chronic Stroke Patients in Response to Motor Skill Challenge, Schaechter, J.D., and K.L. Perdue (2007). Cerebral Cortex, 2007 Jun 29 [Epub ahead of print].
cortical flat-patches
Attentional modulation of human auditory cortex, Petkov, C.I., X. Kang, K. Alho, O. Bertrand, W.E. Yund, and D.L. Woods, (2004). Nature Neuroscience 7:658-663.
FS-FAST
Faces and objects in macaque cerebral cortex, Tsao, D.Y., W.A. Freiwald, T.A. Knutsen, J.B. Mandeville and R.B.H. Tootell, (2003). Nature Neuroscience 6:989-995.
Diffusion Analysis
The relationship between diffusion tensor imaging and volumetry as measures of white matter properties, Anders M Fjell, Lars T Westlye, Doug N. Greve, Bruce Fischl, Thomas Benner, André J. W. van der Kouwe, David Salat, Atle Bjørnerud, Paulina Due-Tønnessen, Kristine B Walhovd. NeuroImage, in press.