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FreeSurfer
Brain imaging software package

FreeSurfer is brain imaging software originally developed by Bruce Fischl, Anders Dale, Martin Sereno, and Doug Greve. Development and maintenance of FreeSurfer is now the primary responsibility of the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. FreeSurfer contains a set of programs with a common focus of analyzing magnetic resonance imaging (MRI) scans of brain tissue. It is an important tool in functional brain mapping and contains tools to conduct both volume based and surface based analysis. FreeSurfer includes tools for the reconstruction of topologically correct and geometrically accurate models of both the gray/white and pial surfaces, for measuring cortical thickness, surface area and folding, and for computing inter-subject registration based on the pattern of cortical folds.

57,541 copies of the FreeSurfer software package have been registered for use as of April 2022 and it is a core tool in the processing pipelines of the Human Connectome Project, the UK Biobank, the Adolescent Brain Cognitive Development Study, and the Alzheimer's Disease Neuroimaging Initiative.

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Usage

The FreeSurfer processing stream is controlled by a shell script called recon-all.9 The script calls component programs that organize raw MRI images into formats easily usable for morphometric and statistical analysis. FreeSurfer automatically segments the volume and parcellates the surface into standardized regions of interest (ROIs). Freesurfer uses a morphed spherical method to average across subjects for statistical (general linear model) analysis with the mri_glmfit10 tool. FreeSurfer contains a range of packages allowing a broad spectrum of uses, including:

  • FreeView, a tool to visualize FreeSurfer output, which can also display common MRI image formats11
  • TRACULA, a tool to construct white matter tract data from diffusion images12
  • FSFAST, a tool for analysis of functional MRI data13
  • XHemi, for Interhemispheric registration14
  • LGI, to calculate the degree of folding or local GI15
  • a Matlab toolbox for linear mixed effects models16

Interoperation

FreeSurfer interoperates easily with the FMRIB Software Library (FSL), a comprehensive library for image analysis written by the Functional MRI of the Brain (FMRIB) group at Oxford, UK. The functional activation results obtained using either the FreeSurfer Functional Analysis Stream (FS-FAST) or the FSL tools can be overlaid onto inflated, sphered or flattened cortical surfaces using FreeSurfer. Data from Statistical Parametric Mapping (SPM) can be integrated into FreeSurfer data sets through tools included in the FreeSurfer package.17 FreeSurfer also uses toolkits from MNI MINC, VXL, Tcl/Tk/Tix/BLT, VTK., KWWidgets and Qt,18 which are all available with the distribution. Other neuroimaging programs like Caret, AFNI/SUMA, MNE, and 3D Slicer can also import data processed by FreeSurfer.

Download

FreeSurfer runs on Mac OS and Linux. Free registration and binary installation are available without a cost, but a license key (text file) is necessary to run the FreeSurfer binaries.19 Documentation can be found on the FreeSurfer Wiki20 and limited support is available from the developers and community through the FreeSurfer mailing list.

Selected references

The following is a sample of references the FreeSurfer team recommends researchers cite when publishing findings obtained through FreeSurfer.21 Citation counts have been obtained through Google Scholar as of August 2019.

TitleYearCitations
Cortical surface-based analysis. I. Segmentation and surface reconstruction.2219996469
Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system.2319994507
High-resolution intersubject averaging and a coordinate system for the cortical surface.2419992339
Measuring the thickness of the human cerebral cortex from magnetic resonance images.2520003863
Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex.2620011258
Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain.2720025066
A hybrid approach to the skull stripping problem in MRI.2820041584
Automatically parcellating the human cerebral cortex.2920042731
An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest.3020064932

See also

  • Free and open-source software portal

References

  1. Fischl, Bruce (15 August 2012). "FreeSurfer". NeuroImage. 62 (2): 774–781. doi:10.1016/j.neuroimage.2012.01.021. ISSN 1053-8119. PMC 3685476. PMID 22248573. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3685476 ↩

  2. "Laboratory for Computational Neuroimaging | MGH/HST Martinos Center for Biomedical Imaging". https://www.nmr.mgh.harvard.edu/lab/lcn ↩

  3. Dale, Anders M.; Fischl, Bruce; Serenob, Martin I. (February 1999). "Cortical Surface-Based Analysis: I. Segmentation and Surface Reconstruction" (PDF). NeuroImage. 9 (2): 179–194. doi:10.1006/nimg.1998.0395. PMID 9931268. S2CID 2807360. Retrieved 29 August 2018. https://surfer.nmr.mgh.harvard.edu/ftp/articles/1999/1999_-_Dale_et_al._-_NeuroImage.pdf ↩

  4. [2] FreeSurfer stats from the official FreeSurfer wiki http://surfer.nmr.mgh.harvard.edu/fswiki/FsStats ↩

  5. Glasser, Matthew F.; Sotiropoulos, Stamatios N; Wilson, J Anthony; Coalson, Timothy S; Fischl, Bruce; Andersson, Jesper L; Xu, Junqian; Jbabdi, Saad; Webster, Matthew; Polimeni, Jonathan R; Van Essen, David C; Jenkinson, Mark (15 October 2013). "The Minimal Preprocessing Pipelines for the Human Connectome Project". NeuroImage. 80: 105–124. doi:10.1016/j.neuroimage.2013.04.127. ISSN 1053-8119. PMC 3720813. PMID 23668970. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3720813 ↩

  6. Smith, Stephen M.; Miller, Karla L.; Matthews, Paul M.; Dragonu, Iulius; Zhang, Hui; Alexander, Daniel C.; Daducci, Alessandro; Rorden, Christopher; McCarthy, Paul; Webster, Matthew; Vidaurre, Diego; Vallee, Emmanuel; Hernandez-Fernandez, Moises; Jbabdi, Saad; Sotiropoulos, Stamatios N.; Douaud, Gwenaëlle; Griffanti, Ludovica; Andersson, Jesper L. R.; Bangerter, Neal K.; Jenkinson, Mark; Alfaro-Almagro, Fidel (24 April 2017). "Image Processing and Quality Control for the first 10,000 Brain Imaging Datasets from UK Biobank". bioRxiv: 130385. doi:10.1101/130385. hdl:11343/256303. https://www.biorxiv.org/content/10.1101/130385v1 ↩

  7. Dale, Anders M.; Jernigan, Terry L.; Brown, Sandra A.; Dowling, Gayathri J.; Grant, Steven J.; Constable, R. Todd; Baskin-Sommers, Arielle; Madden, Pamela A.; Heath, Andrew C.; Glaser, Paul; Anokhin, Andrey P.; Steinberg, Joel; Hettema, John M.; Fuemmeler, Bernard; Charness, Michael E.; Lisdahl, Krista; Larson, Christine; Florsheim, Paul; Potter, Alexandra; Ivanova, Masha; Dumas, Julie A.; Allgaier, Nicholas A.; Yurgelun-Todd, Deborah A.; Renshaw, Perry F.; Prescot, Andrew; McGlade, Erin; Huber, Rebekah; Mason, Michael J.; Mruzek, Daniel W.; et al. (4 November 2018). "Image processing and analysis methods for the Adolescent Brain Cognitive Development Study". bioRxiv. 202: 457739. doi:10.1101/457739. PMC 6981278. PMID 31415884. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6981278 ↩

  8. "ADNI | MRI Tool". http://adni.loni.usc.edu/methods/mri-tool/ ↩

  9. [3] recon-all script usage http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all ↩

  10. "FsTutorial/GroupAnalysisV6.0 – Free Surfer Wiki". surfer.nmr.mgh.harvard.edu. Retrieved 2019-08-30. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0 ↩

  11. "FreeviewGuide/FreeviewIntroduction – Free Surfer Wiki". surfer.nmr.mgh.harvard.edu. Retrieved 2019-08-30. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewIntroduction ↩

  12. "Tracula – Free Surfer Wiki". surfer.nmr.mgh.harvard.edu. Retrieved 2019-08-30. https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula?highlight=(tracula) ↩

  13. "FsFastTutorialV6.0 – Free Surfer Wiki". surfer.nmr.mgh.harvard.edu. Retrieved 2019-08-30. https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0 ↩

  14. "Xhemi – Free Surfer Wiki". https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi ↩

  15. "LGI – Free Surfer Wiki". https://surfer.nmr.mgh.harvard.edu/fswiki/LGI ↩

  16. "LinearMixedEffectsModels – Free Surfer Wiki". https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels ↩

  17. "SPM – Free Surfer Wiki". surfer.nmr.mgh.harvard.edu. 15 August 2012. https://surfer.nmr.mgh.harvard.edu/fswiki/SPM ↩

  18. [4] Developer's Guide http://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide ↩

  19. [5] Archived 2014-11-23 at the Wayback Machine Download notes http://www.freesurfer.net/fswiki/Download#Notes ↩

  20. [6] FreeSurfer Wiki http://surfer.nmr.mgh.harvard.edu/fswiki ↩

  21. "FreeSurferMethodsCitation – Free Surfer Wiki". https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation ↩

  22. Dale, A. M.; Fischl, B.; Sereno, M. I. (February 1999). "Cortical surface-based analysis. I. Segmentation and surface reconstruction". NeuroImage. 9 (2): 179–194. doi:10.1006/nimg.1998.0395. ISSN 1053-8119. PMID 9931268. S2CID 2807360. /wiki/Doi_(identifier) ↩

  23. Fischl, B.; Sereno, M. I.; Dale, A. M. (February 1999). "Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system". NeuroImage. 9 (2): 195–207. doi:10.1006/nimg.1998.0396. ISSN 1053-8119. PMID 9931269. S2CID 3100335. /wiki/Doi_(identifier) ↩

  24. Fischl, Bruce; Sereno, Martin I.; Tootell, Roger B. H.; Dale, Anders M. (1999). "High-resolution intersubject averaging and a coordinate system for the cortical surface". Human Brain Mapping. 8 (4): 272–284. doi:10.1002/(SICI)1097-0193(1999)8:4<272::AID-HBM10>3.0.CO;2-4. ISSN 1097-0193. PMC 6873338. PMID 10619420. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6873338 ↩

  25. Fischl, B.; Dale, A. M. (2000-09-26). "Measuring the thickness of the human cerebral cortex from magnetic resonance images". Proceedings of the National Academy of Sciences of the United States of America. 97 (20): 11050–11055. Bibcode:2000PNAS...9711050F. doi:10.1073/pnas.200033797. ISSN 0027-8424. PMC 27146. PMID 10984517. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC27146 ↩

  26. Fischl, B.; Liu, A.; Dale, A. M. (January 2001). "Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex". IEEE Transactions on Medical Imaging. 20 (1): 70–80. CiteSeerX 10.1.1.3.8686. doi:10.1109/42.906426. ISSN 0278-0062. PMID 11293693. S2CID 954064. /wiki/CiteSeerX_(identifier) ↩

  27. Fischl, Bruce; Salat, David H.; Busa, Evelina; Albert, Marilyn; Dieterich, Megan; Haselgrove, Christian; van der Kouwe, Andre; Killiany, Ron; Kennedy, David (2002-01-31). "Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain". Neuron. 33 (3): 341–355. doi:10.1016/s0896-6273(02)00569-x. ISSN 0896-6273. PMID 11832223. S2CID 9629554. https://doi.org/10.1016%2Fs0896-6273%2802%2900569-x ↩

  28. Ségonne, F.; Dale, A. M.; Busa, E.; Glessner, M.; Salat, D.; Hahn, H. K.; Fischl, B. (July 2004). "A hybrid approach to the skull stripping problem in MRI". NeuroImage. 22 (3): 1060–1075. CiteSeerX 10.1.1.123.7627. doi:10.1016/j.neuroimage.2004.03.032. ISSN 1053-8119. PMID 15219578. S2CID 54432685. /wiki/CiteSeerX_(identifier) ↩

  29. Fischl, Bruce; van der Kouwe, André; Destrieux, Christophe; Halgren, Eric; Ségonne, Florent; Salat, David H.; Busa, Evelina; Seidman, Larry J.; Goldstein, Jill (January 2004). "Automatically parcellating the human cerebral cortex". Cerebral Cortex. 14 (1): 11–22. doi:10.1093/cercor/bhg087. ISSN 1047-3211. PMID 14654453. https://doi.org/10.1093%2Fcercor%2Fbhg087 ↩

  30. Desikan, Rahul S.; Ségonne, Florent; Fischl, Bruce; Quinn, Brian T.; Dickerson, Bradford C.; Blacker, Deborah; Buckner, Randy L.; Dale, Anders M.; Maguire, R. Paul (2006-07-01). "An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest". NeuroImage. 31 (3): 968–980. doi:10.1016/j.neuroimage.2006.01.021. ISSN 1053-8119. PMID 16530430. S2CID 12420386. /wiki/Doi_(identifier) ↩