A screen capture of the FreeView application included in FreeSurfer.
FreeSurfer is brain imaging software originally developed by Bruce Fischl, Anders Dale, Martin Sereno, and Doug Greve.[2] Development and maintenance of FreeSurfer is now the primary responsibility of the Laboratory for Computational Neuroimaging[3] 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.[4] 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[5] and it is a core tool in the processing pipelines of the Human Connectome Project,[6] the UK Biobank,[7] the Adolescent Brain Cognitive Development Study,[8] and the Alzheimer's Disease Neuroimaging Initiative.[9]
FreeSurfer morphs cortical surfaces onto spheres to aide in inter-subject comparisons.
^[1] FreeSurfer Software License page
^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.
^"Laboratory for Computational Neuroimaging | MGH/HST Martinos Center for Biomedical Imaging".
^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.
^[2] FreeSurfer stats from the official FreeSurfer wiki
^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.
^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.
^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.
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