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FreeSurfer
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<h2 id="usage">Usage</h2> <p>The FreeSurfer processing stream is controlled by a shell script called <i>recon-all</i>.<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> 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 <a href="/facts/Region_of_Interest/C8k58oC5">regions of interest</a> (ROIs). Freesurfer uses a morphed spherical method to average across subjects for statistical (<a href="/facts/General_linear_model/yLyjt7aa">general linear model</a>) analysis with the mri_glmfit<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a> tool. FreeSurfer contains a range of packages allowing a broad spectrum of uses, including: </p> <ul><li>FreeView, a tool to visualize FreeSurfer output, which can also display common MRI image formats<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a></li> <li>TRACULA, a tool to construct white matter tract data from diffusion images<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a></li> <li>FSFAST, a tool for analysis of functional MRI data<a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a></li> <li>XHemi, for Interhemispheric registration<a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a></li> <li>LGI, to calculate the degree of folding or local GI<a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a></li> <li>a Matlab toolbox for linear mixed effects models<a class="footnote-ref" id="fnref:16" href="#fn:16"><sup>16</sup></a></li></ul> <h2 id="interoperation">Interoperation</h2> <p>FreeSurfer interoperates easily with the <a href="/facts/FMRIB_Software_Library/hCMGVllw">FMRIB Software Library</a> (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.<a class="footnote-ref" id="fnref:17" href="#fn:17"><sup>17</sup></a> FreeSurfer also uses toolkits from <a href="http://www.bic.mni.mcgill.ca/software">MNI MINC</a>, <a href="/facts/VXL/JHd1QWLY">VXL</a>, <a href="/facts/Tcl/s7fbKYtR">Tcl</a>/<a href="/facts/Tk_(computing)/Y6NBxcbF">Tk</a>/Tix/BLT, <a href="/facts/VTK/SXTm1vTl">VTK</a>., KWWidgets and Qt,<a class="footnote-ref" id="fnref:18" href="#fn:18"><sup>18</sup></a> which are all available with the distribution. Other neuroimaging programs like <a href="/facts/CARET_(Computerized_Anatomical_Reconstruction_and_Editing_Toolkit)/edKLJl0n">Caret</a>, <a href="/facts/AFNI/uSBaTcs1"> AFNI/SUMA</a>, <a href="http://martinos.org/mne/dev/index.html">MNE</a>, and 3D Slicer can also import data processed by FreeSurfer. </p> <h2 id="download">Download</h2> <p>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.<a class="footnote-ref" id="fnref:19" href="#fn:19"><sup>19</sup></a> Documentation can be found on the FreeSurfer Wiki<a class="footnote-ref" id="fnref:20" href="#fn:20"><sup>20</sup></a> and limited support is available from the developers and community through the FreeSurfer mailing list. </p> <h2 id="selected-references">Selected references</h2> <p>The following is a sample of references the FreeSurfer team recommends researchers cite when publishing findings obtained through FreeSurfer.<a class="footnote-ref" id="fnref:21" href="#fn:21"><sup>21</sup></a> Citation counts have been obtained through Google Scholar as of August 2019. </p> <table><tbody><tr><th>Title</th><th>Year</th><th>Citations</th></tr><tr><td>Cortical surface-based analysis. I. Segmentation and surface reconstruction.<a class="footnote-ref" id="fnref:22" href="#fn:22"><sup>22</sup></a></td><td>1999</td><td>6469</td></tr><tr><td>Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system.<a class="footnote-ref" id="fnref:23" href="#fn:23"><sup>23</sup></a></td><td>1999</td><td>4507</td></tr><tr><td>High-resolution intersubject averaging and a coordinate system for the cortical surface.<a class="footnote-ref" id="fnref:24" href="#fn:24"><sup>24</sup></a></td><td>1999</td><td>2339</td></tr><tr><td>Measuring the thickness of the human cerebral cortex from magnetic resonance images.<a class="footnote-ref" id="fnref:25" href="#fn:25"><sup>25</sup></a></td><td>2000</td><td>3863</td></tr><tr><td>Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex.<a class="footnote-ref" id="fnref:26" href="#fn:26"><sup>26</sup></a></td><td>2001</td><td>1258</td></tr><tr><td>Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain.<a class="footnote-ref" id="fnref:27" href="#fn:27"><sup>27</sup></a></td><td>2002</td><td>5066</td></tr><tr><td>A hybrid approach to the skull stripping problem in MRI.<a class="footnote-ref" id="fnref:28" href="#fn:28"><sup>28</sup></a></td><td>2004</td><td>1584</td></tr><tr><td>Automatically parcellating the human cerebral cortex.<a class="footnote-ref" id="fnref:29" href="#fn:29"><sup>29</sup></a></td><td>2004</td><td>2731</td></tr><tr><td>An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest.<a class="footnote-ref" id="fnref:30" href="#fn:30"><sup>30</sup></a></td><td>2006</td><td>4932</td></tr></tbody></table> <h2 id="see-also">See also</h2> <ul> <li>Free and open-source software portal</li></ul> <ul><li><a href="/facts/Analysis_of_Functional_NeuroImages/uSBaTcs1">Analysis of Functional NeuroImages</a></li> <li><a href="/facts/CARET_(Computerized_Anatomical_Reconstruction_and_Editing_Toolkit)/edKLJl0n">Caret</a> Van Essen Lab, Washington University in St. Louis</li> <li>Laboratory of Neuro Imaging, UCLA</li> <li><a href="/facts/Statistical_parametric_mapping/NDJ7qx6M">Statistical parametric mapping</a> (SPM)</li> <li><a href="/facts/Computational_anatomy_toolbox/LX3clAN2">Computational anatomy toolbox</a></li> <li><a href="/facts/Anastasia_Yendiki/0vo1vVQI">Anastasia Yendiki</a></li></ul> <h2 id="external-links">External links</h2> <ul><li><a href="http://www.freesurfer.net/">Official website</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3685476" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3685476</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>"Laboratory for Computational Neuroimaging | MGH/HST Martinos Center for Biomedical Imaging". <a href="https://www.nmr.mgh.harvard.edu/lab/lcn" target="_blank">https://www.nmr.mgh.harvard.edu/lab/lcn</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>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. <a href="https://surfer.nmr.mgh.harvard.edu/ftp/articles/1999/1999_-_Dale_et_al._-_NeuroImage.pdf" target="_blank">https://surfer.nmr.mgh.harvard.edu/ftp/articles/1999/1999_-_Dale_et_al._-_NeuroImage.pdf</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>[2] FreeSurfer stats from the official FreeSurfer wiki <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsStats" target="_blank">http://surfer.nmr.mgh.harvard.edu/fswiki/FsStats</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3720813" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3720813</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>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. <a href="https://www.biorxiv.org/content/10.1101/130385v1" target="_blank">https://www.biorxiv.org/content/10.1101/130385v1</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6981278" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6981278</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>"ADNI | MRI Tool". <a href="http://adni.loni.usc.edu/methods/mri-tool/" target="_blank">http://adni.loni.usc.edu/methods/mri-tool/</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>[3] recon-all script usage <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all" target="_blank">http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>"FsTutorial/GroupAnalysisV6.0 – Free Surfer Wiki". surfer.nmr.mgh.harvard.edu. Retrieved 2019-08-30. <a href="https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0" target="_blank">https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>"FreeviewGuide/FreeviewIntroduction – Free Surfer Wiki". surfer.nmr.mgh.harvard.edu. Retrieved 2019-08-30. <a href="https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewIntroduction" target="_blank">https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewIntroduction</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>"Tracula – Free Surfer Wiki". surfer.nmr.mgh.harvard.edu. Retrieved 2019-08-30. <a href="https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula?highlight=(tracula)" target="_blank">https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula?highlight=(tracula)</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>"FsFastTutorialV6.0 – Free Surfer Wiki". surfer.nmr.mgh.harvard.edu. Retrieved 2019-08-30. <a href="https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0" target="_blank">https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>"Xhemi – Free Surfer Wiki". <a href="https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi" target="_blank">https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> <li id="fn:15"><p>"LGI – Free Surfer Wiki". <a href="https://surfer.nmr.mgh.harvard.edu/fswiki/LGI" target="_blank">https://surfer.nmr.mgh.harvard.edu/fswiki/LGI</a> <a href="#fnref:15" class="footnote-back-ref">↩</a></p></li> <li id="fn:16"><p>"LinearMixedEffectsModels – Free Surfer Wiki". <a href="https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels" target="_blank">https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels</a> <a href="#fnref:16" class="footnote-back-ref">↩</a></p></li> <li id="fn:17"><p>"SPM – Free Surfer Wiki". surfer.nmr.mgh.harvard.edu. 15 August 2012. <a href="https://surfer.nmr.mgh.harvard.edu/fswiki/SPM" target="_blank">https://surfer.nmr.mgh.harvard.edu/fswiki/SPM</a> <a href="#fnref:17" class="footnote-back-ref">↩</a></p></li> <li id="fn:18"><p>[4] Developer's Guide <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide" target="_blank">http://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide</a> <a href="#fnref:18" class="footnote-back-ref">↩</a></p></li> <li id="fn:19"><p>[5] Archived 2014-11-23 at the Wayback Machine Download notes <a href="http://www.freesurfer.net/fswiki/Download#Notes" target="_blank">http://www.freesurfer.net/fswiki/Download#Notes</a> <a href="#fnref:19" class="footnote-back-ref">↩</a></p></li> <li id="fn:20"><p>[6] FreeSurfer Wiki <a href="http://surfer.nmr.mgh.harvard.edu/fswiki" target="_blank">http://surfer.nmr.mgh.harvard.edu/fswiki</a> <a href="#fnref:20" class="footnote-back-ref">↩</a></p></li> <li id="fn:21"><p>"FreeSurferMethodsCitation – Free Surfer Wiki". <a href="https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation" target="_blank">https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation</a> <a href="#fnref:21" class="footnote-back-ref">↩</a></p></li> <li id="fn:22"><p>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. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:22" class="footnote-back-ref">↩</a></p></li> <li id="fn:23"><p>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. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:23" class="footnote-back-ref">↩</a></p></li> <li id="fn:24"><p>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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6873338" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6873338</a> <a href="#fnref:24" class="footnote-back-ref">↩</a></p></li> <li id="fn:25"><p>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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC27146" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC27146</a> <a href="#fnref:25" class="footnote-back-ref">↩</a></p></li> <li id="fn:26"><p>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. <a href="/wiki/CiteSeerX_(identifier)" target="_blank">/wiki/CiteSeerX_(identifier)</a> <a href="#fnref:26" class="footnote-back-ref">↩</a></p></li> <li id="fn:27"><p>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. <a href="https://doi.org/10.1016%2Fs0896-6273%2802%2900569-x" target="_blank">https://doi.org/10.1016%2Fs0896-6273%2802%2900569-x</a> <a href="#fnref:27" class="footnote-back-ref">↩</a></p></li> <li id="fn:28"><p>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. <a href="/wiki/CiteSeerX_(identifier)" target="_blank">/wiki/CiteSeerX_(identifier)</a> <a href="#fnref:28" class="footnote-back-ref">↩</a></p></li> <li id="fn:29"><p>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. <a href="https://doi.org/10.1093%2Fcercor%2Fbhg087" target="_blank">https://doi.org/10.1093%2Fcercor%2Fbhg087</a> <a href="#fnref:29" class="footnote-back-ref">↩</a></p></li> <li id="fn:30"><p>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. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:30" class="footnote-back-ref">↩</a></p></li> </ol>