FreeSurfer

{{Infobox software

| name = FreeSurfer

| screenshot = frameless

| developer = [http://www.nmr.mgh.harvard.edu/martinos/noFlashHome.php Martinos Center for Biomedical Imaging]

| latest_release_version = 7.3

| operating_system = Linux or Mac OS X

| license = FreeSurfer Software License[http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense] FreeSurfer Software License page

| website = [https://freesurfer.net FreeSurfer]

}}

File:FreeviewScreenshot.png

FreeSurfer is brain imaging software originally developed by Bruce Fischl, Anders Dale, Martin Sereno, and Doug Greve.{{cite journal |last1=Fischl |first1=Bruce |title=FreeSurfer |journal=NeuroImage |date=15 August 2012 |volume=62 |issue=2 |pages=774–781 |doi=10.1016/j.neuroimage.2012.01.021 |pmid=22248573 |pmc=3685476 |issn=1053-8119}} Development and maintenance of FreeSurfer is now the primary responsibility of the Laboratory for Computational Neuroimaging{{Cite web|url=https://www.nmr.mgh.harvard.edu/lab/lcn|title=Laboratory for Computational Neuroimaging | MGH/HST Martinos Center for Biomedical Imaging}} 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.{{cite journal |last1=Dale |first1=Anders M. |last2=Fischl |first2=Bruce |last3=Serenob |first3=Martin I. |title=Cortical Surface-Based Analysis: I. Segmentation and Surface Reconstruction |journal=NeuroImage |date=February 1999 |volume=9 |issue=2 |pages=179–194 |doi=10.1006/nimg.1998.0395 |pmid=9931268 |s2cid=2807360 |url=https://surfer.nmr.mgh.harvard.edu/ftp/articles/1999/1999_-_Dale_et_al._-_NeuroImage.pdf |access-date=29 August 2018}} 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[http://surfer.nmr.mgh.harvard.edu/fswiki/FsStats] FreeSurfer stats from the official FreeSurfer wiki and it is a core tool in the processing pipelines of the Human Connectome Project,{{cite journal |last1=Glasser |first1=Matthew F. |last2=Sotiropoulos |first2=Stamatios N |last3=Wilson |first3=J Anthony |last4=Coalson |first4=Timothy S |last5=Fischl |first5=Bruce |last6=Andersson |first6=Jesper L |last7=Xu |first7=Junqian |last8=Jbabdi |first8=Saad |last9=Webster |first9=Matthew |last10=Polimeni |first10=Jonathan R |last11=Van Essen |first11=David C |last12=Jenkinson |first12=Mark |title=The Minimal Preprocessing Pipelines for the Human Connectome Project |journal=NeuroImage |date=15 October 2013 |volume=80 |pages=105–124 |doi=10.1016/j.neuroimage.2013.04.127 |pmid=23668970 |pmc=3720813 |issn=1053-8119}} the UK Biobank,{{cite journal |last1=Smith |first1=Stephen M. |last2=Miller |first2=Karla L. |last3=Matthews |first3=Paul M. |last4=Dragonu |first4=Iulius |last5=Zhang |first5=Hui |last6=Alexander |first6=Daniel C. |last7=Daducci |first7=Alessandro |last8=Rorden |first8=Christopher |last9=McCarthy |first9=Paul |last10=Webster |first10=Matthew |last11=Vidaurre |first11=Diego |last12=Vallee |first12=Emmanuel |last13=Hernandez-Fernandez |first13=Moises |last14=Jbabdi |first14=Saad |last15=Sotiropoulos |first15=Stamatios N. |last16=Douaud |first16=Gwenaëlle |last17=Griffanti |first17=Ludovica |last18=Andersson |first18=Jesper L. R. |last19=Bangerter |first19=Neal K. |last20=Jenkinson |first20=Mark |last21=Alfaro-Almagro |first21=Fidel |title=Image Processing and Quality Control for the first 10,000 Brain Imaging Datasets from UK Biobank |journal=bioRxiv |date=24 April 2017 |pages=130385 |doi=10.1101/130385 |url=https://www.biorxiv.org/content/10.1101/130385v1 |doi-access=free |hdl=11343/256303 |hdl-access=free }} the Adolescent Brain Cognitive Development Study,{{cite journal |last1=Dale |first1=Anders M. |last2=Jernigan |first2=Terry L. |last3=Brown |first3=Sandra A. |last4=Dowling |first4=Gayathri J. |last5=Grant |first5=Steven J. |last6=Constable |first6=R. Todd |last7=Baskin-Sommers |first7=Arielle |last8=Madden |first8=Pamela A. |last9=Heath |first9=Andrew C. |last10=Glaser |first10=Paul |last11=Anokhin |first11=Andrey P. |last12=Steinberg |first12=Joel |last13=Hettema |first13=John M. |last14=Fuemmeler |first14=Bernard |last15=Charness |first15=Michael E. |last16=Lisdahl |first16=Krista |last17=Larson |first17=Christine |last18=Florsheim |first18=Paul |last19=Potter |first19=Alexandra |last20=Ivanova |first20=Masha |last21=Dumas |first21=Julie A. |last22=Allgaier |first22=Nicholas A. |last23=Yurgelun-Todd |first23=Deborah A. |last24=Renshaw |first24=Perry F. |last25=Prescot |first25=Andrew |last26=McGlade |first26=Erin |last27=Huber |first27=Rebekah |last28=Mason |first28=Michael J. |last29=Mruzek |first29=Daniel W. |last30=Freedman |first30=Edward G. |last31=Foxe |first31=John J. |last32=Brima |first32=Tufikameni |last33=Schirda |first33=Claudiu |last34=Luna |first34=Beatriz |last35=Lewis |first35=David A. |last36=Clark |first36=Duncan B. |last37=Calabro |first37=Finnegan J. |last38=Luciana |first38=Monica |last39=Iacono |first39=William G. |last40=Zucker |first40=Robert A. |last41=Sripada |first41=Chandra |last42=Schulenberg |first42=John |last43=Peltier |first43=Scott |last44=Heeringa |first44=Steve |last45=Kennedy |first45=David N. |last46=Reeves |first46=Gloria |last47=Ernst |first47=Thomas |last48=Cloak |first48=Christine |last49=Chang |first49=Linda |last50=Nixon |first50=Sara Jo |last51=Cottler |first51=Linda B. |last52=Tanabe |first52=Jody |last53=Sakai |first53=Joseph |last54=Hopfer |first54=Christian |last55=Hewitt |first55=John K. |last56=Friedman |first56=Naomi |last57=Banich |first57=Marie T. |last58=Sugrue |first58=Leo |last59=Li |first59=Yi |last60=Desikan |first60=Rahul |last61=Shilling |first61=Paul D. |last62=Patrick |first62=Kevin |last63=Jacobus |first63=Joanna |last64=Infante |first64=M. Alejandra |last65=Giedd |first65=Jay |last66=Bagot |first66=Kara |last67=Galvan |first67=Adriana |last68=Dapretto |first68=Mirella |last69=Bookheimer |first69=Susan Y. |last70=Uban |first70=Kristina |last71=Prouty |first71=Devin |last72=Pohl |first72=Kilian M. |last73=Pfefferbaum |first73=Adolf |last74=Goldstone |first74=Aimee |last75=Sturgeon |first75=Darrick T. |last76=Perrone |first76=Anders J. |last77=Nagel |first77=Bonnie J. |last78=Miranda-Dominguez |first78=Oscar |last79=Ewing |first79=Sarah W. Feldstein |last80=DelCarmen-Wiggins |first80=Rebecca |last81=Wolff-Hughes |first81=Dana L. |last82=Weiss |first82=Susan RB |last83=Pariyadath |first83=Vani |last84=Lopez |first84=Marsha |last85=Little |first85=Roger |last86=Hoffman |first86=Elizabeth |last87=Glantz |first87=Meyer |last88=Conway |first88=Kevin |last89=Aklin |first89=Will M. |last90=Noronha |first90=Antonio |last91=Matochik |first91=John A. |last92=Pierpaoli |first92=Carlo |last93=Gray |first93=Kevin M. |last94=Nencka |first94=Andrew S. |last95=Kouwe |first95=Andre van der |last96=Polimeni |first96=Jonathan R. |last97=Simmons |first97=W. Kyle |last98=Paulus |first98=Martin P. |last99=Morris |first99=Amanda Sheffield |last100=Breslin |first100=Florence J. |last101=Bodurka |first101=Jerzy |last102=Sanchez |first102=Mariana |last103=Hawes |first103=Samuel W. |last104=Alvarez |first104=Ruben P. |last105=Sowell |first105=Elizabeth R. |last106=Herting |first106=Megan |last107=Neale |first107=Michael C. |last108=Thompson |first108=Wesley K. |last109=Leon |first109=Octavio Ruiz de |last110=Diaz |first110=Jazmin |last111=Soules |first111=Mary |last112=Baker |first112=Fiona C. |last113=Howlett |first113=Katia D. |last114=Earl |first114=Eric A. |last115=Rosenberg |first115=Monica D. |last116=Hyde |first116=Luke W. |last117=Squeglia |first117=Lindsay M. |last118=Riedel |first118=Michael C. |last119=Tapert |first119=Susan F. |last120=Gonzalez |first120=Raul |last121=Trinh |first121=Thanh T. |last122=Laird |first122=Angela R. |last123=Heitzeg |first123=Mary M. |last124=Xue |first124=Feng |last125=Bartsch |first125=Hauke |last126=Kuperman |first126=Joshua |last127=Sicat |first127=Chelsea S. |last128=Pung |first128=Christopher J. |last129=Hilmer |first129=Laura |last130=Garavan |first130=Hugh P. |last131=Bjork |first131=James M. |last132=Watts |first132=Richard |last133=Harms |first133=Michael P. |last134=Barch |first134=Deanna M. |last135=Casey |first135=B. J. |last136=Sutherland |first136=Matthew T. |last137=Dick |first137=Anthony Steven |last138=Fair |first138=Damien A. |last139=Cornejo |first139=M. Daniela |last140=Makowski |first140=Carolina |last141=Hatton |first141=Sean N. |last142=Hagler |first142=Donald J. |title=Image processing and analysis methods for the Adolescent Brain Cognitive Development Study |journal=bioRxiv |date=4 November 2018 |volume=202 |pages=457739 |doi=10.1101/457739 |pmid=31415884 |pmc=6981278 |display-authors=29 |doi-access=free }} and the Alzheimer's Disease Neuroimaging Initiative.{{cite web |title=ADNI {{!}} MRI Tool |url=http://adni.loni.usc.edu/methods/mri-tool/}}

File:Spherical Registration.png

Usage

The FreeSurfer processing stream is controlled by a shell script called recon-all.[http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all] recon-all script usage 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_glmfit{{Cite web|url=https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0|title=FsTutorial/GroupAnalysisV6.0 – Free Surfer Wiki|website=surfer.nmr.mgh.harvard.edu|access-date=2019-08-30}} 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 formats{{Cite web|url=https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewIntroduction|title=FreeviewGuide/FreeviewIntroduction – Free Surfer Wiki|website=surfer.nmr.mgh.harvard.edu|access-date=2019-08-30}}
TRACULA, a tool to construct white matter tract data from diffusion images{{Cite web|url=https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula?highlight=(tracula)|title=Tracula – Free Surfer Wiki|website=surfer.nmr.mgh.harvard.edu|access-date=2019-08-30}}
FSFAST, a tool for analysis of functional MRI data{{Cite web|url=https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0|title=FsFastTutorialV6.0 – Free Surfer Wiki|website=surfer.nmr.mgh.harvard.edu|access-date=2019-08-30}}
XHemi, for Interhemispheric registration{{Cite web|url=https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi|title = Xhemi – Free Surfer Wiki}}
LGI, to calculate the degree of folding or local GI{{Cite web|url=https://surfer.nmr.mgh.harvard.edu/fswiki/LGI|title=LGI – Free Surfer Wiki}}
a Matlab toolbox for linear mixed effects models{{Cite web|url=https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels|title=LinearMixedEffectsModels – Free Surfer Wiki}}

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.{{cite web |title=SPM – Free Surfer Wiki |url=https://surfer.nmr.mgh.harvard.edu/fswiki/SPM |website=surfer.nmr.mgh.harvard.edu |date=15 August 2012}} FreeSurfer also uses toolkits from [http://www.bic.mni.mcgill.ca/software MNI MINC], VXL, Tcl/Tk/Tix/BLT, VTK., KWWidgets and Qt,[http://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide] Developer's Guide which are all available with the distribution. Other neuroimaging programs like Caret, AFNI/SUMA, [http://martinos.org/mne/dev/index.html 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.[http://www.freesurfer.net/fswiki/Download#Notes] {{Webarchive|url=https://web.archive.org/web/20141123221610/http://freesurfer.net/fswiki/Download#Notes|date=2014-11-23}} Download notes Documentation can be found on the FreeSurfer Wiki[http://surfer.nmr.mgh.harvard.edu/fswiki] FreeSurfer Wiki 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.{{Cite web|url=https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation|title=FreeSurferMethodsCitation – Free Surfer Wiki}} Citation counts have been obtained through Google Scholar as of August 2019.

class="wikitable" \|+
align="left" \| Title ! Year ! Citations
Cortical surface-based analysis. I. Segmentation and surface reconstruction.{{Cite journal\|last1=Dale\|first1=A. M.\|last2=Fischl\|first2=B.\|last3=Sereno\|first3=M. I.\|date=February 1999\|title=Cortical surface-based analysis. I. Segmentation and surface reconstruction\|journal=NeuroImage\|volume=9\|issue=2\|pages=179–194\|doi=10.1006/nimg.1998.0395\|issn=1053-8119\|pmid=9931268\|s2cid=2807360}} \| 1999 \| 6469
Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system.{{Cite journal\|last1=Fischl\|first1=B.\|last2=Sereno\|first2=M. I.\|last3=Dale\|first3=A. M.\|s2cid=3100335\|date=February 1999\|title=Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system\|journal=NeuroImage\|volume=9\|issue=2\|pages=195–207\|doi=10.1006/nimg.1998.0396\|issn=1053-8119\|pmid=9931269}} \| 1999 \| 4507
High-resolution intersubject averaging and a coordinate system for the cortical surface.{{Cite journal\|last1=Fischl\|first1=Bruce\|last2=Sereno\|first2=Martin I.\|last3=Tootell\|first3=Roger B. H.\|last4=Dale\|first4=Anders M.\|date=1999\|title=High-resolution intersubject averaging and a coordinate system for the cortical surface\|journal=Human Brain Mapping\|volume=8\|issue=4\|pages=272–284\|doi=10.1002/(SICI)1097-0193(1999)8:4<272::AID-HBM10>3.0.CO;2-4\|pmid=10619420\|issn=1097-0193\|pmc=6873338}} \| 1999 \| 2339
Measuring the thickness of the human cerebral cortex from magnetic resonance images.{{Cite journal\|last1=Fischl\|first1=B.\|last2=Dale\|first2=A. M.\|date=2000-09-26\|title=Measuring the thickness of the human cerebral cortex from magnetic resonance images\|journal=Proceedings of the National Academy of Sciences of the United States of America\|volume=97\|issue=20\|pages=11050–11055\|doi=10.1073/pnas.200033797\|issn=0027-8424\|pmid=10984517\|pmc=27146\|bibcode=2000PNAS...9711050F\|doi-access=free}} \| 2000 \| 3863
Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex.{{Cite journal\|last1=Fischl\|first1=B.\|last2=Liu\|first2=A.\|last3=Dale\|first3=A. M.\|date=January 2001\|title=Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex\|journal=IEEE Transactions on Medical Imaging\|volume=20\|issue=1\|pages=70–80\|doi=10.1109/42.906426\|issn=0278-0062\|pmid=11293693\|s2cid=954064\|citeseerx=10.1.1.3.8686}} \| 2001 \| 1258
Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain.{{Cite journal\|last1=Fischl\|first1=Bruce\|last2=Salat\|first2=David H.\|last3=Busa\|first3=Evelina\|last4=Albert\|first4=Marilyn\|last5=Dieterich\|first5=Megan\|last6=Haselgrove\|first6=Christian\|last7=van der Kouwe\|first7=Andre\|last8=Killiany\|first8=Ron\|last9=Kennedy\|first9=David\|date=2002-01-31\|title=Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain\|journal=Neuron\|volume=33\|issue=3\|pages=341–355\|doi=10.1016/s0896-6273(02)00569-x\|issn=0896-6273\|pmid=11832223\|s2cid=9629554\|doi-access=free}} \| 2002 \| 5066
A hybrid approach to the skull stripping problem in MRI.{{Cite journal\|last1=Ségonne\|first1=F.\|last2=Dale\|first2=A. M.\|last3=Busa\|first3=E.\|last4=Glessner\|first4=M.\|last5=Salat\|first5=D.\|last6=Hahn\|first6=H. K.\|last7=Fischl\|first7=B.\|date=July 2004\|title=A hybrid approach to the skull stripping problem in MRI\|journal=NeuroImage\|volume=22\|issue=3\|pages=1060–1075\|doi=10.1016/j.neuroimage.2004.03.032\|issn=1053-8119\|pmid=15219578\|s2cid=54432685\|citeseerx=10.1.1.123.7627}} \| 2004 \| 1584
Automatically parcellating the human cerebral cortex.{{Cite journal\|last1=Fischl\|first1=Bruce\|last2=van der Kouwe\|first2=André\|last3=Destrieux\|first3=Christophe\|last4=Halgren\|first4=Eric\|last5=Ségonne\|first5=Florent\|last6=Salat\|first6=David H.\|last7=Busa\|first7=Evelina\|last8=Seidman\|first8=Larry J.\|last9=Goldstein\|first9=Jill\|date=January 2004\|title=Automatically parcellating the human cerebral cortex\|journal=Cerebral Cortex \|volume=14\|issue=1\|pages=11–22\|doi=10.1093/cercor/bhg087\|issn=1047-3211\|pmid=14654453\|doi-access=free}} \| 2004 \| 2731
An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest.{{Cite journal\|last1=Desikan\|first1=Rahul S.\|last2=Ségonne\|first2=Florent\|last3=Fischl\|first3=Bruce\|last4=Quinn\|first4=Brian T.\|last5=Dickerson\|first5=Bradford C.\|last6=Blacker\|first6=Deborah\|last7=Buckner\|first7=Randy L.\|last8=Dale\|first8=Anders M.\|last9=Maguire\|first9=R. Paul\|date=2006-07-01\|title=An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest\|journal=NeuroImage\|volume=31\|issue=3\|pages=968–980\|doi=10.1016/j.neuroimage.2006.01.021\|issn=1053-8119\|pmid=16530430\|s2cid=12420386}} \| 2006 \| 4932

class="wikitable"

align="left" | Title

! Year

! Citations

Cortical surface-based analysis. I. Segmentation and surface reconstruction.{{Cite journal|last1=Dale|first1=A. M.|last2=Fischl|first2=B.|last3=Sereno|first3=M. I.|date=February 1999|title=Cortical surface-based analysis. I. Segmentation and surface reconstruction|journal=NeuroImage|volume=9|issue=2|pages=179–194|doi=10.1006/nimg.1998.0395|issn=1053-8119|pmid=9931268|s2cid=2807360}}

| 1999

| 6469

Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system.{{Cite journal|last1=Fischl|first1=B.|last2=Sereno|first2=M. I.|last3=Dale|first3=A. M.|s2cid=3100335|date=February 1999|title=Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system|journal=NeuroImage|volume=9|issue=2|pages=195–207|doi=10.1006/nimg.1998.0396|issn=1053-8119|pmid=9931269}}

| 1999

| 4507

High-resolution intersubject averaging and a coordinate system for the cortical surface.{{Cite journal|last1=Fischl|first1=Bruce|last2=Sereno|first2=Martin I.|last3=Tootell|first3=Roger B. H.|last4=Dale|first4=Anders M.|date=1999|title=High-resolution intersubject averaging and a coordinate system for the cortical surface|journal=Human Brain Mapping|volume=8|issue=4|pages=272–284|doi=10.1002/(SICI)1097-0193(1999)8:4<272::AID-HBM10>3.0.CO;2-4|pmid=10619420|issn=1097-0193|pmc=6873338}}

| 1999

| 2339

Measuring the thickness of the human cerebral cortex from magnetic resonance images.{{Cite journal|last1=Fischl|first1=B.|last2=Dale|first2=A. M.|date=2000-09-26|title=Measuring the thickness of the human cerebral cortex from magnetic resonance images|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=97|issue=20|pages=11050–11055|doi=10.1073/pnas.200033797|issn=0027-8424|pmid=10984517|pmc=27146|bibcode=2000PNAS...9711050F|doi-access=free}}

| 2000

| 3863

Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex.{{Cite journal|last1=Fischl|first1=B.|last2=Liu|first2=A.|last3=Dale|first3=A. M.|date=January 2001|title=Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex|journal=IEEE Transactions on Medical Imaging|volume=20|issue=1|pages=70–80|doi=10.1109/42.906426|issn=0278-0062|pmid=11293693|s2cid=954064|citeseerx=10.1.1.3.8686}}

| 2001

| 1258

Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain.{{Cite journal|last1=Fischl|first1=Bruce|last2=Salat|first2=David H.|last3=Busa|first3=Evelina|last4=Albert|first4=Marilyn|last5=Dieterich|first5=Megan|last6=Haselgrove|first6=Christian|last7=van der Kouwe|first7=Andre|last8=Killiany|first8=Ron|last9=Kennedy|first9=David|date=2002-01-31|title=Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain|journal=Neuron|volume=33|issue=3|pages=341–355|doi=10.1016/s0896-6273(02)00569-x|issn=0896-6273|pmid=11832223|s2cid=9629554|doi-access=free}}

| 2002

| 5066

A hybrid approach to the skull stripping problem in MRI.{{Cite journal|last1=Ségonne|first1=F.|last2=Dale|first2=A. M.|last3=Busa|first3=E.|last4=Glessner|first4=M.|last5=Salat|first5=D.|last6=Hahn|first6=H. K.|last7=Fischl|first7=B.|date=July 2004|title=A hybrid approach to the skull stripping problem in MRI|journal=NeuroImage|volume=22|issue=3|pages=1060–1075|doi=10.1016/j.neuroimage.2004.03.032|issn=1053-8119|pmid=15219578|s2cid=54432685|citeseerx=10.1.1.123.7627}}

| 2004

| 1584

Automatically parcellating the human cerebral cortex.{{Cite journal|last1=Fischl|first1=Bruce|last2=van der Kouwe|first2=André|last3=Destrieux|first3=Christophe|last4=Halgren|first4=Eric|last5=Ségonne|first5=Florent|last6=Salat|first6=David H.|last7=Busa|first7=Evelina|last8=Seidman|first8=Larry J.|last9=Goldstein|first9=Jill|date=January 2004|title=Automatically parcellating the human cerebral cortex|journal=Cerebral Cortex |volume=14|issue=1|pages=11–22|doi=10.1093/cercor/bhg087|issn=1047-3211|pmid=14654453|doi-access=free}}

| 2004

| 2731

An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest.{{Cite journal|last1=Desikan|first1=Rahul S.|last2=Ségonne|first2=Florent|last3=Fischl|first3=Bruce|last4=Quinn|first4=Brian T.|last5=Dickerson|first5=Bradford C.|last6=Blacker|first6=Deborah|last7=Buckner|first7=Randy L.|last8=Dale|first8=Anders M.|last9=Maguire|first9=R. Paul|date=2006-07-01|title=An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest|journal=NeuroImage|volume=31|issue=3|pages=968–980|doi=10.1016/j.neuroimage.2006.01.021|issn=1053-8119|pmid=16530430|s2cid=12420386}}

| 2006

| 4932