Differences between revisions 1 and 109 (spanning 108 versions)
⇤ ← Revision 1 as of 2004-07-22 12:01:25 →
Size: 2094
Editor: DavidTuch
Comment:
← Revision 109 as of 2006-02-01 16:40:42 → ⇥
Size: 4684
Editor: EvelinaBusa
Comment: added references
Deletions are marked like this. Additions are marked like this.
Line 3: Line 3:
#acl WikiUserGroup:read,write,delete,revert All:read
Line 5: Line 6:
  Welcome to the FreeSurferWiki. FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. The FreeSurferWiki provides a documentation forum for investigators at the [http://www.martinos.org Athinoula A. Martinos Center For Biomedical Imaging].  * Welcome to the FreeSurferWiki. The FreeSurferWiki is the central documentation source for FreeSurfer.

 * '''''NEW USERS:''''' Please see the FreeSurferBeginnersGuide to get started.

 * 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 [[MailTo(freesurfer AT nmr DOT mgh DOT harvard DOT edu, freesurfer mailing list)]]. Bugs reports should be directed to the [[MailTo(analysis-bugs AT nmr DOT mgh DOT harvard DOT edu, analysis-bugs mailing list)]].

= Software =

 * [wiki:Self:DownloadAndInstall FreeSurfer download and install]
 * [wiki:Self:MiscellaneousDownloads Miscellaneous downloads]
 * [wiki:Self:InternalFreeSurferDistributions Information for internal (Martinos Center) users]
 * [wiki:Self:FtpFileExchange Information on FTP file exchange]
 * [wiki:Self:RemoteAccess Information on remote access]
Line 9: Line 24:
  * FreeSurferInstallation
  * FreeSurferGuide
  * FreeSurferTutorial
  * FreeSurferTools		 ## * FreeSurferDistributions - Description of !FreeSurfer distributions
 * FreeSurferAnalysisPipelineOverview - Overview of the !FreeSurfer analysis pipeline.
 * WorkFlows - Information on the how the !FreeSurfer tools are used in a processing stream.
 * ArticlesSlidesAndPosters - Background describing the techniques used in the !FreeSurfer tools, and their usage in research.
 * ["Tutorials"] - A walk-through of a !FreeSurfer work-flow, covering editing and troubleshooting techniques in-depth, as well as a group study example.
 * ["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).
Line 15: Line 35:
  FreeSurferSupport  * FreeSurferSupport - Mailing lists and helplines which provide user support for !FreeSurfer

= WikiGuidelines =
 * CulturalGuidelines
 * StyleGuidelines

= BeginnersGuides =
 * WikiBeginnersGuide
 * FreeSurferBeginnersGuide

= Feedback =
 * The FreeSurfer development team values your feedback. Please take a moment to visit the ["Priorities"] page and register your priority. Thanks.
 * You can add your comments or suggestions on our FeedBack page.
Line 18: Line 50:
FreeSurfer is brought to you by [http://www.cortechs.net CorTechs] and NCRR/P41RR14075  * !FreeSurfer is brought to you by [http://www.cortechs.net CorTechs], [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6641264&p_grant_num=5P41RR014075-05&p_query=&ticket=10459360&p_audit_session_id=48433183&p_keywords= NCRR/P41RR14075], [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6936484&p_grant_num=5R01RR01659404&p_query=&ticket=16737375&p_audit_session_id=78570196&p_keywords= R01 RR16594-01A1], and our ["Contributors"].
Line 20: Line 52:
= MoinMoin Wiki = = References =
Line 22: Line 54:
A WikiWikiWeb is a collaborative hypertext environment, with an emphasis on easy access to and modification of information. This wiki can also link to InterWiki space. For more technical descriptions of the software capabilities, see:
Line 24: Line 56:
MoinMoin is a Python Wiki:WikiClone, based on Wiki:PikiPiki. The name is a common German slang expression explained on the MoinMoin page. If you run a Wiki using MoinMoin, please add it to the MoinMoin:MoinMoinWikis page. Contributed code is on the MoinMoin:MacroMarket, MoinMoin:ActionMarket and MoinMoin:ParserMarket pages. For more details and further topics, see the MoinMoin page. Fischl B, van der Kouwe A, Destrieux C, Halgren E, Segonne F, Salat DH, Busa E, Seidman LJ, Goldstein J, Kennedy D, Caviness V, Makris N, Rosen B, Dale AM. Automatically parcellating the human cerebral cortex. Cereb Cortex. 2004 Jan;14(1):11-22.
Line 26: Line 58:
----
You can edit any page by pressing the link at the bottom of the page. Capitalized words joined together form a WikiName, which hyperlinks to another page. The highlighted title searches for all pages that link to the current page. Pages which do not yet exist are linked with a question mark: just follow the link and you can add a definition.		 Fischl B, Salat DH, van der Kouwe AJ, Makris N, Segonne F, Quinn BT, Dale AM. Sequence-independent segmentation of magnetic resonance images.
Neuroimage. 2004;23 Suppl 1:S69-84.
Line 29: Line 61:
To get an overview over this site and what it contains, see the SiteNavigation page. Fischl B, Salat DH, Busa E, Albert M, Dieterich M, Haselgrove C, van der Kouwe A, Killiany R, Kennedy D, Klaveness S, Montillo A, Makris N, Rosen B, Dale AM. Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. Neuron. 2002 Jan 31;33(3):341-55.
Line 31: Line 63:
To learn more about what a WikiWikiWeb is, read about MoinMoin:WhyWikiWorks and the MoinMoin:WikiNature. Also, consult the MoinMoin:WikiWikiWebFaq. Segonne F, Dale AM, Busa E, Glessner M, Salat D, Hahn HK, Fischl B. A hybrid approach to the skull stripping problem in MRI. Neuroimage. 2004 Jul;22(3):1060-75.
Line 33: Line 65:
----
Interesting starting points:
  * RecentChanges: see where people are currently working
  * HelpForBeginners: to get you going
  * WikiSandBox: feel free to change this page and experiment with editing
  * FindPage: search or browse the database in various ways
  * SyntaxReference		 Fischl B, Liu A, Dale AM. Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex.
Line 41: Line 67:
Fischl B, Dale AM. Measuring the thickness of the human cerebral cortex from magnetic resonance images. Proc Natl Acad Sci U S A. 2000 Sep 26;97(20):11050-5.

Fischl B, Sereno MI, Dale AM. Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system. Neuroimage. 1999 Feb;9(2):195-207.

Dale AM, Fischl B, Sereno MI. Cortical surface-based analysis. I. Segmentation and surface reconstruction. Neuroimage. 1999 Feb;9(2):179-94.

Welcome

Software

Documentation

  • FreeSurferAnalysisPipelineOverview - Overview of the FreeSurfer analysis pipeline.

  • WorkFlows - Information on the how the FreeSurfer tools are used in a processing stream.

  • ArticlesSlidesAndPosters - Background describing the techniques used in the FreeSurfer tools, and their usage in research.

  • ["Tutorials"] - A walk-through of a FreeSurfer work-flow, covering editing and troubleshooting techniques in-depth, as well as a group study example.

  • ["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).

Support

  • FreeSurferSupport - Mailing lists and helplines which provide user support for FreeSurfer

WikiGuidelines

BeginnersGuides

Feedback

  • The FreeSurfer development team values your feedback. Please take a moment to visit the ["Priorities"] page and register your priority. Thanks.

  • You can add your comments or suggestions on our FeedBack page.

Acknowledgements

References

For more technical descriptions of the software capabilities, see:

Fischl B, van der Kouwe A, Destrieux C, Halgren E, Segonne F, Salat DH, Busa E, Seidman LJ, Goldstein J, Kennedy D, Caviness V, Makris N, Rosen B, Dale AM. Automatically parcellating the human cerebral cortex. Cereb Cortex. 2004 Jan;14(1):11-22.

Fischl B, Salat DH, van der Kouwe AJ, Makris N, Segonne F, Quinn BT, Dale AM. Sequence-independent segmentation of magnetic resonance images. Neuroimage. 2004;23 Suppl 1:S69-84.

Fischl B, Salat DH, Busa E, Albert M, Dieterich M, Haselgrove C, van der Kouwe A, Killiany R, Kennedy D, Klaveness S, Montillo A, Makris N, Rosen B, Dale AM. Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. Neuron. 2002 Jan 31;33(3):341-55.

Segonne F, Dale AM, Busa E, Glessner M, Salat D, Hahn HK, Fischl B. A hybrid approach to the skull stripping problem in MRI. Neuroimage. 2004 Jul;22(3):1060-75.

Fischl B, Liu A, Dale AM. Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex.

Fischl B, Dale AM. Measuring the thickness of the human cerebral cortex from magnetic resonance images. Proc Natl Acad Sci U S A. 2000 Sep 26;97(20):11050-5.

Fischl B, Sereno MI, Dale AM. Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system. Neuroimage. 1999 Feb;9(2):195-207.

Dale AM, Fischl B, Sereno MI. Cortical surface-based analysis. I. Segmentation and surface reconstruction. Neuroimage. 1999 Feb;9(2):179-94.

FreeSurferWiki (last edited 2023-06-14 23:16:55 by buildqa)