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= FreeSurfer =

##<<Include(FreeSurfer)>>
!FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the [[https://www.martinos.org/lab/lcn|Laboratory for Computational Neuroimaging]] at the [[http://martinos.org/|Athinoula A. Martinos Center for Biomedical Imaging.]] !FreeSurfer is the structural MRI analysis software of choice for the [[https://github.com/Washington-University/Pipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage|Human Connectome Project.]]

 * '''[[FreeSurferSoftwareLicense|License:]]''' The open source license agreement that allows you to use !FreeSurfer
 * '''[[ReleaseNotes|Release notes and downloads:]]''' New features and changes in each version of !FreeSurfer - '''current stable release is v7.4.1'''
 * '''[[DownloadAndInstall|Installation guide:]]''' How to download and install !FreeSurfer on your computer

 * '''Documentation:''' [[QuickInstall|Getting started]]; [[Tutorials|step-by-step tutorials]]; [[UserContributions/FAQ|FAQ]]; [[FsTutorial/Glossary|glossary]]; [[ReconAllTable | Table of commands in processing stream]]

 * '''[[FreeSurferMethodsCitation|Citing FreeSurfer:]]''' Short description and citations for core !FreeSurfer methods 

 * '''[[https://www.zotero.org/freesurfer|Publications:]]''' A Zotero library of articles on the methods in !FreeSurfer and the studies that use !FreeSurfer

 * '''[[FreeSurferSupport | User support:]]''' How to get help with problems that you encounter when using !FreeSurfer

 * '''[[CourseDescription | Hands-on training:]]''' Information on the !FreeSurfer courses that we organize in Boston and around the world

 * '''[[FsStats | Stats:]]''' Stats on !FreeSurfer usage, citations, and development

 * '''[[UserContributions | User contributions:]]''' Scripts and techniques from users of !FreeSurfer

 * '''[[ThirdPartySoftware | Other software:]]''' Third-party software packages that are interoperable or related to !FreeSurfer

 * '''[[FreesurferAcknowledgements|Acknowledgements:]]''' The funding agencies and collaborators that have contributed to the research behind !FreeSurfer

 * '''Social media''': Find us on [[http://facebook.com/FreeSurferMRI|Facebook]] [[http://facebook.com/FreeSurferMRI|{{attachment:facebook_32.png|Find FreeSurferMRI on Facebook|height="18"}}]] as ''FreeSurferMRI'', follow us on [[http://www.twitter.com/FreeSurferMRI|Twitter]] [[http://www.twitter.com/FreeSurferMRI|{{attachment:twitter_32.png|Follow FreeSurferMRI on Twitter|height="20"}}]] or join our [[https://www.linkedin.com/groups/FreeSurfer-8173404|LinkedIn]] group [[https://www.linkedin.com/groups/FreeSurfer-8173404|{{attachment:linkedin_32.png|!LinkedIn FreeSurfer Group|height="20"}}]].

 * '''[[DiversityAndInclusion|Diversity and Inclusion]]'''

= Our tools =

=== Structural MRI ===

!FreeSurfer provides a full processing stream for structural MRI data, including: 
 * Skull stripping, B1 bias field correction, and gray-white matter segmentation
 * Reconstruction of cortical surface models (gray-white boundary surface and pial surface)
 * Labeling of regions on the cortical surface, as well as subcortical brain structures
 * Nonlinear registration of the cortical surface of an individual with a stereotaxic atlas
 * Statistical analysis of group morphometry differences

For more information, see:
 * '''[[FreeSurferAnalysisPipelineOverview|Overview:]]''' General description of the functionality in !FreeSurfer
 * '''Recommended acquisition protocols:'''
  * [[attachment:FreeSurfer_Suggested_Morphometry_Protocols.pdf|Suggested morphometry protocols for optimal FreeSurfer reconstruction|&do=get]]
  * [[http://adni.loni.usc.edu/methods/documents/mri-protocols/|Alternative morphometry protocols, from ADNI]]
 * '''Longitudinal studies:'''
  * [[LongitudinalProcessing|The longitudinal FreeSurfer stream]] 
  * [[LongitudinalStatistics | Longitudinal linear mixed effects statistics]]
 * '''Troubleshooting:'''
  * Manual editing [[Edits|for the basic stream]] and [[LongitudinalEdits|for the longitudinal stream]]
  * [[ReconAllTableStableV6.0|Output files:]] A table of files created and used during a standard !FreeSurfer analysis
 * '''Advanced:'''
  * [[WorkFlows|Work flows:]] How to use the !FreeSurfer stream to accomplish specific tasks
  * [[ToolsAndCommands|Tools and commands:]] GUI and command-line tool documentation
  * [[FileFormats|File formats:]] Description of native !FreeSurfer file formats, as well as external file formats recognized by !FreeSurfer
  * [[CoordinateSystems|Coordinate systems:]] Details on the voxel and RAS coordinate systems used in !FreeSurfer

=== Functional MRI ===
 * '''[[FsFast|FreeSurfer Functional Analysis Stream (FS-FAST):]]''' FS-FAST is a set of tools for performing functional MRI data analyses on the cortical surface. 

=== Diffusion MRI ===
* '''[[Tracula|TRActs Constrained by UnderLying Anatomy (TRACULA):]]''' TRACULA is a tool for automated global probabilistic tractography with anatomical priors. It reconstructs a set of major white-matter pathways by incorporating prior information on the structural segmentation labels that each pathway goes through or next to, as a function of position along the length of the pathway. It includes a specialized stream for processing longitudinal diffusion MRI data.

* '''AnatomiCuts''' : An unsupervised hierarchical streamline clustering algorithm based on anatomical similarity. AnatomiCuts is currently in the developing branch (https://github.com/freesurfer/freesurfer/tree/dev/anatomicuts).

* '''DiffusionTool''' : This tool can help generating the configuration file of TRACULA and setting up the parameters to run AnatomiCuts. The DiffusionTool is currently in the developing branch (https://github.com/freesurfer/freesurfer/tree/dev/diffusion_tool).

=== PETsurfer PET Kinetic Modeling and Partial Volume Correction (PVC) ===
 * '''[[PetSurfer|PETSurfer:]]''' PETSurfer is a tool for performing ROI-based, surface-based, and whole-brain analysis of PET data integrated with FreeSurfer anatomical analysis.

=== Multimodal ===
 * '''[[FreeSurferCommandsRegistration|Registration tools:]]''' !FreeSurfer offers a range of tools for both within-subject and across-subject registration.

## * DevelopersGuide - Information for developers of the !FreeSurfer code-base (Martinos Center internal).

=== Quick Links for LCN Members ===

 * LCN Members can navigate to the LcnInternal wiki page with quicklinks to regularly requested resources or wiki pages