![FreeviewScreenshot](https://upload.wikimedia.org/wikipedia/commons/4/47/FreeviewScreenshot.png)
FreeSurfer is a brain
imaging software package originally developed by Bruce Fischl,
Anders Dale, Martin Sereno, and Doug Greve. Development and maintenance of FreeSurfer is now the primary responsibility of the Laboratory for Computational Neuroimaging 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
Brain mapping is a set of neuroscience techniques predicated on the mapping of (biological) quantities or properties onto spatial representations of the (human or non-human) brain resulting in maps.
According to the definition established in ...
and contains tools to conduct both volume based and surface based analysis. FreeSurfer includes tools for the reconstruction of topologically correct and geometrically accurate models of both the gray/white and
pial
Pia mater ( or ),[Entry "pia mater"](_blank)
in
Human Connectome Project
The Human Connectome Project (HCP) is a five-year project sponsored by sixteen components of the National Institutes of Health, split between two consortia of research institutions. The project was launched in July 2009 as the first of three Grand ...
, the
UK Biobank
UK Biobank is a large long-term biobank study in the United Kingdom (UK) which is investigating the respective contributions of genetic predisposition and environmental exposure (including nutrition, lifestyle, medications etc.) to the developme ...
, the Adolescent Brain Cognitive Development Study, and the
Alzheimer's Disease Neuroimaging Initiative.
Usage
The FreeSurfer processing stream is controlled by a shell script called ''recon-all''. 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
The general linear model or general multivariate regression model is a compact way of simultaneously writing several multiple linear regression models. In that sense it is not a separate statistical linear model. The various multiple linear regr ...
) analysis with the mri_glmfit tool.
FreeSurfer contains a range of packages allowing a broad spectrum of uses, including:
* FreeView, a tool to visualize FreeSurfer output, can also display common MRI image formats.
* TRACULA, a tool to construct white matter tract data from diffusion images
* FSFAST, a tool for analysis of functional MRI data
* XHemi, for Interhemispheric registration
* LGI, to calculate the degree of folding or local GI.
* a Matlab toolbox for linear mixed effects models
Interoperation
FreeSurfer interoperates easily with the
FMRIB Software Library
The FMRIB Software Library, abbreviated FSL, is a software library containing image analysis and statistical tools for functional, structural and diffusion MRI brain imaging data.
FSL is available as both precompiled binaries and source code ...
(FSL), which is 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. FreeSurfer also uses toolkits fro
MNI MINC VXL,
Tcl
TCL or Tcl or TCLs may refer to:
Business
* TCL Technology, a Chinese consumer electronics and appliance company
**TCL Electronics, a subsidiary of TCL Technology
* Texas Collegiate League, a collegiate baseball league
* Trade Centre Limited ...
/
Tk/Tix/BLT,
VTK., KWWidgets and Qt, which are all available with the distribution. Other neuroimaging programs like
Caret
Caret is the name used familiarly for the character , provided on most QWERTY keyboards by typing . The symbol has a variety of uses in programming and mathematics. The name "caret" arose from its visual similarity to the original proofreade ...
,
AFNI/SUMAMNE 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. Documentation can be found on the 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.
Citation counts have been obtained through Google Scholar as of August 2019.
See also
*
Analysis of Functional NeuroImages
*
Caret
Caret is the name used familiarly for the character , provided on most QWERTY keyboards by typing . The symbol has a variety of uses in programming and mathematics. The name "caret" arose from its visual similarity to the original proofreade ...
Van Essen Lab, Washington University in St. Louis
*
Laboratory of Neuro Imaging, UCLA
*
Statistical parametric mapping (SPM)
References
External links
*
{{Image Processing Software
Computing in medical imaging
Neuroimaging
Neuroimaging software
Software that uses VTK