FreeSurfer
Encyclopedia
FreeSurfer is an MRI brain imaging software package developed by the Athinoula A. Martinos Center for Biomedical Imaging
at Massachusetts General Hospital
. It is an important tool in functional brain mapping
and facilitates the visualization of the functional regions of the highly-folded cerebral cortex
. It contains both volume based and surface based analysis, which primarily use the white matter surface . 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. In addition, an automated labeling of 35 non-cortical regions is included in the package.
images into formats easily usable for morphometric and functional MRI statistical analysis with the FS-FAST package. Freesurfer uses a morphed spherical method to average across subjects for a GLM
group analysis with the QDEC tool. Two editing and visualization tools, Tkmedit and Tksurfer, respectively, are included in the package, but they will be replaced by Freeview when it is completed. FreeSurfer automatically segments the volume and parcellates the surface into standardized regions of interest (ROIs). The package has a broad spectrum of other uses, including retinotopy and cortical thickness analysis.
(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 overlayed onto inflated, sphered or flattened cortical surfaces using FreeSurfer. FreeSurfer also uses toolkits from MNI MINC, VXL
, Tcl
/Tk/Tix/BLT, VTK
., KWWidgets and Qt, which are all available with the distribution. Other neuroimaging programs like Caret
, AFNI/SUMA
, and 3D Slicer can also import data processed by FreeSurfer.
Athinoula A. Martinos Center for Biomedical Imaging
The Athinoula A. Martinos Center for Biomedical Imaging, usually referred to as just the "Martinos Center," is a major hub of neuropsychological research and nuclear magnetic resonance research and development in Boston. The center has two sites, one in the Massachusetts General Hospital East...
at Massachusetts General Hospital
Massachusetts General Hospital
Massachusetts General Hospital is a teaching hospital and biomedical research facility in the West End neighborhood of Boston, Massachusetts...
. It is an important tool in functional brain mapping
Brain mapping
Brain mapping is a set of neuroscience techniques predicated on the mapping of quantities or properties onto spatial representations of the brain resulting in maps.- Overview :...
and facilitates the visualization of the functional regions of the highly-folded cerebral cortex
Cerebral cortex
The cerebral cortex is a sheet of neural tissue that is outermost to the cerebrum of the mammalian brain. It plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It is constituted of up to six horizontal layers, each of which has a different...
. It contains both volume based and surface based analysis, which primarily use the white matter surface . 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. In addition, an automated labeling of 35 non-cortical regions is included in the package.
Usage
The FreeSurfer processing stream is controlled by a shell script called recon-all. The script calls component programs that organize raw MRIMagnetic resonance imaging
Magnetic resonance imaging , nuclear magnetic resonance imaging , or magnetic resonance tomography is a medical imaging technique used in radiology to visualize detailed internal structures...
images into formats easily usable for morphometric and functional MRI statistical analysis with the FS-FAST package. Freesurfer uses a morphed spherical method to average across subjects for a GLM
GLM
The three-letter acronym GLM may refer to:*Generalized linear model*General linear model*Geostationary Lightning Mapper, an instrument being designed for the GOES-R series of satellites...
group analysis with the QDEC tool. Two editing and visualization tools, Tkmedit and Tksurfer, respectively, are included in the package, but they will be replaced by Freeview when it is completed. FreeSurfer automatically segments the volume and parcellates the surface into standardized regions of interest (ROIs). The package has a broad spectrum of other uses, including retinotopy and cortical thickness analysis.
Interoperation
FreeSurfer interoperates easily with the FMRIB Software LibraryFMRIB Software Library
The FMRIB Software Library is a software library containing image analysis and statistical tools for functional, structural and diffusion MRI brain imaging data....
(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 overlayed onto inflated, sphered or flattened cortical surfaces using FreeSurfer. FreeSurfer also uses toolkits from MNI MINC, VXL
VXL
VXL, the Vision-something-Library,' is a collection of open source C++ libraries for Computer Vision. The idea is to replace X with one of many letters, ie. G is a geometry library, N is a numerics library, I is an image processing library, etc. These libraries can be used for general scientific...
, Tcl
Tcl
Tcl is a scripting language created by John Ousterhout. Originally "born out of frustration", according to the author, with programmers devising their own languages intended to be embedded into applications, Tcl gained acceptance on its own...
/Tk/Tix/BLT, VTK
VTK
The Visualization Toolkit is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. Kitware, whose team created and continues to...
., KWWidgets and Qt, which are all available with the distribution. Other neuroimaging programs like Caret
CARET (Computerized Anatomical Reconstruction and Editing Toolkit)
CARET is a software application for the structural and functional analysis of the cerebral and cerebellar cortex. CARET is developed in the Van Essen Laboratory in the Department of Anatomy and Neurobiology at the Washington University School of Medicine in St...
, AFNI/SUMA
AFNI
Analysis of Functional NeuroImages is an open-source environment for processing and displaying functional MRI data—a technique for mapping human brain activity....
, and 3D Slicer can also import data processed by FreeSurfer.
Download
FreeSurfer runs on Mac OS and Linux. Free registration and installation are available. Documentation can be found on the FreeSurfer Wiki and limited support is available from the developers and community through the FreeSurfer mailing list.See also
- Analysis of Functional NeuroImages
- CaretCARET (Computerized Anatomical Reconstruction and Editing Toolkit)CARET is a software application for the structural and functional analysis of the cerebral and cerebellar cortex. CARET is developed in the Van Essen Laboratory in the Department of Anatomy and Neurobiology at the Washington University School of Medicine in St...
Van Essen Lab, Washington University in St. Louis - Laboratory of Neuro ImagingLaboratory Of Neuro ImagingThe Laboratory of Neuro Imaging is a research laboratory within the Department of Neurology at the UCLA David Geffen School of Medicine. The laboratory conducts a wide variety of brain imaging studies of normal brain anatomy and function, development, aging, and disease...
, UCLA - Statistical parametric mappingStatistical parametric mappingStatistical parametric mapping or SPM is a statistical technique created by Karl Friston for examining differences in brain activity recorded during functional neuroimaging experiments using neuroimaging technologies such as fMRI or PET...
(SPM)