Developer(s) | Martinos Center for Biomedical Imaging |
---|---|
Stable release | 7.3 |
Repository | |
Operating system | Linux or Mac OS X |
Type | Neuroimaging data analysis |
License | FreeSurfer Software License [1] |
Website | FreeSurfer |
FreeSurfer is brain imaging software originally developed by Bruce Fischl, Anders Dale, Martin Sereno, and Doug Greve. [2] Development and maintenance of FreeSurfer is now the primary responsibility of the Laboratory for Computational Neuroimaging [3] 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. [4] 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 [5] and it is a core tool in the processing pipelines of the Human Connectome Project, [6] the UK Biobank, [7] the Adolescent Brain Cognitive Development Study, [8] and the Alzheimer's Disease Neuroimaging Initiative. [9]
The FreeSurfer processing stream is controlled by a shell script called recon-all. [10] 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 [11] tool. FreeSurfer contains a range of packages allowing a broad spectrum of uses, including:
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. [18] FreeSurfer also uses toolkits from MNI MINC, VXL, Tcl/Tk/Tix/BLT, VTK., KWWidgets and Qt, [19] which are all available with the distribution. Other neuroimaging programs like Caret, AFNI/SUMA, MNE, and 3D Slicer can also import data processed by FreeSurfer.
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. [20] Documentation can be found on the FreeSurfer Wiki [21] and limited support is available from the developers and community through the FreeSurfer mailing list.
The following is a sample of references the FreeSurfer team recommends researchers cite when publishing findings obtained through FreeSurfer. [22] Citation counts have been obtained through Google Scholar as of August 2019.
Title | Year | Citations |
---|---|---|
Cortical surface-based analysis. I. Segmentation and surface reconstruction. [23] | 1999 | 6469 |
Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system. [24] | 1999 | 4507 |
High-resolution intersubject averaging and a coordinate system for the cortical surface. [25] | 1999 | 2339 |
Measuring the thickness of the human cerebral cortex from magnetic resonance images. [26] | 2000 | 3863 |
Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex. [27] | 2001 | 1258 |
Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. [28] | 2002 | 5066 |
A hybrid approach to the skull stripping problem in MRI. [29] | 2004 | 1584 |
Automatically parcellating the human cerebral cortex. [30] | 2004 | 2731 |
An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. [31] | 2006 | 4932 |
In neuroanatomy, the precuneus is the portion of the superior parietal lobule on the medial surface of each brain hemisphere. It is located in front of the cuneus. The precuneus is bounded in front by the marginal branch of the cingulate sulcus, at the rear by the parieto-occipital sulcus, and underneath by the subparietal sulcus. It is involved with episodic memory, visuospatial processing, reflections upon self, and aspects of consciousness.
Neuroscience and intelligence refers to the various neurological factors that are partly responsible for the variation of intelligence within species or between different species. A large amount of research in this area has been focused on the neural basis of human intelligence. Historic approaches to studying the neuroscience of intelligence consisted of correlating external head parameters, for example head circumference, to intelligence. Post-mortem measures of brain weight and brain volume have also been used. More recent methodologies focus on examining correlates of intelligence within the living brain using techniques such as magnetic resonance imaging (MRI), functional MRI (fMRI), electroencephalography (EEG), positron emission tomography and other non-invasive measures of brain structure and activity.
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Connectomics is the production and study of connectomes: comprehensive maps of connections within an organism's nervous system. More generally, it can be thought of as the study of neuronal wiring diagrams with a focus on how structural connectivity, individual synapses, cellular morphology, and cellular ultrastructure contribute to the make up of a network. The nervous system is a network made of billions of connections and these connections are responsible for our thoughts, emotions, actions, memories, function and dysfunction. Therefore, the study of connectomics aims to advance our understanding of mental health and cognition by understanding how cells in the nervous system are connected and communicate. Because these structures are extremely complex, methods within this field use a high-throughput application of functional and structural neural imaging, most commonly magnetic resonance imaging (MRI), electron microscopy, and histological techniques in order to increase the speed, efficiency, and resolution of these nervous system maps. To date, tens of large scale datasets have been collected spanning the nervous system including the various areas of cortex, cerebellum, the retina, the peripheral nervous system and neuromuscular junctions.
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Anders Martin Dale is a prominent neuroscientist and professor of radiology, neurosciences, psychiatry, and cognitive science at the University of California, San Diego (UCSD), and is one of the world's leading developers of sophisticated computational neuroimaging techniques. He is the founding Director of the Center for Multimodal Imaging Genetics (CMIG) at UCSD.
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