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| BrainSuite is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head. | BrainSuite is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human brain. The major functionality of these tools is to extract and parameterize the inner and outer surfaces of the cerebral cortex and to segment and label gray and white matter structures. BrainSuite also provides several tools for [[http://brainsuite.org/visualization|visualizing]] and [[http://brainsuite.org/interaction|interacting]] with the data. |
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| BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. We have written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C++ using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. | BrainSuite is collaboratively developed between David Shattuck at the Laboratory of Neuro Imaging (LONI), UCLA and Richard Leahy in the Biomedical Imaging Group, USC. Other contributors to the development of the methods embodied in this software include: Anand A. Joshi, Belma Dogdas, Stephanie Sandor-Leahy, Bijan Timsari, and Paul M. Thompson. |
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| BrainSuite has been written to be compatible with our [[Brainsuite/../brainstorm|BrainStorm Software]] package for the analysis of MEG and EEG data. Cortical surfaces extracted using BrainSuite can be used for part of a cortically constrained minimum norm imaging; brain, skull and scalp surfaces can be used to solve forward calculations using BEM or FEM functions in BrainStorm. BrainStorm also includes utilities to downsample surface tessellations and build FEM meshes from segmented volumes and surfaces. | The currently released version of the software (BrainSuite11a) can be dowloaded here. This release includes both the graphical user interface version, available for Windows platforms, and command line versions of the the routines used for cortical surface extraction (available for Mac OSX, and Linux). The GUI can also be run on Linux and Mac OSX using [[http://www.winehq.org/|WINE]], [[http://www.kronenberg.org/wine/|Darwine (Mac OSX)]], or [[http://www.codeweavers.com/products/|Crossover (commercial)]], or using virtual machine software such as [[http://www.virtualbox.org/|Virtual Box]] or [[http://www.vmware.com/products/fusion/overview.html|VMWare Fusion]] |
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| BrainSuite was written by Dr. David W. Shattuck and is produced and distributed as a collaborative project between the [[http://www.loni.ucla.edu/index.shtml|Laboratory of Neuro Imaging]] at the University of California Los Angeles (Director: Dr. Arthur W. Toga) and the [[Brainsuite/../|Biomedical Imaging Research Group]] at the University of Southern California (Director: Dr. Richard M. Leahy). The work is supported by grants from the National Institute of Biomedical Imaging and Bioengineering (R01 EB002010, PI: R.M. Leahy) and from the National Center for Research Resources (P41 RR013642, PI: A.W. Toga). | Current BrainSuite features include: |
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| Contributors to the development of the methods embodied in this software include: David Shattuck, Anand Joshi, Belma Dogdas, Stephanie Sandor-Leahy, Bijan Timsari, Paul Thompson and Richard M. Leahy. | * Visualization tools, such as MRI visualization in 3 orthogonal views (either seperately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. Tools include brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Interactive labeling of sulcal landmarks in surface and orthogonal views * Skull and scalp surface extraction |
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| BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either seperately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. Tools include brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction |
A new version of BrainSuite will be released soon that will include coregistration of cortical surfaces to an atlas and surface-constrained volume registration to an atlas that produces a one-to-one mapping between cortical surfaces. |
BrainSuite homepage has moved: click here
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BrainSuite documentation: click here
BrainSuite
BrainSuite is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human brain. The major functionality of these tools is to extract and parameterize the inner and outer surfaces of the cerebral cortex and to segment and label gray and white matter structures. BrainSuite also provides several tools for visualizing and interacting with the data.
BrainSuite is collaboratively developed between David Shattuck at the Laboratory of Neuro Imaging (LONI), UCLA and Richard Leahy in the Biomedical Imaging Group, USC. Other contributors to the development of the methods embodied in this software include: Anand A. Joshi, Belma Dogdas, Stephanie Sandor-Leahy, Bijan Timsari, and Paul M. Thompson.
The currently released version of the software (BrainSuite11a) can be dowloaded here. This release includes both the graphical user interface version, available for Windows platforms, and command line versions of the the routines used for cortical surface extraction (available for Mac OSX, and Linux). The GUI can also be run on Linux and Mac OSX using WINE, Darwine (Mac OSX), or Crossover (commercial), or using virtual machine software such as Virtual Box or VMWare Fusion
Current BrainSuite features include:
- Visualization tools, such as MRI visualization in 3 orthogonal views (either seperately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp
- Cortical surface extraction, using a multi-stage user friendly approach. Tools include brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation
- Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology
- Interactive labeling of sulcal landmarks in surface and orthogonal views
- Skull and scalp surface extraction
A new version of BrainSuite will be released soon that will include coregistration of cortical surfaces to an atlas and surface-constrained volume registration to an atlas that produces a one-to-one mapping between cortical surfaces.