Welcome to the BrainSuite Website
BrainSuite is a collection of open source software tools that enable largely automated processing of magnetic resonance images (MRI) of the human brain. The major functionality of these tools is to extract and parameterize the inner and outer surfaces of the cerebral cortex, to segment and label gray and white matter structures, and to analyze diffusion imaging data. BrainSuite also provides several tools for visualizing and interacting with the data.
We are pleased to announce the release of BrainSuite version 21a. BrainSuite21a includes many recently added features, including automated parameter tuning for skull-stripping, estimation of cortical thickness using the Anisotropic Laplace Equation, and new diffusion modeling tools.
A new version of the BrainSuite BIDS App now available
- The BrainSuite BIDS App provide containerized workflows for processing and analyzing anatomical, diffusion, and functional MRI data primarily using software we have developed for the BrainSuite project.
- By using the BIDS and BIDS App standards , BrainSuite BIDS App can be rapidly deployed to provide a complete framework for performing end-to-end data analysis.
- We developed the BrainSuite Dashboard, a browser-based quality control system that can be run concurrently with a set of BrainSuite BIDS App instances to facilitate real-time visual assessment of processing outputs.
The BrainSuite Statistics toolbox in R (bssr) is a software package developed in R that performs statistical analysis of population-level neuroimaging data processed using BrainSuite. Specifically, it provides statistical tools for conducting cortical thickness analysis, tensor based morphometry, and analysis of diffusion measures.
For more details, please see the bssr page.
Joshi AA, Choi S, Chong M, Sonkar G, Gonzalez-Martinez J, Nair D, Wisnowski JL, Haldar JP, Shattuck DW, Damasio H, Leahy RM (2022) A Hybrid High-Resolution Anatomical MRI Atlas with Sub-parcellation of Cortical Gyri using Resting fMRI. Journal of Neuroscience Methods 374:109566.
We recently released the USCBrain atlas, a hybrid high-resolution Anatomical MRI atlas with subparcellation of cortical gyri using resting fMRI. The USCBrain atlas is constructed using both anatomical and functional information to guide the parcellation of the cortex.
- consists of consistent volumetric and surface-based parcellations and labels.
- contains a total of 159 regions of interest (130 cortical, 29 noncortical) defined with respect to the volumetric space
- The surface-based component of the atlas as the same 130 sub-gyral (cortical) regions delineated and labeled in addition to the identification of 76 sulcal curves and delineation of gyral crowns and sulcal banks for each gyrus.
- The USCBrain atlas was developed to be used with BrainSuite to register individual structural T1-weighted scans to this atlas and perform structural labeling.
- The atlas is included in the BrainSuite21a Release.
- The atlas can also be used with other brain imaging software packages, including FSL and FreeSurfer.
The latest version of BrainSuite (v.21a) is available for download.
This release features:
- GUI for Windows, Mac OSX, and Linux platforms
- USCBrain Atlas — A Hybrid High-Resolution Anatomical MRI Atlas with Subparcellation of Cortical Gyri using Resting fMRI — now included in the distribution
- New rewind feature for each stage of the BrainSuite anatomical (T1-weighted) pipeline
- Automated skull-stripping parameter tuning
- Command line tools for performing cortical surface extraction, surface/volume registration, and processing of diffusion weighted images
- Ability to create and use custom brain atlases.
- Compiled MATLAB code now uses MATLAB R2019b Matlab Compiler Runtime, which provides improved compatibility with more recent versions of Mac OS X.
For more details on the updates to BrainSuite in this release, please see the BrainSuite21a Release Page.
BrainSuite User Interface
BrainSuite provides an easy-to-use interface for performing data processing, analysis, and visualization of brain MRI data. The GUI is available for Mac, Windows, and Linux.
Cortical Surface Extraction
BrainSuite provides a flexible set of tools for performing rapid automated extraction of cortical surface models.
Surface-constrained Volumetric Registration
BrainSuite uses the novel Surface-constrained Volumetric Registration (SVReg) to align subject MRI to a labeled atlas.
BrainSuite Diffusion Pipeline
The BrainSuite Diffusion Pipeline (BDP) provides a set of tools for processing diffusion weighted MRI (dMRI). This functionality includes:
- Correction of geometric distortion in EPI data using a T1-weighted structural as an anatomical reference
- Tensor fitting and estimation of diffusion parameters aligned with the T1-weighted MRI.
- Orientation distribution function (ODF) estimation using FRT, FRACT, and 3D-SHORE