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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, to analyze diffusion imaging data, and to process functional MRI. BrainSuite also provides several tools for visualizing and interacting with the data.

New: BrainSuite BIDS App — We have just released an updated version of the BrainSuite BIDS App, which provides containerized workflows for analyzing anatomical, diffusion, and functional MRI organized according to the BIDS standard. A prebuilt image is available for download from Docker Hub and the code is also available on the BIDS App Github site. For more details, please see the BrainSuite BIDS App documentation or read the preprint on bioRxiv.

A new version of the BrainSuite BIDS App is now available.

  • BrainSuite BIDS App adopts the BIDS App model to facilitate reproducible analyses.
  • Provides participant-level workflows for structural, diffusion, and functional MRI.
  • Group-level structural and diffusion analysis generates statistical reports using R.
  • Group-level fMRI analysis uses BrainSync to align the time-series data temporally.
  • BrainSuite Dashboard provides real-time updates of participant-level processing.

Please visit the BrainSuite BIDS App documentation page for details on how to to install and use it. For a detailed description of the BrainSuite BIDS App, please see our recent preprint:
Kim Y, Joshi AA, Choi S, Joshi SH, Bhushan C, Varadarajan D, Haldar JP, Leahy RM, Shattuck DW (2023) BrainSuite BIDS App: Containerized Workflows for MRI Analysis. bioRxiv 2023.03.14.532686; doi: 10.1101/2023.03.14.532686

We will also be presenting this work as a poster at OHBM2023 (see abstract).

BrainSuite Dashboard

The BrainSuite Dashboard is a new component that we have released with the BrainSuite BIDS App.

For more details, please see the BrainSuite BIDS App documentation.

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.

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.

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