Our manuscript describing the registration and distortion correction methods used in the BrainSuite Diffusion Pipeline has been accepted to be published in NeuroImage.

The paper is available on ScienceDirect.

Bhushan C, Haldar JP, Choi S, Joshi AA, Shattuck DW, and Leahy RM (2015) Co-registration and Distortion Correction of Diffusion and Anatomical Images Based on Inverse Contrast Normalization, NeuroImage 115:269-89.

Abstract:
Diffusion MRI provides quantitative information about microstructural properties which can be useful in neuroimaging studies of the human brain. Echo planar imaging (EPI) sequences, which are frequently used for acquisition of diffusion images, are sensitive to inhomogeneities in the primary magnetic (B0) field that cause localized distortions in the reconstructed images. We describe and evaluate a new method for correction of susceptibility-induced distortion in diffusion images in the absence of an accurate B0 fieldmap. In our method, the distortion field is estimated using a constrained non-rigid registration between an undistorted T1-weighted anatomical image and one of the distorted EPI images from diffusion acquisition. Our registration framework is based on a new approach, INVERSION (Inverse contrast Normalization for VERy Simple registratION), which exploits the inverted contrast relationship between T1- and T2-weighted brain images to define a simple and robust similarity measure. We also describe how INVERSION can be used for rigid alignment of diffusion images and T1-weighted anatomical images. Our approach is evaluated with multiple in vivo datasets acquired with a different acquisition parameters. Compared to other methods, INVERSION shows robust and consistent performance in rigid registration and shows improved alignment of diffusion and anatomical images relative to normalized mutual information for non-rigid distortion correction.

We have released an updated version of the BrainSuite Statistical Toolbox (BSS). For details please see the BSS page. The BrainSuite statistics toolbox allows the application of advanced statistical models to surface and curve based outputs generated from BrainSuite. This enables population or group modeling of cortical or sulcal morphology.

New in this version-

• ROI statistical analysis (ANOVA/GLMs) for gray matter volume, thickness, and cortical surface area
• Math operations on surface valued data – addition, subtraction

Source code for BSS is available under the GPL v2 license and may be downloaded here: https://bitbucket.org/bmapdev/bss.

The latest version of BrainSuite (v.14c) is available for download from the BrainSuite download page. This release includes a graphical user interface version for both Windows and Mac OSX platforms, as well as command line tools for performing cortical surface extraction, surface/volume registration, and processing of diffusion weighted images. BrainSuite 14c also features an improved installation process.

The recent update to Mac OS X (Yosemite) causes the MATLAB R2012a MCR to stop working, which is needed to run SVReg and BDP. This can be fixed with three simple steps.

If you are using these tools on Mac OS X 10.10 Yosemite, please visit this page: https://brainsuite.org/quickstart/installation/mac/yosemite/ for instructions on how to fix this issue.

We have recently released a new version of BrainSuite (v 14a1), which includes updates to all three components of the software. The BrainSuite GUI has been updated with many bug fixes and improvements, including support for multiple SVReg brain atlases, better NiFTI support, greater stability, and improved support for higher resolution displays (e.g., Mac Retina). SVReg has been updated to include a new single-subject atlas (the BCI DNI brain atlas), and has improved cross-platform consistency. The BrainSuite Diffusion Pipeline has also been updated, and provides better cross-platform consistency and also features numerous bug fixes and memory optimization.

The software can be downloaded here.

We are pleased to announce a new release of our BrainSuite software, which includes several updates to the graphical user interface, the SVReg registration and labeling software, and the BrainSuite Diffusion Pipeline (BDP). The new release is BrainSuite13a4, and can be downloaded here. This latest version contains several bug fixes and other improvements, and we strongly encourage users to switch to this version.

Please note that we have migrated to a new download system on our brainsuite.org site, and you will need to create a new user account to download the software. You may register for an account here.