We are still testing BrainSuite for Sierra, but we have recently been alerted to issues that arise when BrainSuite is installed on MacOS Sierra (10.12). These issues are due to changes in Apple’s security policies, which affect programs that are distributed via the Apple App Store. Specifically, these programs will be run in randomized folder locations rather than their installed location (e.g., BrainSuite will not be run in /Applications/BrainSuite16a1/, but instead it will be run in a folder located in /private/var/folders/). When the BrainSuite GUI is first run, it uses its location to find the locations of its related data and other programs. These locations are stored persistently, and reused when the program is launched again. With the Sierra security update, the randomization of the file locations prevents this from working properly.
We are evaluating permanent solutions to this issue, but have explored possible workarounds for users of Sierra. These include (note that this assumes you have installed BrainSuite16a1 into your /Applications folder):
1. Using Finder, move the BrainSuite folder out of /Applications/BrainSuite16a1/ to a different location (e.g., the desktop), and then back to /Applications/BrainSuite16a1/. This will reset the security setting, and enable BrainSuite to run in the correct folder. Note that this can only be done with Finder, and not with the bash mv command.
2. Run BrainSuite from the command line. After opening a terminal, run /Applications/BrainSuite16a1/BrainSuite16a1.app/Contents/MacOS/BrainSuite16a1 from the command window.
If you have already run BrainSuite, and it now shows strange paths for its files in the BrainSuite Log, you may need to clear the stored file locations. To do this, run:
and select [Yes] when prompted. This will reset the stored settings, and the next time you run the BrainSuite GUI, BrainSuite will search for its required files.
We are still working to resolve this more fully, and will update these notes as we find better and more permanent solutions.
If you encounter issues with BrainSuite and Sierra, please share them with us in the BrainSuite forums so we can work to resolve them.
BrainSuite v.16a1 is now available for download from the BrainSuite download page. This release includes a graphical user interface version for Windows, Mac OSX, and Linux platforms, as well as command line tools for performing cortical surface extraction, surface/volume registration, and processing of diffusion weighted images. Source code is provided under a GPLv2 license. This version now uses MATLAB R2015b MCR, which offers improved compatibility with more recent versions of Mac OS X.
The two major changes in v16a1 relative to v16a are:
– A bug has been fixed in the topology algorithm, which previously could cause BrainSuite to crash for large or complex image volumes.
– A build of the BrainSuite GUI for Linux is now included.
BrainSuite v.16a is now available for download from the BrainSuite download page. This release includes a graphical user interface version for Windows and Mac OS X platforms. Command line tools for performing cortical surface extraction, surface/volume registration, and processing of diffusion weighted images are also included. Source code is provided under a GPLv2 license. This version now uses MATLAB R2015b MCR, which offers improved compatibility with more recent versions of Mac OS X.
The latest version of BrainSuite (v.15c) 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. Source code is provided under a GPLv2 license. The Linux GUI may be built from the source code.
New NeuroImage article describing BDP registration and distortion correctionby shattuck | 28-Mar-2015
Our manuscript describing the registration and distortion correction methods used in the BrainSuite Diffusion Pipeline has been accepted to be published in NeuroImage.
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.
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.
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.
Configuring Mac OS X 10.10 Yosemite to work with SVReg and BDPby shattuck | 19-Oct-2014
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: http://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.
The BrainSuite Diffusion Pipeline (BDP) and Surface and Volume Registration (SVReg) programs distributed with BrainSuite 13a have received significant updates since the original April release. Besides bug fixes and performance tweaks, SVReg now has the ability to output statistics based on ROIs (BDP will output statistics in its next release). Rigid alignment in BDP has been improved and it performs consistently with images acquired with high b-values.
Due to the number of improvements we recommend everyone update to this latest version. The software is available for download from the software download site.
We are pleased to announce the release of BrainSuite13, which is the first version of BrainSuite that runs natively on both Mac and Windows platforms (a Linux release is also planned). BrainSuite13 includes many new features for processing, analyzing, and visualizing MRI data. In addition to the cortical surface extraction tools upon which BrainSuite was initially developed, we have also added new functionality for performing brain image registration using SVReg (Surface/Volume Registration), which uses the surface extraction results to initialize an automated registration procedure. We are also introducing the BrainSuite Diffusion Pipeline (BDP), which provides new tools for correcting distortion in diffusion MR images and registering them to a structural T1-weighted image, computing various diffusion products including tensors and ODFs. BDP can compute ODFs using the recently developed Funk-Radon and Cosine Transform (FRACT). The results of BDP can be combined with the results of SVReg, enabling the analysis of diffusion and connectivity in the context of neuroanatomical ROIs. The software is available for download from the download page.
Justin Haldar and David Shattuck will be presenting work at the 18th Annual Meeting of the Organization for Human Brain Mapping to be held June 10-14, 2012 in Beijing (www.humanbrainmapping.org/OHBM2012/). Come see us at these posters:
#408 Haldar JP, Shattuck DW, Damasio H, Leahy RM (2012) Improved Diffusion Tractography with the Funk-Radon and Cosine Transform, 18th Annual Meeting of the Organization for Human Brain Mapping, Beijing, China, June 2012.
#602 Joshi AA, Shattuck DW, Leahy RM (2012) Refinement of Automated Cortical Surface Registration and Labelling using Gradient Curvature Flow, 18th Annual Meeting of the Organization for Human Brain Mapping, Beijing, China, June 2012.
We will also be available to show demos of the latest BrainSuite tools for our upcoming software release.