BrainSuite on MacOS Sierra (10.12)
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 16a1 repackaged for Windows and Linux
We have updated the Windows and Linux packages for BrainSuite v.16a1. These changes are to address library issues that prevented BrainSuite from running on some platforms without the installation of additional libraries or due to potential conflicts with other installed libraries. The changes do not affect the outputs of the programs.
The specific issues addressed are:
Windows : two programs in SVReg were previously compiled for 32-bit Windows rather than 64-bit Windows, requiring additional runtime libraries to be installed if they were not already present. The repackaged installer includes the 64-bit builds of these programs, reducing dependencies. The difference in 32-bit vs. 64-bit does not affect the results of the programs, which produce identical outputs between the two versions.
Linux : on fresh installations of Ubuntu 14, the presence of Qt libraries on the system could present version conflicts. Specifically, the presence of an older version of libQt5Svg in /usr/lib/x86_64-linux-gnu/, from Qt 5.2.1, would lead to BrainSuite trying to load this library, which is incompatible with the Qt 5.6.1 libraries. We have now included libQt5Svg in the BrainSuite distribution, which prevents the incorrect version from being loaded and resolves the issue, enabling BrainSuite16a1 to be run on Ubuntu 14 without additional steps.
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.
BrainSuite at the 2016 UCLA NITP Advanced Neuroimaging Summer Program
We are pleased to be presenting a lecture and lab on BrainSuite at this year’s UCLA Advanced Neuroimaging Summer Program. More details, and archived slides and video of the presentation, can be found on here: http://brainsuite.org/nitp2016/.