Welcome to USPS.com. Find information on our most convenient and affordable shipping and mailing services. Use our quick tools to find locations, calculate prices, look up a ZIP Code, and get Track & Confirm info. Use the MatlabComponentRuntime dmg to install the MATLAB Runtime Component, allowing you to run standalone MATLAB applications. Use 'Terminal' and, while in the hhsim31macPPC directory, type (assuming you installed MCR in the default location).

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System Requirements

Operating System: Windows 10 (64-bit); Mac OS X 10.8+; Linux 64-bit
Memory: 2 GB (4+ GB recommended)
Processor: x86

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The BrainSuite software is distributed as a GUI for Windows, Macintosh OS X, and Linux platforms. Command line programs for cortical surface extraction and diffusion processing are also provided. The related software for Surface/Volume Registration (SVReg) is provided as a collection of command-line programs callable from BrainSuite’s GUI, while the BrainSuite Diffusion Pipeline (BDP) is a command-line only program.

The software may be downloaded here.

Installing on Mac OS X

Mac OS X Platforms

Note: if you are using MacOS Sierra (10.12), please see this page.

BrainSuite for Mac OS X is distributed as a disk image (BrainSuite16a1.dmg) file. To install:

1. Open BrainSuite16a1.dmg and drag the BrainSuite16a1 folder into your Applications folder, as indicated in the pop-up window.
2. Download and install the 2015b MATLAB Compiler Runtime, available from Mathworks. See the Mathworks MCR page for more details.
3. Open your Applications folder (or Launch Pad on the dock) and start BrainSuite21a from within the BrainSuite21a folder.
4. Verify that the program has been installed correctly by checking that no red text warnings appear in the log at the bottom of the BrainSuite window.

Installing on Windows

Windows Platforms

On Windows, the software is distributed as an installer package (BrainSuite21a_win64.exe). To install:

1. Run BrainSuite21a_win64.exe. This will initiate the BrainSuite Installer.
2. Follow the instructions for the Setup, indicating the folder in which you would like to save BrainSuite and its shortcuts.
3. The Setup program will check to see if you have the correct version of the Matlab runtime libraries installed. If you do not, it will offer to download the MATLAB Compiler Runtime for you. Install this, and then continue the setup procedure.
4. When Setup has finished, launch BrainSuite.
5. Verify that the program has been installed correctly by checking that no red text warnings appear in the log at the bottom of the BrainSuite window.

Installing on Linux

Linux Platforms

On Linux, the software is distributed as gzipped tar file (BrainSuite21a.linux.tgz). This file can be installed to whichever location is most appropriate for your system. A typical location, provided you have administrator privileges, would be /opt/BrainSuite16a1/. For individual use, you may want to locate the program in your home directory.

1. Unzip and untar BrainSuite21a.linux.tgz file. This will create a BrainSuite21a folder which includes the files for CSE, BDP, and SVReg.

This can be done on the command line using

Note that you can unpack BrainSuite into the /opt directory by using

sudo tar xvfz BrainSuite21a.linux.tgz -C /opt/
2. If necessary, move the folder to its desired location. You may need to use sudo to do this.
3. Download and install the , 2015b MATLAB Compiler Runtime for Linux, available from Mathworks. See the Mathworks MCR page for more details.
4. To run the GUI on Linux (requires glibc 2.14, glibc++ 3.4.19 or greater), launch BrainSuite16a1 in the bin folder from the terminal, e.g., /opt/BrainSuite16a1/bin/BrainSuite16a1. Doing so will launch the user interface:
5. We have run the BrainSuite GUI on Ubuntu 14.04LTS, 15.04, and 16.04LTS.
6. For Ubuntu 12.04LTS, a newer version of glibc++ must be installed. One way to do this is to install g++ 4.8. See this page for details.

   sudo add-apt-repository ppa:ubuntu-toolchain-r/test

   sudo apt-get update

   sudo apt-get install g++-4.8

   Another is to copy a recent version (3.4.19 or greater) of libg++.so to the lib directory inside BrainSuite16a1/bin.

7. There are a variety of Linux flavors, so if you encounter difficulties with the installation, please visit the BrainSuite forums for assistance.

Building from Source

We highly recommend using the pre-compiled versions of BrainSuite, which have been tested for cross-platform compatibility. If you do wish do build the software from the source code, instructions for how to do this are provided on this page.

Compiled versions of RetroTS.m that do not require Matlab to be installed are available here. These can be used in cases where either Matlab is not installed or Matlab toolboxes are missing. The program, McRetroTS, is provided as a wrapper to the RetroTS.m program. The RetroTS.m program requires both the Statistical toolbox and the Signal Processing toolbox in addition to Matlab while the compiled version provides a stand-alone solution (with no additional cost). The code takes as input the respiration movement and pulse oximetry data and provides as output a series of curves that are appropriate as regressors for RETROICORR processing (now handled in afni_proc.py). Linux (64-bit), Mac Intel and Mac PPC versions are available.

This is an example of the usage of the program, McRetroTS:

McRetroTS resp.dat pulsox.dat 4 50 20 0
or generally

McRetroTS Respdatafile ECGdatafile VolTR Nslices SamplingFreq(PhysFS) ShowGraphs

The output is a file named oba.slibase.1D. The ShowGraphs option here is new allowing you to turn off figures from appearing. Setting that to 0 turns off the figures. Setting it to 1 turns the figures on, so graphs will appear. With the graphs on, the program waits for user input before exiting. With the graphs off, the program does not wait and continues, making it more appropriate for use in scripts. The number of options is limited compared to the Matlab version because they need to be explicily set. Also because the compilation is not yet automated, the compiled versions will not be updated frequently and will lag behind the Matlab version distributed with AFNI's Matlab library. If options or features are missing that you need, please let us know.

In a script, this program can be repeated called like this:

foreach run ( `count -digits 2 0 8`)
McRetroTS Resp_${run}.dat ECG_${run}.dat 2.3 38 50 0
mv oba.slibase.1D r${run}.slibase.1D
end

Then use the -ricor_regress_option for afni_proc.py to use these regressor files.

The installation of the compiled program requires several environment variables to be set so that the program knows where to find the dynamic libraries required for Matlab compiled code, the MCR (Matlab Compiler Runtime) libraries.

For the Mac versions, install the MCR libraries by using the DMG package installer included in the distribution. If Matlab is already installed, then this step is not necessary. A script is supplied to set the environment variables and run the McRetroTS program, but setting the environment variables separately can done also, as for the Linux version.

For the Linux version, untar the package from the distribution link, run MCRinstaller.bin the first time you run this and then run the setMcRetro.csh script (included in the distribution and copied below) to setup the environment variables for the appropriate directories.

tar xzvf McRetro_Linux.tgz

cd McRetro

unzip McRetroTS_pkg

./MCRInstaller.bin

# edit the setMcRetro.csh script to point to the correct directories

# updating the mcr_root directory to the location where it was downloaded

# and the version to the version of Matlab (V76). If there is no preexisting version

# of Matlab, keep the version the same.

# alternatively, add the environment variable definitions to your .cshrc file

source ./setMcRetro.csh

You can then add the McRetroTS directory to your path or copy the McRetroTS program to your afni directory.

#!/bin/tcsh
# setMcRetro.csh
# set up environment variables for call Matlab compiled code
# usage:

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# run MCR installer.bin once to get this to work
# Install into the directory that you will specify as mcr_root below
# call this with source./setMcRetro.csh
# or put these environment variable settings in the .cshrc file or equivalent for your shell
# may want to put these files in a separate directory,
# mkdir McRetro; cd McRetro
# tar xzvf McRetroTS.tgz
# unzip McRetroTS_pkg
# install Matlab compiler runtime libraries
# install using GUI (there are options to do this silently and no user interaction though)
# ./MCRInstaller.bin

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set mcr_root = '/misc/tungsten2/dglen/McRetro'
set version = v76

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# slightly different from the Matlab help - also need bin/glnxa64
setenv LD_LIBRARY_PATH
${mcr_root}/${version}/runtime/glnxa64:${mcr_root}/${version}/bin/glnxa64:${mcr_root}/${version}/sys/os/glnxa64:${mcr_root}/${version}/sys/java/jre/glnxa64/jre1.5.0/lib/amd64/native_threads:${mcr_root}/${version}/sys/java/jre/glnxa64/jre1.5.0/lib/amd64/server:${mcr_root}/${version}/sys/java/jre/glnxa64/jre1.5.0/lib/amd64
setenv XAPPLRESDIR ${mcr_root}/${version}/X11/app-defaults

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