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• 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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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

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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

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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:
# 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
# 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

Release (MATLAB Runtime Version#)	Windows	Linux	Mac
R2021a (9.10)	64-bit	64-bit	Intel 64-bit
R2020b (9.9)	64-bit	64-bit	Intel 64-bit
R2020a (9.8)	64-bit	64-bit	Intel 64-bit
R2019b (9.7)	64-bit	64-bit	Intel 64-bit
R2019a (9.6)	64-bit	64-bit	Intel 64-bit
R2018b (9.5)	64-bit	64-bit	Intel 64-bit
R2018a (9.4)	64-bit	64-bit	Intel 64-bit
R2017b (9.3)	64-bit	64-bit	Intel 64-bit
Apply Updates to R2016a-R2017a versions of MATLAB Runtime after installing the runtime Important security fixes are available for the R2016a, R2016b, and R2017a releases of the MATLAB Runtime. After installing the MATLAB Runtime for one of these releases, you should apply the latest Update by clicking on the appropriate Update link below. Note this applies only if your application uses MATLAB apps authored with MATLAB App Designer (.mlapp files). For more information see this bug report. R2017a (9.2) 64-bit | Update 64-bit | Update Intel 64-bit | Update R2016b (9.1) 64-bit | Update 64-bit | Update Intel 64-bit | Update R2016a (9.0.1) 1, 2 64-bit | Update 64-bit | Update Intel 64-bit | Update
R2015b (9.0) 1, 2, 3	32-bit / 64-bit	64-bit	Intel 64-bit
R2015aSP1 (8.5.1) 1	32-bit / 64-bit	64-bit	Intel 64-bit
R2015a (8.5) 1	32-bit / 64-bit	64-bit	Intel 64-bit
R2014b (8.4) 1	32-bit / 64-bit	64-bit	Intel 64-bit
R2014a (8.3) 1	32-bit / 64-bit	64-bit	Intel 64-bit
R2013b (8.2)	32-bit / 64-bit	64-bit	Intel 64-bit
R2013a (8.1)	32-bit / 64-bit	64-bit	Intel 64-bit
R2012b (8.0)	32-bit / 64-bit	64-bit	Intel 64-bit
R2012a (7.17)	32-bit / 64-bit	32-bit / 64-bit	Intel 64-bit
R2011b and earlier 4	Open MATLAB and run the command mcrinstaller to locate MATLAB Runtime for redistribution with your compiled components.