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SPM/Standalone

< SPM
The latest reviewed version was checked on 2 December 2020. There are template/file changes awaiting review.

Introduction

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A standalone SPM is a version of SPM that has been compiled using the MATLAB Compiler so that it does not require the availability of a MATLAB licence (you might want to check first here whether you have access to a MATLAB campus license).

A standalone version of SPM12 is available for download from the SPM website (select "SPM Standalone" for "SPM Version"). Please contact fil.spm@ucl.ac.uk if you need assistance.

Installation

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Following your request, you will be given instructions to download the following components:

  • The MATLAB Runtime: it contains a set of libraries that enables the execution of compiled MATLAB applications. You need to install the one that corresponds to your platform (Windows, Linux or macOS) and to the version that was used to compile SPM. The default SPM standalone requires the MATLAB Compiler Runtime (MCR) 7.13 of MATLAB R2010a available from the MCR folder from the link you will have been given. Otherwise more recent MATLAB Runtimes are downloadable from here.
  • The SPM Standalone itself containing the compiled SPM, as a ZIP file.

Installation of the MATLAB Runtime

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You need to do this operation only once, even if you use several versions of standalone SPM.

Run the MCRInstaller executable you downloaded and follow the instructions.

Windows installation requires to have administrative privileges and you might also have to install the Visual C++ Redistributable Package (vcredist_*.exe), that can be found in the same folder as the MCRInstaller. We also recommend you restart Windows at this point.

If you run into problems, or want to learn more, see:

To install the MCR on Linux from the command line, type: 

chmod 755 MCRInstaller.bin
./MCRInstaller.bin -P bean421.installLocation="MCR" -silent

Installation of the SPM Standalone

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  • Unzip the spm12_rxxx.zip archive containing the SPM Standalone in an appropriate folder. It contains a number of small executables for each supported platform and a large spm12.ctf file containing the compiled version of SPM12 itself.
  • The first time the standalone application will be executed, the CTF file will be unpacked in a subfolder so if you installed the CTF in a folder that requires administrative permission for write access, you should execute the application once under those privileges -- see below.
  • On Mac, you also need to unzip the spm12_maci64.zip archive.

Usage

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To start SPM graphical user interface:

  • on Windows: double-click on spm12_wxx.exe
  • on Linux, type
./run_spm12.sh /usr/local/MATLAB/MATLAB_Compiler_Runtime/v713/

where the argument is the path to your MCR installation.

  • on Mac, type
./run_spm12.sh /Applications/MATLAB/MATLAB_Compiler_Runtime/v713/

where the argument is the path to your MCR installation.

The first execution should take longer to start as the CTF file will be unpacked. When installing SPM system-wide, you should do the first unpacker execution as root, i.e. 

./run_spm12.sh /usr/local/MATLAB/MATLAB_Compiler_Runtime/v713/ quit

On Linux/Mac, you can edit the Shell script run_spm12.sh to hardcode the location of the MCR installation, thus removing the need of providing it on the command line.

The other arguments that can be used are the modality (as in `spm fmri`) or the keyword `batch` to start directly the batch system window, e.g.: 

./run_spm12.sh /Applications/MATLAB/MATLAB_Compiler_Runtime/v713/ fmri
./run_spm12.sh /Applications/MATLAB/MATLAB_Compiler_Runtime/v713/ batch

Furthermore, `batch` followed by a batch filename (*.mat or *.m) will start SPM, execute the batch and quit: 

./run_spm12.sh /Applications/MATLAB/MATLAB_Compiler_Runtime/v713/ batch mybatch.mat

Trouble-shooting

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  • Why do I receive an error regarding missing mclmcrrt7x.dll ?

The first thing to try is restarting your computer, if you haven't already, since Windows can fail to find this dll even when the path is correctly set if it hasn't been restarted. If you still have problems, see: http://www.mathworks.com/support/solutions/en/data/1-1IW46N/

  • What to do if I get the error "Unable to obtain exclusive lock on CTF directory because of a file access error."?

You need to set variable MCR_INHIBIT_CTF_LOCK to 1, see this.

  • What to do if I get the error "readlink: illegal option -- f" on a Mac?

Change the last line of run_spm12.sh so that it reads: 

`dirname $0`/${MACAPP}spm12_${MWE_ARCH} $*
  • How to have the standalone version using a single computational thread?

All recent versions of the standalone SPM are compiled with the "-R -singleCompThread" flag in mcc so that they will use a single thread at runtime.

Previous version r4290, was not using this compilation option so you might want to have your MATLAB script to start with maxNumCompThreads(1); to have the same effect.

  • Why do I get a warning "Process manager already initialized -- can't fully enable headless mode." followed by a crash on Mac OS?

Try installing XQuartz (you must logout and back in again after installing XQuartz).

  • What to do if I get the error "Error: libXp.so.6: cannot open shared object file: No such file or directory"?

You need to install the package containing libXp on your Linux platform: 

yum install libXp.x86_64

If you don't find this package on Ubuntu, try installing libXp manually (compilation might require to install packages autoconf autogen xutils-dev and x11proto-print-dev): 

git clone git://anongit.freedesktop.org/xorg/lib/libXp
cd libXp
./autogen.sh
./configure
make
sudo make install

Alternatively you can find packages for Ubuntu or Debian that can be installed after download with dpkg -i libxp6_1.0.2-2_amd64.deb.

  • What to do if I get the error "This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported."?

Run the standalone as root once, i.e. start the command line with sudo.

  • Why do I get an error "Library not loaded: /usr/X11/lib/libXext.6.dylib" on Mac?

Have a look at [1], you probably have to reinstall XQuartz.

  • Why does standalone SPM crash when starting the GUI?

This is discussed here and can be fixed by adding the following in run_spm12.sh: 

SPM_HTML_BROWSER=0

Frequently Asked Questions

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  • Will it run faster?

No: https://www.mathworks.com/matlabcentral/answers/94695

  • Is it possible to add other SPM toolboxes?

No: only core SPM toolboxes are available, contributed SPM toolboxes are not present and cannot be added without a whole recompilation.

  • How to compile the SPM standalone by myself?

Have a look at config/spm_make_standalone.m and spm_standalone.m in your SPM installation.

Open MATLAB, at the command line, addpath the SPM directory (if not done already), run spm_jobman('initcfg'), then run spm_make_standalone. The compilation process takes several minutes. By default, the newly compiled standalone SPM will be saved in a standalone directory.

  • How to create a shortcut on your Desktop for a faster launch?

On Linux, for achieving menu entries, you can install an appropriate .desktop file and an icon file for SPM. For example, save the following as spm12.desktop (modify according to your needs/MCR version): 

 [Desktop Entry]
 Name=spm12
 GenericName=SPM12
 Comment=Statistical Parametric Mapping
 Exec=/usr/local/SPM/spm12/run_spm12.sh /usr/local/MATLAB/MATLAB_Compiler_Runtime/v713
 Icon=spm
 Terminal=false
 Type=Application
 Categories=Education;Science;

Additionally get the SPM icon from https://www.fil.ion.ucl.ac.uk/spm/favicon.ico and convert it to an png file, name it spm.png (this is the one referred to in the .desktop file as icon).

Then (package xdg-utils required) execute in a terminal: 

 xdg-desktop-menu install --novendor spm12.desktop
 xdg-icon-resource install --novendor --size 32 spm.png

To deinstall desktop and icon file run 

 xdg-icon-resource uninstall --size 32 spm
 xdg-desktop-menu uninstall spm12.desktop

Documentation

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The MATLAB Compiler Toolbox presentation:

The MATLAB Compiler Toolbox documentation:

The MATLAB Compiler Support page:

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