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Standalone SPM

Introduction

What is Standalone SPM?

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

The download contains:

  • The MATLAB Runtime: a set of libraries that enables the execution of compiled MATLAB applications. The version has to match the one that was used to compile SPM.
  • The SPM Standalone itself containing the compiled SPM, as a ZIP file.

Installation

  1. Download the SPM Standalone ZIP file from the newest GitHub release for your OS

  2. Unzip spm_standalone_<version>_<OS>.zip in a folder of your choice, such as C:\Users\login\Documents\spm_standalone

  3. Install the MATLAB Runtime via the provided installer in the ZIP file under runtime_installer. It will install the minimal MATLAB Runtime that is required to run SPM (~2.5GB). This can be optionally performed without a GUI via the command line, e.g. on Linux/Mac:

    chmod 755 runtime_installer/Runtime_R2024b_for_spm_standalone_24.11.install
    runtime_installer/Runtime_R2024b_for_spm_standalone_24.11.install -agreeToLicense yes
    

First Run

  • 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.

Usage

To start SPM graphical user interface:

Double-click on spmxx.exe

Type in bash:

./run_spmxx.sh /usr/local/MATLAB/MATLAB_Runtime/<matlab_version>/

where the argument is the path to your Matlab Runtime installation. On macOS this might be under /Applications/MATLAB/MATLAB_Runtime/<matlab_version>/

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_spmxx.sh /usr/local/MATLAB/MATLAB_Runtime/<matlab_version>/ quit

For more conveniently running SPM, you can create an alias in ~/.bashrc or edit the Shell script run_spmxx.sh to hardcode the location of the MCR installation, thus removing the need of providing it on the command line.

When run via the command line, 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_spmxx.sh /Applications/MATLAB/MATLAB_Runtime/<matlab_version>/ fmri
./run_spmxx.sh /Applications/MATLAB/MATLAB_Runtime/<matlab_version>/ batch

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

./run_spmxx.sh /Applications/MATLAB/MATLAB_Compiler_Runtime/<matlab_version>/ batch mybatch.mat

Troubleshooting

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_spmxx.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 modefollowed by a crash on macOS?

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](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 here, 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_spmxx.sh:

SPM_HTML_BROWSER=0

Frequently Asked Questions

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.

The GitHub release action might also be an interesting reference.

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 download the SPM icon and convert it to a 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 uninstall desktop and icon file run:

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

Documentation

The MATLAB Compiler Toolbox presentation:

The MATLAB Compiler Toolbox documentation:

The MATLAB Compiler Support page: