SPM Installation with MATLAB¶

Prerequisites

The SPM software is a collection of MATLAB functions and thus requires the MATLAB software to be installed on your computer in order to run. SPM requires only core MATLAB to run (no special toolboxes are required - unless stated otherwise).

Each SPM version was written for a particular MATLAB version and will not work with earlier versions. MATLAB versions released after SPM can have some peculiarities but SPM developers try to provide compatibility fixes in the updates.

Installation¶

WindowsmacOSLinux

Download spm12.zip from the SPM website.
Unzip spm12.zip in a folder of your choice, such as C:\Users\login\Documents\MATLAB\spm12.
Start MATLAB and add SPM to your path, either using:

Home Set Path Add Folder...: select the directory containing your SPM installation then click on Save and Close.

or type the following at the MATLAB prompt:
```
addpath('C:\Users\<login>\Documents\MATLAB\spm12')
savepath % if you want to save the current MATLAB path
```
If you are using MATLAB without its desktop, you can open the Set Path dialog box by typing pathtool at the MATLAB prompt.

Download spm12.zip from the SPM website in your home directory.

If using Apple Silicon and Matlab 2023b or higher, download the development version of SPM or the maintenance branch of SPM12 from GitHub.
Uncompress the archive by typing the following in a Terminal:
```
cd /Users/<login>
unzip spm12.zip
```
Start MATLAB and add SPM to your path, either using: File Set Path Add Folder...

or typing the following at the MATLAB prompt:
```
addpath /Users/<login>/spm12
savepath % if you want to save the current MATLAB path
```

Using Apple Silicon with Matlab 2023b (onwards)

If, after installation, you get an error indicating that the MEX files for MACA64 are missing:

Error using spm_check_installation>check_basic
SPM uses a number of MEX files, which are compiled functions.
These need to be compiled for the various platforms on which SPM
is run. It seems that the compiled files for your computer platform
are missing or not compatible. See
https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Mac_OS_(Intel)
for information about how to compile MEX files for MACA64
in MATLAB 23.2.0.2365128 (R2023b).

This is because you are running native Apple silicon MATLAB (R2023b onwards) and the MEX files are not available for that platform in SPM12. Instead download and install the development version of SPM or the maintenance branch of SPM12 where the *.mexmaca64 MEX files have been compiled.

Then complete the steps detailed below if you receive a MEX file validation error, such as:

"*.mexmaca64" cannot be opened because the developer cannot be verified.
macOS cannot verify that this app is free from malware

or:

Code signature not valid for use in process using Library Validation: library load disallowed by system policy

Open a Terminal, cd to the SPM directory and type:

find . -name "*.mexmaca64" -exec xattr -d com.apple.quarantine {} \;

If it doesn’t work, please try this equivalent alternative, replacing SPM_PATH with the path of your SPM installation:

sudo xattr -r -d com.apple.quarantine SPM_PATH
sudo find SPM_PATH -name "*.mexmaca64" -exec spctl --add {} \;

Using any other Mac and Matlab version combination

If you have validation issues with MEX files with one of these errors:

"*.mexmaci64" cannot be opened because the developer cannot be verified.
macOS cannot verify that this app is free from malware

or:

Code signature not valid for use in process using Library Validation: library load disallowed by system policy

Open a Terminal, cd to the SPM directory and type:

find . -name "*.mexmaci64" -exec xattr -d com.apple.quarantine {} \;

If it doesn’t work, please try this equivalent alternative, replacing SPM_PATH with the path of your SPM installation:

sudo xattr -r -d com.apple.quarantine SPM_PATH
sudo find SPM_PATH -name "*.mexmaci64" -exec spctl --add {} \;

Download spm12.zip from the SPM website in your home directory.
Uncompress the archive by typing the following in a terminal:
```
cd /home/<login>
unzip spm12.zip
```
Start MATLAB and add SPM into your path, either using:

File Set Path Add Folder...

or typing the following at the MATLAB prompt:
```
addpath /home/<login>/spm12
savepath % if you want to save the current MATLAB path
```

Crash at startup

The following concerns a situation where MATLAB generates a segmentation fault when opening the SPM interface with errors like:

BadWindow (invalid Window parameter)

serial 20133 error_code 3 request_code 20 minor_code 0

Pango-CRITICAL **: pango_font_description_from_string: assertion 'str != NULL' failed

GLib-CRITICAL **: g_once_init_leave: assertion 'result != 0' failed

GLib-GObject-CRITICAL **: g_type_register_dynamic: assertion 'parent_type > 0' failed

This is likely to be an issue with the display of the welcoming message in the Graphics window as a web document.

One fix is to comment one line in spm.m.. Another fix not requiring to modify the SPM source code is to define an environment variable.:

setenv('SPM_HTML_BROWSER','0')

Danger

If using the graphical interface, make sure to use the Add Folder... button and not Add with Subfolders.... SPM will automatically add the appropriate subfolders to the MATLAB path at runtime.

You can then launch SPM by typing spm at the MATLAB prompt.

Update¶

If you have just downloaded the spm12.zip archive, it already contains the latest set of updates. To update SPM when a new version is released:

Download spm12_updates_rxxxx.zip.
Uncompress spm12_updates_rxxxx.zip on top of the folder containing your SPM installation so that newer files overwrite existing files.

Alternatively, you can use the spm_update.m function:

spm_update

If a new version is available, it can be applied to your local installation by typing:

spm_update update