spm-python 25.1a1.dev1

Python bindings for the SPM software.

   ___  ____  __  __
  / __)(  _ \(  \/  )  
  \__ \ )___/ )    (   Statistical Parametric Mapping
  (___/(__)  (_/\/\_)  SPM - https://www.fil.ion.ucl.ac.uk/spm/

Copyright (C) 1991,1994-2024 Wellcome Centre for Human Neuroimaging

Python bindings for SPM

[!WARNING] This project is currently under construction and might contain bugs. If you experience any issues, please let us know!

Installation instructions:

0. Install Python and Pip. Python installation made from Microsoft Store on Windows will not work (raises DeclarativeService.dll not found), intall it from Python website.
1. Install Matlab Runtime 2024b
2. Install SPM:

   pip install git+https://github.com/spm/spm-python.git
   

3. That's all!

Minimal example

Here is a minimal set of examples showcasing changes to do to use existing Matlab code in Python (taken from the OPM tutorial).

1. Importing and setting up SPM

In Matlab:

 spm('defaults', 'eeg');

In Python:

from spm import *
spm('defaults', 'eeg');

2. Constructing objects

In Matlab:

S = [];
S.data = 'OPM_meg_001.cMEG';
S.positions = 'OPM_HelmConfig.tsv';
D = spm_opm_create(S);

In Python, create a Struct() instead of a struct:

S = Struct()
S.data='OPM_meg_001.cMEG'
S.positions='OPM_HelmConfig.tsv'
D = spm_opm_create(S)

Here, D will be a meeg object which contains a virtual representation of the Matlab object. Class methods should work as expected, e.g.:

D.fullfile()
>>> './OPM_meg_001.mat'

Note that the alternative call that exist in Matlab (i.e., fullfile(D)) will not work.

3. Creating and handling figures

In Matlab:

S = [];
S.triallength = 3000; 
S.plot = 1;
S.D = D;
S.channels = 'MEG';
spm_opm_psd(S);
ylim([1,1e5])

In Python:

S = Struct()
S.triallength = 3000
S.plot = 1
S.D = D
S.channels = 'MEG'
spm_opm_psd(S)

This opens a Matlab figure, but we do not have the possibility of manipulating it yet (e.g., calling ylim). As of now, we can view the figures, have GUI interactions, but cannot manipulate figures with Python code.

4. Variable number of output arguments

In Matlab:

S = [];
S.triallength = 3000; 
S.plot = 1;
S.D = mD;
[~,freq] = spm_opm_psd(S);

In Python, the number of output arguments must be specified by the nargout keyword argument:

S = Struct()
S.triallength = 3000
S.plot=1
S.D=mD
[_,freq] = spm_opm_psd(S, nargout=2)

5. Other examples

In Matlab:

S=[];
S.D=D;
S.freq=[10];
S.band = 'high';
fD = spm_eeg_ffilter(S);

S = [];
S.D = fD;
S.freq = [70];
S.band = 'low';
fD = spm_eeg_ffilter(S);

In Python:

S = Struct()
S.D = D
S.freq = 10
S.band = 'high'
fD = spm_eeg_ffilter(S)

S = Struct()
S.D = fD
S.freq = 70
S.band = 'low'
fD = spm_eeg_ffilter(S)