Installation#

Requirements#

This SPM toolbox runs with Matlab and Octave.

Dependencies

Minimum required

Used for testing in CI

MATLAB

2014

2023b on Ubuntu 22.04, Windowns and MacOS

Octave

6.4.0

6.4.0 on Ubuntu 22.04

SPM12

7219

7771

Some functionalities require some extra SPM toolbox to work: for example the ALI toolbox for brain lesion segmentation.

Installation#

If you are only going to use this toolbox for a new analysis and you are not planning to edit the code base of bidspm itself, we STRONGLY suggest you use this template repository to create a new project with a basic structure of folders and with the bidspm code already set up.

Otherwise you can clone the repo with all its dependencies with the following git command:

git clone --recurse-submodules https://github.com/cpp-lln-lab/bidspm.git

If you need the latest development, then you must clone from the dev branch:

Initialization#

Warning

In general DO NOT ADD bidspm PERMANENTLY to your MATLAB / Octave path.

You just need to initialize for a given session with:

bidspm()

This will add all the required folders to the path.

You can also remove bidspm from the path with:

bidspm uninit

BIDS app Command line Interface (CLI)#

bidspm comes with a BIDS app CLI.

Requirements#

If you are using MATLAB, you need to edit the file src/matlab.py, so that it returns the fullpath to the MATLAB executable on your computer.

For this you first need to know where is the MATLAB application. Here are the typical location depending on your operating system (where XXx corresponds to the version you use).

  • Windows: C:\Program Files\MATLAB\R20XXx\bin\matlab.exe

  • Mac: /Applications/Matlab_R20XXx.app/bin/matlab

  • Linux: /usr/local/MATLAB/R20XXx/bin/matlab

You can then install the bidspm CLI from within the bidspm folder with:

pip install .

You can then type the following in your terminal to see which command you have access to:

bidspm --help

BIDS validation#

After installing bidspm python package, you can get access to extra validation options.

BIDS stats model validation#

Please see the documentation

BIDS dataset validation#

To run the bids-validator when running bidspm, you will need:

You can then install:

  • the bids validator

by running from the command line in the root folder of the repository:

make install

or

npm install -g bids-validator

Octave compatibility#

The following features do not yet work with Octave:

Not (yet) tested with Octave:

  • MACS toolbox workflow for model selection

  • ALI toolbox workflow for model selection