BIDS for MATLAB / Octave
This repository aims at centralising MATLAB/Octave tools to interact with datasets conforming to the BIDS (Brain Imaging Data Structure) format.
For more information about BIDS, visit https://bids.neuroimaging.io/.
Join our chat on the bids-matlab channel on the brainhack mattermost.
See also PyBIDS for Python and the BIDS Starter Kit.
Installation
Download this repository and add it to your MATLAB/Octave path.
unzip('https://github.com/bids-standard/bids-matlab/archive/master.zip');
addpath('bids-matlab-master');If your version of MATLAB/Octave does not support JSON natively, please also install SPM12 or JSONio.
Usage
BIDS = bids.layout('/home/data/ds000117');
bids.query(BIDS, 'subjects')A tutorial is available as a Jupyter Notebook and can be run interactively via Binder.
Requirements
BIDS-MATLAB works with MATLAB R2014a or newer, or Octave 4.2.2 or newer. (It may also work with older versions, but those are not actively supported.)
If you are using MATLAB R2016b or newer, nothing else needs to be installed.
If you are using MATLAB R2016a or older, or using Octave, you need to install a supported JSON library for your MATLAB or Octave. This can be any of:
Implementation
Starting point was spm_BIDS.m from SPM12 (documentation) reformatted in a +bids package with dependencies to other SPM functions removed.
Other tools (MATLAB only)
- dicm2nii: A DICOM to BIDS converter
- imtool3D_BIDS: A 3D viewer for BIDS directory
- Brainstorm: Comprehensive brain analysis toolbox (includes BIDS import and export and different examples dealing with BIDS datasets (e.g. group analysis from a MEG visual dataset, resting state analysis from OMEGA datasets )
Contributors ✨
Thanks goes to these wonderful people (emoji key):
 Guillaume 💻 🎨 📖 💡 🤔 🚇 🚧 💬 👀 |
 Remi Gau 💻 🎨 📖 💡 🤔 🚧 💬 👀 |
 Andrew Janke 💻 🎨 📖 🤔 |
 tanguyduval 💻 📖 🤔 |
 Robert Oostenveld 💻 📖 🤔 👀 |
This project follows the all-contributors specification. Contributions of any kind welcome!