CPP_BIDS

A set of function for matlab and octave to create BIDS-compatible folder structure and filenames for the output of behavioral, EEG, fMRI, eyetracking studies.

Installation

Use the CPP templates for PsychToolBox experiments

The easiest way to use this repository is to create a new repository by using the template PTB experiment repository: this creates a new repository on your github account with all the basic folders, files and submodules (including CPP_BIDS) already set up. You only have to then clone the repository and you are good to go.

Download with git

cd fullpath_to_directory_where_to_install

# use git to download the code and the submodules
git clone --recurse-submodules https://github.com/cpp-lln-lab/CPP_BIDS.git

Then get the latest commit:

# from the directory where you downloaded the code
git pull origin master

To work with a specific version, create a branch at a specific version tag number

# creating and checking out a branch that will be called version1 at the version tag v0.0.1
git checkout -b version1 v2.2.1

Add as a submodule

Add it as a submodule in the repo you are working on.

cd fullpath_to_directory_where_to_install

# use git to download the code
git submodule add https://github.com/cpp-lln-lab/CPP_BIDS.git

To get the latest commit you then need to update the submodule with the information on its remote repository and then merge those locally.

git submodule update --remote --merge

Remember that updates to submodules need to be committed as well.

Example

So say you want to clone a repo that has some nested submodules, then you would type this to get the content of all the submodules at once (here with assumption that you want to clone my experiment repo):

# clone the repo
git clone https://github.com/user_name/myExperiment.git

# go into the directory
cd myExperiment

# initialize and get the content of the first level of submodules
git submodule init
git submodule update

# get the nested submodules JSONio and BIDS-matlab for CPP_BIDS
git submodule foreach --recursive 'git submodule init'
git submodule foreach --recursive 'git submodule update'

Demos

How to use it: jupyter notebooks

Documentation

General documentation

Contributing

Feel free to open issues to report a bug and ask for improvements.

If you want to contribute, have a look at our contributing guidelines that are meant to guide you and help you get started. If something is not clear or you get stuck: it is more likely we did not do good enough a job at explaining things. So do not hesitate to open an issue, just to ask for clarification.