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cpp_bids

a set of matlab / octave function to create BIDS comptible folder structure and filenames

https://github.com/cpp-lln-lab/cpp_bids

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
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  • ○
    Scientific vocabulary similarity
    Low similarity (14.1%) to scientific vocabulary

Keywords

bids eeg eyetracker fmri matlab octave
Last synced: 6 months ago · JSON representation ·

Repository

a set of matlab / octave function to create BIDS comptible folder structure and filenames

Basic Info
Statistics
  • Stars: 1
  • Watchers: 4
  • Forks: 9
  • Open Issues: 14
  • Releases: 7
Topics
bids eeg eyetracker fmri matlab octave
Created almost 6 years ago · Last pushed 12 months ago
Metadata Files
Readme License Citation

README.md

Binder Documentation Status: stable DOI codecov All Contributors

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

```bash cd fullpathtodirectorywhereto_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:

```bash

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

```bash

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.

```bash cd fullpathtodirectorywhereto_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.

bash 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):

```bash

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.

Contributors ✨

Thanks goes to these wonderful people (emoji key):


CerenB
💻 🎨 📖 📓 🤔 🐛
marcobarilari
💻 🎨 📖 📓 🤔 🐛
Remi Gau
💻 🎨 📖 🐛 📓 🤔 🚇 🚧 ⚠️ 💬
Tomas Lenc
💻 🤔 ⚠️
iqrashahzad14
🐛 ⚠️

This project follows the all-contributors specification. Contributions of any kind welcome!

Owner

  • Name: Crossmodal Perception and Plasticity laboratory
  • Login: cpp-lln-lab
  • Kind: organization
  • Location: Louvain la Neuve, Belgium

Citation (CITATION.cff) 

cff-version: 1.2.0

title: "CPP BIDS"

version: 2.2.0

abstract: A lightweight Octave/MATLAB toolbox to help create BIDS data sets from source.

message: "If you use this software, please cite it as below."

repository-code: "https://github.com/cpp-lln-lab/CPP_BIDS"

identifiers:
  - description: This is the collection of archived snapshots of all releases of CPP BIDS
    type: doi
    value: "10.5281/zenodo.4007674"

contact:
  - affiliation: "Université catholique de Louvain"
    email: remi.gau@uclouvain.be
    family-names: Gau
    given-names: Rémi

authors:
- family-names: "Gau"
  given-names: "Rémi"
  orcid: "https://orcid.org/0000-0002-1535-9767"
  affiliation: "Université catholique de Louvain"

- family-names: "Barilari"
  given-names: "Marco"
  orcid: "https://orcid.org/0000-0002-3313-3120"
  affiliation: "Université catholique de Louvain"

- family-names: "Battal"
  given-names: "Ceren"
  orcid: "https://orcid.org/0000-0002-9844-7630"
  affiliation: "Université catholique de Louvain"


- family-names: "Lenc"
  given-names: "Thomas"
  orcid: "https://orcid.org/0000-0001-5796-1388"
  affiliation: "Université catholique de Louvain"

license: MIT

keywords:
  - BIDS
  - brain imaging data structure
  - neuroscience
  - MATLAB
  - Octave

GitHub Events

Total
  • Delete event: 7
  • Push event: 6
  • Pull request event: 13
  • Create event: 8
Last Year
  • Delete event: 7
  • Push event: 6
  • Pull request event: 13
  • Create event: 8

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 20
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 month
  • Total issue authors: 0
  • Total pull request authors: 4
  • Average comments per issue: 0
  • Average comments per pull request: 0.1
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 18
Past Year
  • Issues: 0
  • Pull requests: 8
  • Average time to close issues: N/A
  • Average time to close pull requests: 14 days
  • Issue authors: 0
  • Pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 7
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Top Authors
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  • dependabot[bot] (14)
  • pre-commit-ci[bot] (5)
  • Remi-Gau (1)
  • marcobarilari (1)
Top Labels
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dependencies (14) github_actions (14)

Dependencies

binder/environment.yml conda
  • octave_kernel
requirements.txt pypi
  • Sphinx *
  • miss_hit ==0.9.29
  • notebook *
  • octave_kernel *
  • sphinx_rtd_theme *
  • sphinxcontrib-matlabdomain *
  • sphinxcontrib-napoleon *
.github/workflows/bids_validator.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
.github/workflows/check_md_links.yml actions
  • actions/checkout v3 composite
  • gaurav-nelson/github-action-markdown-link-check v1 composite
.github/workflows/codespell.yml actions
  • actions/checkout v3 composite
  • codespell-project/actions-codespell master composite
.github/workflows/run_tests.yml actions
  • actions/checkout v3 composite
  • codecov/codecov-action v3 composite
  • joergbrech/moxunit-action v1.2.0 composite