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UnfoldBIDS

https://github.com/unfoldtoolbox/unfoldbids.jl

Science Score: 44.0%

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    Found CITATION.cff file
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    Scientific vocabulary similarity
    Low similarity (11.7%) to scientific vocabulary

Keywords

bids eeg julia modeling
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: unfoldtoolbox
  • License: mit
  • Language: Julia
  • Default Branch: main
  • Homepage:
  • Size: 2.56 MB
Statistics
  • Stars: 8
  • Watchers: 4
  • Forks: 3
  • Open Issues: 14
  • Releases: 6
Topics
bids eeg julia modeling
Created about 4 years ago · Last pushed 9 months ago
Metadata Files
Readme License Citation

README.md

UnfoldBIDS

Dev Build Status Coverage

|Estimation|Visualisation|Simulation|BIDS pipeline|Decoding|Statistics|MixedModelling| |---|---|---|---|---|---|---| | Unfold.jl Logo | UnfoldMakie.jl Logo|UnfoldSim.jl Logo|UnfoldBIDS.jl Logo|UnfoldDecode.jl Logo|UnfoldStats.jl Logo|UnfoldMixedModels.jl logo|

Sub/Wrapper-Package of Unfold.jl to automatically load a Dataset in BIDS format and apply unfold-style processing to all participants in one go. Additionally gives the means to apply MNE preprocessing.

Install

Installing Julia

Click to expand The recommended way to install julia is [juliaup](https://github.com/JuliaLang/juliaup). It allows you to, e.g., easily update Julia at a later point, but also test out alpha/beta versions etc. TL:DR; If you dont want to read the explicit instructions, just copy the following command #### Windows AppStore -> JuliaUp, or `winget install julia -s msstore` in CMD #### Mac & Linux `curl -fsSL https://install.julialang.org | sh` in any shell

Installing Unfold

julia using Pkg Pkg.add("UnfoldBIDS")

Quickstart

julia using UnfoldBIDS

Look up the paths of all subjects and store in a Dataframe

Note: UnfoldBIDS.jl currently only works on paths and filenames, but ignores information from .json files.

```julia layoutdf = bidslayout(bidsPath::AbstractString; kwargs) """

Input

bidsPath::AbstractString; # Path to BIDS root folder

Kwargs

  • derivatives::Bool=true: Do you want to us the derivative/ processed data?
  • specific_folder::Union{Nothing,AbstractString}=nothing: If you want a specific folder in derivatives or root specify here
  • exclude_folder::Union{Nothing,AbstractString}=nothing: You can exclude specific folders when not looking for a specific sub-folder
  • ses::Union{Nothing,AbstractString}=nothing: Specify session; will load all sessions if not specified
  • task::Union{Nothing,AbstractString}=nothing: Specify task; will load all tasks if not specified
  • run::Union{Nothing,AbstractString}=nothing): Specify run; will load all runs if not specified

""" ```

Load all data into memory/ one dataframe:

julia eeg_df = load_bids_eeg_data(layout_df; verbose::Bool=true, kwargs...)

Run Unfold model

julia models_df = run_unfold(eeg_df, bf_dict; eventcolumn="event", removeTimeexpandedXs=true, extract_data = raw_to_data, verbose::Bool=true, kwargs...) (bf_dict = basis functions dictionary; see Unfold.jl):

For dataframe containing tidy results

julia results_df = bids_coeftable(models_df)

Unpack single subject tidy results into one big tidy DataFrame, with subject information

julia results = unpack_results(results_df)

Supported EEG file types

  • edf
  • vhdr
  • fif
  • set

Contributions

Contributions are very welcome. These could be typos, bugreports, feature-requests, speed-optimization, new solvers, better code, better documentation.

How-to Contribute

You are very welcome to raise issues and start pull requests!

Adding Documentation

  1. We recommend to write a Literate.jl document and place it in docs/literate/FOLDER/FILENAME.jl with FOLDER being HowTo, Explanation, Tutorial or Reference (recommended reading on the 4 categories).
  2. Literate.jl converts the .jl file to a .md automatically and places it in docs/src/generated/FOLDER/FILENAME.md.
  3. Edit make.jl with a reference to docs/src/generated/FOLDER/FILENAME.md.

Contributors

Benedikt Ehinger
Benedikt Ehinger
🐛 💻 📆 🤔		 René Skukies
René Skukies
👀 🤔 💻 🐛

This project follows the all-contributors specification.

Contributions of any kind welcome! You can find the emoji key for the contributors here

Citation

Acknowledgements

Funded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany´s Excellence Strategy – EXC 2075 – 390740016

Owner

  • Name: unfoldtoolbox
  • Login: unfoldtoolbox
  • Kind: organization
  • Email: info@unfoldtoolbox.org

Unfold your potentials...

Citation (CITATION.bib) 

@misc{UnfoldBIDS.jl,
	author  = {Rene Skukies, Benedikt Ehinger, Jan Haas},
	title   = {UnfoldBIDS.jl},
	url     = {https://github.com/reneskukies/UnfoldBIDS.jl},
	version = {v0.1.0},
	year    = {2021},
	month   = {12}
}

GitHub Events

Total
  • Create event: 10
  • Release event: 4
  • Issues event: 16
  • Watch event: 5
  • Delete event: 7
  • Issue comment event: 24
  • Push event: 74
  • Pull request review event: 3
  • Pull request review comment event: 4
  • Pull request event: 12
Last Year
  • Create event: 10
  • Release event: 4
  • Issues event: 16
  • Watch event: 5
  • Delete event: 7
  • Issue comment event: 24
  • Push event: 74
  • Pull request review event: 3
  • Pull request review comment event: 4
  • Pull request event: 12

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 3
  • Total pull requests: 7
  • Average time to close issues: 7 months
  • Average time to close pull requests: 15 days
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 0.67
  • Average comments per pull request: 0.43
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 7
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 15 days
  • Issue authors: 2
  • Pull request authors: 3
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.43
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ReneSkukies (17)
  • behinger (5)
  • JuliaTagBot (1)
Pull Request Authors
  • ReneSkukies (10)
  • allcontributors[bot] (5)
  • behinger (2)
  • xuyg16 (2)
Top Labels
Issue Labels
enhancement (10) bug (5) documentation (2)
Pull Request Labels
bug (2) enhancement (1)

Packages

  • Total packages: 1
  • Total downloads:
    • julia 2 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
juliahub.com: UnfoldBIDS
  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 2 Total
Rankings
Dependent repos count: 9.6%
Average: 24.1%
Dependent packages count: 38.7%
Last synced: 6 months ago

Dependencies

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.github/workflows/CompatHelper.yml actions
.github/workflows/TagBot.yml actions
  • JuliaRegistries/TagBot v1 composite