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ieeg

A repo of current preprocessing methods for the Cogan Lab

https://github.com/coganlab/ieeg_pipelines

Science Score: 62.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 11 committers (18.2%) from academic institutions
  • ✓
    Institutional organization owner
    Organization coganlab has institutional domain (coganlab.pages.oit.duke.edu)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary

Keywords

bids-apps eeg ieeg matlab neuroscience python
Last synced: 6 months ago · JSON representation ·

Repository

A repo of current preprocessing methods for the Cogan Lab

Basic Info
Statistics
  • Stars: 5
  • Watchers: 1
  • Forks: 2
  • Open Issues: 20
  • Releases: 0
Topics
bids-apps eeg ieeg matlab neuroscience python
Created almost 5 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Citation

README.md

IEEG_Pipelines

A repo of current preprocessing pipelines for the Cogan Lab

Brain

Documentation

Documentation Status

Lab Wiki

Pipeline Functionality

Python (3.10 - 3.13) on Windows/Linux/Mac

MATLAB latest

codecov

Installation

MATLAB

  1. Install MATLAB
  2. Clone this repository into your userpath (Documents/MATLAB by default)

  3. Run commands:

    MATLAB path = fullfile(userpath, 'IEEG_Pipelines', 'MATLAB'); addpath(genpath(path));

Python

Version 3.10 - 3.13 supported

Conda

  1. Install Anaconda

  2. Create an anaconda environment with python and pip packages installed

    bash conda create -n <YOUR_NAME> python<3.14 pip

  3. Activate the environment

    bash conda activate <YOUR_NAME>

  4. Run

    bash pip install ieeg

Pip

  1. Install Python

  2. Run:

    bash python -m venv <PATH TO VENV>/<YOUR_NAME> source activate <PATH TO VENV>/<YOUR_NAME> python -m pip install ieeg

Usage

MATLAB (INCOMPLETE)

  1. Load .dat file using convertOpenErec2mat.m
  2. Create the ieeg data structure from the ieegStructClass.m
  3. TBD

Python (INCOMPLETE)

  1. Load BIDS files from BIDS directory using pybids

    python from bids import BIDSLayout import ieeg layout = BIDSLayout(<BIDS_root>) data = ieeg.io.raw_from_layout(layout)

  2. Perform line noise filtering

  3. Check Spectrograms

  4. Plot the high gamma responses

  5. Run the cluster correction and permutation test

Owner

  • Name: coganlab
  • Login: coganlab
  • Kind: organization
  • Email: coganlab_github@googlegroups.com
  • Location: United States of America

Citation (citation.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Earle-Richardson
    given-names: Aaron
title: "IEEG_Pipelines"
version: 0.6.1
date-released: 2024-12-03

GitHub Events

Total
  • Create event: 4
  • Commit comment event: 1
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 1
  • Push event: 160
  • Pull request event: 8
Last Year
  • Create event: 4
  • Commit comment event: 1
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 1
  • Push event: 160
  • Pull request event: 8

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 943
  • Total Committers: 11
  • Avg Commits per committer: 85.727
  • Development Distribution Score (DDS): 0.507
Past Year
  • Commits: 375
  • Committers: 5
  • Avg Commits per committer: 75.0
  • Development Distribution Score (DDS): 0.211
Top Committers
Name Email Commits
Aaronearlerichardson j****1@g****m 465
Aaron Earle-Richardson J****1@g****m 368
Raymond Xiong r****4@g****m 49
dsuseendar@gmail.com 4****r 43
Aaron Earle-Richardson 3****n 6
Aaron Earle-Richardson a****6@d****u 4
Zac Spalding s****c@g****m 3
Jim j****5@g****m 2
Daniel Sexton d****3@d****u 1
Suseendrakumar Duraivel s****l@t****m 1
coganlab 8****b 1
Committer Domains (Top 20 + Academic)
duke.edu: 2 tneuro.com: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 67
  • Total pull requests: 89
  • Average time to close issues: 3 months
  • Average time to close pull requests: 10 days
  • Total issue authors: 6
  • Total pull request authors: 5
  • Average comments per issue: 0.55
  • Average comments per pull request: 0.27
  • Merged pull requests: 77
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 8
  • Average time to close issues: 1 day
  • Average time to close pull requests: 9 days
  • Issue authors: 2
  • Pull request authors: 3
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Aaronearlerichardson (37)
  • jimzhang629 (8)
  • coganlab (6)
  • rayarxti (2)
  • itsyuchao (1)
  • ncl24 (1)
Pull Request Authors
  • Aaronearlerichardson (72)
  • rayarxti (7)
  • jimzhang629 (5)
  • dsuseendar (4)
  • coganlab (2)
Top Labels
Issue Labels
bug (11) enhancement (9) documentation (6) good first issue (2)
Pull Request Labels
documentation (2) bug (1) enhancement (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 61 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 9
  • Total maintainers: 2
pypi.org: ieeg

A Python package for iEEG data processing.

  • Homepage: https://github.com/coganlab/IEEG_Pipelines
  • Documentation: https://ieeg-pipelines.readthedocs.io/en/latest/
  • License: MIT License Copyright (c) 2023 coganlab Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  • Latest release: 0.7.0
    published 8 months ago
  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 61 Last month
Rankings
Dependent packages count: 9.5%
Average: 36.1%
Dependent repos count: 62.7%
Maintainers (2)
Aaronearlerichardson rayarxti
Last synced: 6 months ago

Dependencies

envs/environment.yml pypi
.github/workflows/MATLAB-CI.yml actions
  • actions/checkout v2 composite
  • matlab-actions/run-tests v1 composite
  • matlab-actions/setup-matlab v1 composite
.github/workflows/Python-CI.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • codecov/codecov-action v3 composite
  • conda-incubator/setup-miniconda v2 composite
  • pyvista/setup-headless-display-action main composite
envs/requirements.txt pypi
  • EDFlib-Python *
  • bids >=0.0
  • coverage *
  • dipy *
  • h5io *
  • joblib *
  • matplotlib *
  • mne-bids *
  • mne-qt-browser *
  • naplib *
  • nipype *
  • numpy *
  • pandas *
  • psutil *
  • pytest *
  • pytest-cov *
  • pytest-pycodestyle *
  • pytest-xdist *
  • pytz *
  • pyvistaqt *
  • scikit-image *
  • scipy *
  • tqdm *