IEEG_Pipelines

A repo of current preprocessing pipelines for the Cogan Lab

Documentation

Pipeline Functionality

Installation

MATLAB

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

Run commands:

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

Python

Version 3.10 - 3.13 supported

Conda

Install Anaconda
Create an anaconda environment with python and pip packages installed
```
conda create -n <YOUR_NAME> python<3.14 pip
```
Activate the environment
```
conda activate <YOUR_NAME>
```
Run
```
pip install ieeg
```

Pip

Install Python

Run:

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

Usage

MATLAB (INCOMPLETE)

Load .dat file using convert_OpenE_rec2mat.m
Create the ieeg data structure from the ieegStructClass.m
TBD

Python (INCOMPLETE)

Load BIDS files from BIDS directory using pybids

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

Perform line noise filtering
Check Spectrograms
Plot the high gamma responses
Run the cluster correction and permutation test

Metadata

Release files for ieeg 0.7.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for ieeg 0.7.0
File	Size	Uploaded
ieeg-0.7.0.tar.gz	620.1 kB	Jun 24, 2025	Details

Built distributions (wheels)

Table of built distributions (wheels) for ieeg 0.7.0
File	Interpreter	ABI	Platform	Reset
ieeg-0.7.0-cp310-cp310-musllinux_1_2_x86_64.whl 1.7 MB Jun 24, 2025	CPython 3.10	CPython 3.10	Linux musl 1.2+ x86-64	Details
ieeg-0.7.0-cp310-cp310-musllinux_1_2_i686.whl 1.7 MB Jun 24, 2025	CPython 3.10	CPython 3.10	Linux musl 1.2+ x86-32	Details
ieeg-0.7.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 1.6 MB Jun 24, 2025	CPython 3.10	CPython 3.10	Linux glibc 2.17+ x86-64	Details
ieeg-0.7.0-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl 1.6 MB Jun 24, 2025	CPython 3.10	CPython 3.10	Linux glibc 2.17+ x86-32, Linux glibc 2.5+ x86-32	Details

Total release size: 7.2 MB

Release files / ieeg-0.7.0.tar.gz

Download URL	ieeg-0.7.0.tar.gz
Size	620.1 kB
Tags	Source
SHA-256 checksum How to use checksums	`847ddb9b4d1d829035a5eb4cd341a814ce9c8983236f5a288e5d48849f1099ed`
BLAKE2b-256 checksum How to use checksums	`1b7154e0572ef712fc32c39c8a8c6eed975d6bd1e359eb1d6caade082f1520d5`
Upload date	Jun 24, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/coganlab/IEEG_Pipelines
Publishing commit: github.com/coganlab/IEEG_Pipelines/tree/b2ad2c8ec842419f00db1c59af1373fbb75dce34

Workflow

Publishing configuration: github.com/coganlab/IEEG_Pipelines/blob/b2ad2c8ec842419f00db1c59af1373fbb75dce34/.github/workflows/Package.yml
Publishing logs: github.com/coganlab/IEEG_Pipelines/actions/runs/15854323407/attempts/1

Artifact

Subject: ieeg-0.7.0.tar.gz
SHA-256 checksum: 847ddb9b4d1d829035a5eb4cd341a814ce9c8983236f5a288e5d48849f1099ed Verifying attestations

Release files / ieeg-0.7.0-cp310-cp310-musllinux_1_2_x86_64.whl

Download URL	ieeg-0.7.0-cp310-cp310-musllinux_1_2_x86_64.whl
Size	1.7 MB
Tags	CPython 3.10 Linux musl 1.2+ x86-64
SHA-256 checksum How to use checksums	`246c536e87f03659aa7d7b46b01c882f7a18cb19ae9c35b1a4fba6ef40001789`
BLAKE2b-256 checksum How to use checksums	`a258d544f6beeda010ceb2ba4d00a472fd2deca31c8d1734e8bfcb71898896d6`
Upload date	Jun 24, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/coganlab/IEEG_Pipelines
Publishing commit: github.com/coganlab/IEEG_Pipelines/tree/b2ad2c8ec842419f00db1c59af1373fbb75dce34

Workflow

Publishing configuration: github.com/coganlab/IEEG_Pipelines/blob/b2ad2c8ec842419f00db1c59af1373fbb75dce34/.github/workflows/Package.yml
Publishing logs: github.com/coganlab/IEEG_Pipelines/actions/runs/15854323407/attempts/1

Artifact

Subject: ieeg-0.7.0-cp310-cp310-musllinux_1_2_x86_64.whl
SHA-256 checksum: 246c536e87f03659aa7d7b46b01c882f7a18cb19ae9c35b1a4fba6ef40001789 Verifying attestations

Release files / ieeg-0.7.0-cp310-cp310-musllinux_1_2_i686.whl

Download URL	ieeg-0.7.0-cp310-cp310-musllinux_1_2_i686.whl
Size	1.7 MB
Tags	CPython 3.10 Linux musl 1.2+ x86-32
SHA-256 checksum How to use checksums	`3e28644a9bf196a58113780b89608547e17ec2ea8d13f8cf5131288efe6be5db`
BLAKE2b-256 checksum How to use checksums	`55af4092165b629cf1d93c80a59c3c19b358483ac98c6247d179f7a090520b19`
Upload date	Jun 24, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/coganlab/IEEG_Pipelines
Publishing commit: github.com/coganlab/IEEG_Pipelines/tree/b2ad2c8ec842419f00db1c59af1373fbb75dce34

Workflow

Publishing configuration: github.com/coganlab/IEEG_Pipelines/blob/b2ad2c8ec842419f00db1c59af1373fbb75dce34/.github/workflows/Package.yml
Publishing logs: github.com/coganlab/IEEG_Pipelines/actions/runs/15854323407/attempts/1

Artifact

Subject: ieeg-0.7.0-cp310-cp310-musllinux_1_2_i686.whl
SHA-256 checksum: 3e28644a9bf196a58113780b89608547e17ec2ea8d13f8cf5131288efe6be5db Verifying attestations

Release files / ieeg-0.7.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Download URL	ieeg-0.7.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Size	1.6 MB
Tags	CPython 3.10 Linux glibc 2.17+ x86-64
SHA-256 checksum How to use checksums	`3141bebeac4ce8a86d08249a25708b0040181bb4fac3c4b8da77518864330f3a`
BLAKE2b-256 checksum How to use checksums	`a715c5bab254cfc86a1838167150b5eb255281d45bef62cfce254d595cf0082b`
Upload date	Jun 24, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/coganlab/IEEG_Pipelines
Publishing commit: github.com/coganlab/IEEG_Pipelines/tree/b2ad2c8ec842419f00db1c59af1373fbb75dce34

Workflow

Publishing configuration: github.com/coganlab/IEEG_Pipelines/blob/b2ad2c8ec842419f00db1c59af1373fbb75dce34/.github/workflows/Package.yml
Publishing logs: github.com/coganlab/IEEG_Pipelines/actions/runs/15854323407/attempts/1

Artifact

Subject: ieeg-0.7.0-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
SHA-256 checksum: 3141bebeac4ce8a86d08249a25708b0040181bb4fac3c4b8da77518864330f3a Verifying attestations

Release files / ieeg-0.7.0-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl

Download URL	ieeg-0.7.0-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl
Size	1.6 MB
Tags	CPython 3.10 Linux glibc 2.17+ x86-32 Linux glibc 2.5+ x86-32
SHA-256 checksum How to use checksums	`b402064e475a628d86c2a55c1956fcd040e8aee9834bd813b0811c7a4e133b00`
BLAKE2b-256 checksum How to use checksums	`422dd1257c0e381876bab54622a6385559b2ec9661e0a9d1185efaeb4786c77d`
Upload date	Jun 24, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/coganlab/IEEG_Pipelines
Publishing commit: github.com/coganlab/IEEG_Pipelines/tree/b2ad2c8ec842419f00db1c59af1373fbb75dce34

Workflow

Publishing configuration: github.com/coganlab/IEEG_Pipelines/blob/b2ad2c8ec842419f00db1c59af1373fbb75dce34/.github/workflows/Package.yml
Publishing logs: github.com/coganlab/IEEG_Pipelines/actions/runs/15854323407/attempts/1

Artifact

Subject: ieeg-0.7.0-cp310-cp310-manylinux1_i686.manylinux2014_i686.manylinux_2_17_i686.manylinux_2_5_i686.whl
SHA-256 checksum: b402064e475a628d86c2a55c1956fcd040e8aee9834bd813b0811c7a4e133b00 Verifying attestations