app-rereference

This is an app that takes EEG data in MNE Epochs format and recomputes the reference from collection mode to chosen (defaults to average reference)

1. Input file is mne/Epochs
2. Input is a choice of average, REST (Reference Electrode Standardization Technique infinity reference), or a list of channels to use.
3. The output file is mne/Epochs, as well.

Authors

• Kamilya Salibayeva

Copyright (c) 2022 brainlife.io The University of Texas at Austin

Funding Acknowledgement

brainlife.io is publicly funded and for the sustainability of the project it is helpful to Acknowledge the use of the platform. We kindly ask that you acknowledge the funding below in your code and publications. Copy and past the following lines into your repository when using this code.

Citations

We ask that you the following articles when publishing papers that used data, code or other resources created by the brainlife.io community.

1. Avesani, P., McPherson, B., Hayashi, S. et al. The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services. Sci Data 6, 69 (2019). https://doi.org/10.1038/s41597-019-0073-y

Running the App

On Brainlife.io

You can submit this App online at https://doi.org/10.25663/bl.app.444 via the "Execute" tab.

Running Locally (on your machine)

1. git clone this repo.
2. Inside the cloned directory, create config.json with something like the following content with paths to your input files.

{
"t1": "t1.nii.gz"
}

3. Launch the App by executing main

./main

Sample Datasets

If you don't have your own input file, you can download sample datasets from Brainlife.io, or you can use Brainlife CLI.

npm install -g brainlife
bl login
mkdir input
bl dataset download 5a0f0fad2c214c9ba8624376#5a050966eec2b300611abff2 && mv 5a0f0fad2c214c9ba8624376#5a050966eec2b300611abff2 .

Output

All output file (a resampled T1w NIFTI-1 file) will be generated inside the current working directory (pwd), inside a specifc directory called:

out_dir

Dependencies

This App requires MNE/Python to run.