opm-preproc

OPM preprocessing pipeline built on mne-python and osl-ephys.

Grateful for advice from Lukas Rier and Robert Seymour.

Installation

git clone https://github.com/harrisonritz/opm-preproc.git
cd opm-preproc
conda env create -f environment.yml
conda activate opm-preproc

Core Functions

• src/opm_format_bids.py: BIDSify Cerca OPM data, annotating experimental events
• src/opm_preproc.py: run preprocessing pipeline for a single participant
  • set_participant_params(): set participant information
  • set_preproc_params(): set pipeline options
  • run_preproc(): run pipeline (top-level function)

Pipeline Steps

1. reject channels [osl]
2. harmonic field correction
3. temporal filter
4. continuous segment reject [osl]
5. fit ICA
6. epoch, apply ICA, and resample
7. reject epochs [osl]

todo

• source reconstruction
• argument handling for batch scripting