analyse_OPMEG
Scripts to analyse data acquired from the OP-MEG Lab, UCL
Copyright (C) 2020-21 Wellcome Trust Centre for Neuroimaging
Authors:
- Robert Seymour (rob.seymour@ucl.ac.uk)
- Nic Alexander (n.alexander@ucl.ac.uk);
- Tim West
- George O’Neill
Load in data
Data from the UCL OP-MEG lab is stored in .bin format, with BIDS-compliant descriptor files, for example: channels.tsv, meg.json, coordinatesystem.json, positions.tsv.
Method 1:
%% Load the OPM data
% Read in the BIDS-organised raw data
disp('Loading data...');
cfg = [];
cfg.folder = data_dir; % This is overall BIDS directory
cfg.precision = 'single';
cfg.bids.task = 'aef';
cfg.bids.sub = '001';
cfg.bids.ses = '001';
cfg.bids.run = '001';
rawData = ft_opm_create(cfg);
Method 2:
%% Load the OPM data
% Read in the BIDS-organised raw data
disp('Loading data...');
cfg = [];
cfg.data = path_to_bin_file;
% (requires .json and _channels.tsv in same folder
% with same name as the .bin file)
rawData = ft_opm_create(cfg);
Calculate PSD
cfg = [];
cfg.channel = ft_channelselection('MEG',rawData,'qzfm_g2');
cfg.trial_length = 10;
cfg.method = 'tim';
cfg.foi = [0.1 150];
cfg.plot = 'yes';
cfg.plot_chans = 'yes';
cfg.plot_ci = 'no';
cfg.plot_legend = 'no';
cfg.transparency = 0.3;
[pow1 freq] = ft_opm_psd(cfg,rawData);
Compare PSDs (before and after pre-processing)
% Plot PSD
cfg = [];
cfg.channel = ft_channelselection('MEG',rawData,'qzfm_g2');
cfg.trial_length = 10;
cfg.method = 'tim';
cfg.foi = [0.1 100];
cfg.plot = 'yes';
cfg.plot_chans = 'yes';
cfg.plot_ci = 'no';
cfg.plot_legend = 'no';
cfg.transparency = 0.3;
[pow freq] = ft_opm_psd_compare(cfg,data1,data2);
Implemented Interference Suppression Algorithms
- HFC (Coming Soon)
- Zapline
- Synthetic Gradiometry
- Regress motion capture data from OPM data
Example Analysis Pipelines
Outlined in Seymour et al., (2021). Interference suppression techniques for OPM-based MEG: Opportunities and challenges. Under Review.
1. Auditory evoked field paradigm during participant movement
- Data: https://doi.org/10.5281/zenodo.5539414
- Script: pipeline_tutorial_1.m
2. Motor-beta power changes during a finger-tapping paradigm
- Data: https://doi.org/10.5281/zenodo.5539414
- Script: pipeline_tutorial_2.m
Other messier scripts can be found here: https://github.com/FIL-OPMEG/opm_benchmarking_2020