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bioRxiv · 10.64898/2026.06.03.729876

The ENIGMA MEG Pipeline: Automated cortically localized spectral analysis of multi-site resting state MEG datasets

Nugent, A. C.·Namyst, A. M.·Carver, F. W.·Thompson, P. M.·Stout, J. D.
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Abstract

BackgroundMagnetoencephalography (MEG) is a unique technique in human neuroimaging combining high temporal resolution (millisecond or faster) with moderate spatial resolution (several millimeter). While many software packages for MEG data analysis exist, there is no pipeline developed for the specific purpose of enabling the automated analysis of very large, multi-site datasets. ResultsThe ENIGMA consortium was developed to enable large scale collaborations in the fields of neuroimaging and genetics. To facilitate ENIGMA MEG working group data analysis, we developed the ENIGMA MEG pipeline. The first ENIGMA MEG working group project involves spectral analysis of resting state MEG data, thus our current pipeline is designed to carry out that task. The goals of the ENIGMA MEG pipeline include ease of use, automated processing wherever possible, detailed logging and quality assurance (QA) features, the use of the brain imaging data structure (BIDS) format, anonymized output, and consistent processing across vendors. The pipeline is built using the MNE-Python framework and incorporates a re-trained version of the MEGnet deep neural network algorithm for automated artifact detection. QA tools are designed to enable high throughput evaluation of a large number of subject datasets. All software is open source and available on GitHub (https://github.com/nih-megcore/enigma_MEG). We used our pipeline to process data from three publicly available MEG cohorts, demonstrating its functionality and compatibility with large-scale processing. ConclusionsWhile the current ENIGMA pipeline is limited to resting state data and spectral analysis for the current working group project, the software is highly modularized, allowing straightforward extension to other analysis questions. Further development of the tool to enable connectivity and task-based MEG analysis are planned. The ENIGMA MEG pipeline represents an important first step to augment the existing arsenal of analysis tools, enabling multi-site, high throughput data analysis.

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Nugent, A. C., Namyst, A. M., Carver, F. W., Thompson, P. M., Stout, J. D.. 2026-06-08. The ENIGMA MEG Pipeline: Automated cortically localized spectral analysis of multi-site resting state MEG datasets. https://doi.org/10.64898/2026.06.03.729876

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