Outputs

Outputs#

MEGPrep writes Nextflow execution files under output_dir and processing derivatives under preproc_dir. By default:

preproc_dir = ${params.output_dir}/preprocessed

Top-Level Output Layout#

Path

Description

<output_dir>/work/

Nextflow work directory.

<output_dir>/report.html

Nextflow execution report when run through the Docker entrypoint.

<output_dir>/timeline.html

Nextflow timeline when run through the Docker entrypoint.

<output_dir>/trace.txt

Nextflow process trace. The static report uses it to populate per-subject Task Details when available.

<output_dir>/nextflow.config

Effective config copied from the Docker run config.

<output_dir>/static_html_report/

Portable MEGPrep QC report. Depending on static_task_log_mode, this may include packaged Nextflow .command* log excerpts.

<output_dir>/preprocessed/

MEGPrep processing derivatives.

Preprocessed Directory#

Path

Contents

preprocessed/<recording>/

Continuous preprocessed raw files, ICA-clean raw files, and selected QA plots.

preprocessed/artifact_report/<recording>/

Bad-channel files, bad-segment annotation files, and artifact review images.

preprocessed/ica_report/<recording>/

ICA model, component labels, ECG/EOG score files, component figures, and overlay/PSD plots.

preprocessed/epochs/<recording>/

Epoch FIF files, rejection logs, and epoch-level figures.

preprocessed/covariance/<recording>/

Noise covariance FIF file and covariance visualization figures.

preprocessed/trans/<recording>/

MEG-MRI transform, coregistration distance CSV, and staged coregistration figures.

preprocessed/forward_solution/<recording>/

Forward model outputs and head model figures.

preprocessed/source_recon/<recording>/

Source reconstruction outputs and visualization figures.

preprocessed/logs/

Nextflow log, MEGPrep run manifest, and config snapshots when available.

preprocessed/deepprep/

DeepPrep outputs when anatomy_preprocess_method = "deepprep" and anatomy processing is enabled.

Important Sidecar Files#

File pattern

Meaning

*_preproc-raw.fif

Continuous output from OSL preprocessing.

*_bad_channels.txt

One bad channel name per line.

*_bad_segments.txt

MNE annotation file containing bad time spans.

*_ica.fif

Fitted ICA model.

marked_components.txt

ICA component indices selected for exclusion.

ecg_eog_scores.json

ECG/EOG candidate indices and scores when produced by ICA labeling.

*_clean_raw.fif

Continuous raw file after ICA application.

*-epo.fif

Epoch output.

*_reject_epoch_log.txt

Rejected epoch indices and estimated remaining epoch count.

bl-cov.fif

Noise covariance estimate.

dists.csv

Coregistration distance summary in mm.

coreg-trans.fif

MEG-MRI transform used by forward modeling.

megprep_run_manifest.json

Pipeline mode, selected stages, path snapshot, and runtime metadata.

The exact set of outputs depends on params.steps. For example, meg_artifacts does not produce ICA, epoch, covariance, forward, or source outputs, while report only rebuilds the static report from existing files.

Contents