Drop Bad Epochs

Description

Drops (rejects) bad epochs from MNE Epochs files by their indices using MNE-Python's Epochs.drop() method. This app is useful for:

• Removing epochs marked as artifacts or bad quality
• Removing epochs by index from a separate quality control analysis
• Cleaning up epoched data for subsequent analysis

The app generates:

• An epochs file with the specified epochs removed
• A text summary of the dropped epochs
• An HTML report with before/after epoch visualizations
• A product.json with metadata about the dropped epochs

Inputs

• mne (neuro/meeg/mne/epochs): epoched file to remove epochs from (required)
• events (neuro/meg/fif-override): special-case input whose events.tsv contains a single line of comma-separated indices of bad trials to drop (optional)

Outputs

• out_dir/meg-epo.fif (neuro/meeg/mne/epochs): epochs file with the specified epochs removed
• out_dir/info.txt: summary of dropped and remaining epochs
• out_figs/: PNG plots of epochs before dropping and of the epochs dropped from the events file / drop config
• out_report/report.html: HTML report with the original, dropped, and remaining epochs
• product.json: metadata about dropped epochs

Configuration Parameters

key	type	default	description
mne	input (neuro/meeg/mne/epochs)	required	path to the input MNE epochs file (.fif format)
events	input (neuro/meg/fif-override)	"" (optional)	path to an events.tsv-style file whose contents are a comma-separated list of epoch indices to drop
drop	string	"" (optional)	comma-separated list of epoch indices to drop (e.g., "1, 5, 16")

If both events and drop are provided, the union of both sets of indices is used.

Usage

Running on Brainlife.io

1. Go to the drop-bad-epo app page on Brainlife.io.
2. Select an MNE epochs file as the mne input.
3. Optionally select an events input, and/or set the drop parameter to a comma-separated list of epoch indices.
4. Submit the process and retrieve the resulting epochs file, report, and product.json once it completes.

Local Testing

# Set up a config.json, e.g.:
# {
#     "mne": "in_dir/meg-epo.fif",
#     "drop": "1,5,10"
# }

./main

Technical Details

• Execution: Python with MNE-Python and the shared brainlife_utils library
• Data format: MNE .fif format (compatible with all downstream Brainlife.io apps)
• Epoch dropping: Uses MNE's Epochs.drop() method for reliable epoch removal
• Index handling: Supports comma-separated indices or file-based index lists

Authors

• Maximilien Chaumon, Paris Brain Institute

Citations

We kindly ask that you cite the following articles when publishing papers and code using this app:

Hayashi, S., Caron, B.A., Heinsfeld, A.S. et al. brainlife.io: a decentralized and open-source cloud platform to support neuroscience research. Nat Methods 21, 809–813 (2024). https://doi.org/10.1038/s41592-024-02237-2

Gramfort, A. et al. MEG and EEG data analysis with MNE-Python. Front. Neurosci. 7, 267 (2013). https://doi.org/10.3389/fnins.2013.00267

Funding Acknowledgement

brainlife.io is publicly funded and for the sustainability of the project we kindly ask that you acknowledge the following funding sources:

License

Copyright (c) 2026 MEEG Brainlife team. Licensed under AGPL-3.0, see license.txt.