fNIRS App: Quality Reports

This fNIRS App will produce data quality reports for all measurements in your BIDS dataset. Reports are html documents. See an example report here.

Usage

To run the app you must have docker installed. See here for details about installing fNIRS Apps. You do NOT need to have MATLAB or python installed, and you do not need any scripts. See this tutorial for an introduction to fNIRS Apps.

To run the app you must inform it where the bids_dataset resides. This is done by passing the location of the dataset using the -v command to the app. To run this app use the command:

docker run -v /path/to/data/:/bids_dataset ghcr.io/rob-luke/fnirs-apps-quality-reports/app

By default the app will process all subject and tasks. You can modify the behaviour of the script using the options below.

Arguments

	Required	Default	Note
subject-label	optional	[]	Subjects to process. Default is to process all.
session-label	optional	[]	Sessions to process. Default is to process all.
task-label	optional	[]	Task name to use for data. Defaults to use all.
sci-threshold	optional	0.0	Threshold applied in the scalp coupling index figures.
pp-threshold	optional	0.0	Threshold applied in the peak power figures.

An example of how to use these arguments:

docker run -v /path/to/data/:/bids_dataset ghcr.io/rob-luke/fnirs-apps-quality-reports/app --sci-threshold 0.5 --pp-threshold 0.6 --participant-label 06

Updating

To update to the latest version run.

docker pull ghcr.io/rob-luke/fnirs-apps-quality-reports/app

Or to run a specific version:

docker run -v /path/:/bids_dataset ghcr.io/rob-luke/fnirs-apps-quality-reports/app:v1.4.2

Additional information

Boutiques

This app is boutiques compatible. In addition to the methods described above, this app can also be run using boutiques bosh command. You can see an example usage of this app with boutiques at https://github.com/rob-luke/fnirs-apps-demo.

Acknowledgements

This app is directly based on BIDS Apps and BIDS Execution. Please cite those projects when using this app.

BIDS Apps: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005209

BIDS Execution: bids-standard/bids-specification#313

This app uses MNE-Python, MNE-BIDS, and MNE-NIRS under the hood. Please cite those package accordingly.

MNE-Python: https://mne.tools/dev/overview/cite.html

MNE-BIDS: https://github.com/mne-tools/mne-bids#citing

MNE-NIRS: https://github.com/mne-tools/mne-nirs#acknowledgements