fNIRS App: Scalp Coupling Index

This fNIRS App will calculate the scalp coupling index for each channel in your BIDS dataset.

This app evaluates the channel quality of your data using the scalp coupling index metric. The extracted metric is saved as a column in the channels.tsv BIDS file. If a threshold is specified, then the status column in channels.tsv will also be set. Additionally the peak power metric is extracted, and the average value across the measurement is stored per channel in the channels.tsv BIDS file.

If you prefer a visual report of the data quality see: fNIRS App: Quality Reports

Feedback is welcome!! Please let me know your experience with this app by raising an issue.

The metrics computed in this program are from the following manuscripts. Please cite these accordingly:

Pollonini L et al., “PHOEBE: a method for real time mapping of
optodes-scalp coupling in functional near-infrared spectroscopy” in
Biomed. Opt. Express 7, 5104-5119 (2016).
Hernandez, Samuel Montero, and Luca Pollonini. "NIRSplot: a tool for
quality assessment of fNIRS scans." Optics and the Brain.
Optical Society of America, 2020.

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-scalp-coupling-index/app

You can also specify additional parameters by passing arguments to the app. A complete list of arguments is provided below. A more complete example that only runs on participant 6 and also specifies a threshold, below which channels are marked as bad, can be set as:

docker run -v /path/to/data/:/bids_dataset ghcr.io/rob-luke/fnirs-apps-scalp-coupling-index/app \
  --threshold 0.7 \
  --subject-label 06

Arguments

	Required	Default	Note
threshold	optional	[]	If not present then the status column is not modified.
subject-label	optional	[]	Subjects to process. Default is to process all.
task-label	optional	[]	Tasks to process. Default is to process all.
h-freq	optional	1.5	High frequency limit for metrics (Hz).
h-trans-bandwidth	optional	0.3	Width of the high frequency transition band (Hz).

For arguments h-freq and h-trans-bandwidth detailed explanations can be found in the MNE-NIRS documentation.

Updating

To update to the latest version run.

docker pull ghcr.io/rob-luke/fnirs-apps-scalp-coupling-index/app

Or to run a specific version:

docker run -v /path/:/bids_dataset ghcr.io/rob-luke/fnirs-apps-scalp-coupling-index/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.