This fNIRS App will runs a GLM pipeline on your data and export subject and group level results.
Feedback is welcome!! Please let me know your experience with this app by raising an issue.
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 the software 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-glm-pipeline/app
By default the app will process all subject and tasks. 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 3 and also specifies that short channel regression should not be used, can be run as:
docker run -v /path/to/data/:/bids_dataset ghcr.io/rob-luke/fnirs-apps-glm-pipeline/app \
--subject-label 03 \
--short-regression False
--sample-rate X
to resample to user specified value.--short-regression True
is specified the short channels will be added as regressors to the design matrix for the GLM computation.Required | Default | Note | |
---|---|---|---|
short-regression | optional | True | Include short channels as regressor. |
export-drifts | optional | False | Export the drift coefficients in csv. |
sample-rate. | optional | 0.6. | Sample rate the data will be resampled to. |
export-shorts | optional | False | Export the short channel coefficients in csv. |
subject-label | optional | [] | Sujects to process. Default is to process all. |
task-label | optional | [] | Tasks to process. Default is to process all. |
For example
docker run -v /path/to/data/:/bids_dataset ghcr.io/rob-luke/fnirs-apps-glm-pipeline/app --short-regression True --export-shorts True --subject-label 02 04
To update to the latest version run.
docker pull ghcr.io/rob-luke/fnirs-apps-glm-pipeline/app
Or to run a specific version:
docker run -v /path/:/bids_dataset ghcr.io/rob-luke/fnirs-apps-glm-pipeline/app:v1.4.2
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.
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: https://github.com/bids-standard/bids-specification/issues/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