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https://github.com/rob-luke/fnirs-apps-quality-reports
fNIRS Apps: Quality Reports
https://github.com/rob-luke/fnirs-apps-quality-reports
Last synced: 12 days ago
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fNIRS Apps: Quality Reports
- Host: GitHub
- URL: https://github.com/rob-luke/fnirs-apps-quality-reports
- Owner: rob-luke
- License: bsd-3-clause
- Created: 2021-06-16T10:49:26.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2022-10-21T22:54:12.000Z (about 2 years ago)
- Last Synced: 2024-10-15T18:31:09.468Z (24 days ago)
- Language: Python
- Homepage: http://fnirs-apps.org
- Size: 9.89 MB
- Stars: 7
- Watchers: 3
- Forks: 2
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# fNIRS App: Quality Reports
[](https://github.com/rob-luke/fnirs-apps-quality-reports/actions/workflows/ghregistry.yml)
[](https://doi.org/10.5281/zenodo.4999160)
This [*fNIRS App*](http://fnirs-apps.org) will produce data quality reports for all measurements in your BIDS dataset.
Reports are html documents.
See an example report [here](https://rob-luke.github.io/fnirs-apps-quality-reports/example_report.html).
## Usage
To run the app you must have [docker installed](https://docs.docker.com/get-docker/). See here for details about [installing fNIRS Apps](http://fnirs-apps.org/overview//). 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](http://fnirs-apps.org/tutorial/).
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:
```bash
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:
```bash
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.
```bash
docker pull ghcr.io/rob-luke/fnirs-apps-quality-reports/app
```
Or to run a specific version:
```bash
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](https://boutiques.github.io).
In addition to the methods described above, this app can also be run using [boutiques bosh command](https://boutiques.github.io/doc/index.html).
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: 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