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poquirion committed Nov 27, 2017
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[![Build Status](https://circleci.com/gh/BIDS-Apps/niak.png?circle-token=:circle-token)](https://circleci.com/gh/BIDS-Apps/niak) [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
# Niak
The neuroimaging analysis kit (NIAK) is a library of pipelines for the preprocessing and mining of large functional neuroimaging data, using GNU Octave or Matlab(r), and distributed under a MIT license. This includes but is not limited to the preprocessing pipeline implemented in this app. Essential documentation can be found on the [NIAK website](http://niak.simexp-lab.org/).
The neuroimaging analysis kit (NIAK) is a library of pipelines for the preprocessing and mining of large functional neuroimaging data, using GNU Octave or Matlab(r), and distributed under a MIT license. This includes but is not limited to the preprocessing pipeline implemented in this app. Essential documentation can be found on the [NIAK website](http://niak.simexp-lab.org/).

# In this Bids-apps

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If the problems seems to be related to the app itself, you can always create a [new issue on our github page.](https://github.com/BIDS-Apps/niak/issues)
If is seems to come from NIAK itself, please [report you issues on the NIAK github page](https://github.com/SIMEXP/niak/issues)

## Usage
## Usage
To run NIAK Fmri preprocessing pipeline on your bids data set:
```
docker run -it --read-only --volumes-from data bids/niak /bids_dataset /outputs participant --participant_label "XXX-YYY"
docker run -it --read-only --volumes-from data bids/niak /bids_dataset /outputs group --participant_label "XXX-YYY"
```
docker run -it --rm -v /path/to/bids_dataset:/bids_dataset:ro -v path_to_result_dir:/outputs bids/niak /bids_dataset /outputs participant --participant_label "XXX-YYY"
docker run -it --rm -v /path/to/bids_dataset:/bids_dataset:ro -v path_to_result_dir:/outputs bids/niak /bids_dataset /outputs group --participant_label "XXX-YYY"
```
For more details, type:
```
docker run -it --read-only --volumes-from data bids/niak --help
docker run bids/niak --help
```

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