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INSTALL.md

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How to install NARPS Open Pipelines ?

1 - Fork the repository

Fork the repository, so you have your own working copy of it.

2 - Clone the code

First, install Datalad. This will allow you to access the NARPS data easily, as it is included in the repository as datalad subdatasets.

Then, clone the project :

# Replace YOUR_GITHUB_USERNAME in the following command.
datalad install --recursive https://github.com/YOUR_GITHUB_USERNAME/narps_open_pipelines.git

Warning

It is still possible to clone the fork using git ; but by doing this, you will only get the code.

# Replace YOUR_GITHUB_USERNAME in the following command.
git clone https://github.com/YOUR_GITHUB_USERNAME/narps_open_pipelines.git

3 - Get the data

Now that you cloned the repository using Datalad, you are able to get the data :

# Move inside the root directory of the repository.
cd narps_open_pipelines

# Select the data you want to download. Here is an example to get data of the first 4 subjects.
datalad get data/original/ds001734/sub-00[1-4] -J 12
datalad get data/original/ds001734/derivatives/fmriprep/sub-00[1-4] -J 12

Note

For further information and alternatives on how to get the data, see the corresponding documentation page docs/data.md.

4 - Set up the environment

Install Docker then pull the Docker image :

docker pull elodiegermani/open_pipeline:latest

Once it's done you can check the image is available on your system :

docker images
   REPOSITORY                               TAG       IMAGE ID        CREATED         SIZE
   docker.io/elodiegermani/open_pipeline    latest    0f3c74d28406    9 months ago    22.7 GB

Note

Feel free to read this documentation page docs/environment.md to get further information about this environment.

5 - Run the project

Start a Docker container from the Docker image :

# Replace PATH_TO_THE_REPOSITORY in the following command (e.g.: with /home/user/dev/narps_open_pipelines/)
docker run -it -v PATH_TO_THE_REPOSITORY:/home/neuro/code/ elodiegermani/open_pipeline

Install NARPS Open Pipelines inside the container :

source activate neuro
cd /home/neuro/code/
pip install .

Finally, you are able to run pipelines :

python narps_open/runner.py
  usage: runner.py [-h] -t TEAM (-r RSUBJECTS | -s SUBJECTS [SUBJECTS ...] | -n NSUBJECTS) [-g | -f] [-c]

Note

For further information, read this documentation page docs/running.md.