environment.md

Set up the environment to run pipelines

Run a docker container 🐳

Start a container using the command below:

docker run -ti \
		-p 8888:8888 \
		elodiegermani/open_pipeline

On this command line, you need to add volumes to be able to link with your local files (original dataset and git repository). If you stored the original dataset in data/original, just make a volume with the narps_open_pipelines directory:

docker run 	-ti \
		-p 8888:8888 \
		-v /users/egermani/Documents/narps_open_pipelines:/home/ \
		elodiegermani/open_pipeline

If it is in another directory, make a second volume with the path to your dataset:

docker run 	-ti \
		-p 8888:8888 \
		-v /Users/egermani/Documents/narps_open_pipelines:/home/ \
		-v /Users/egermani/Documents/data/NARPS/:/data/ \
		elodiegermani/open_pipeline

After that, your container will be launched!

Other useful docker commands

START A CONTAINER

docker start [name_of_the_container]

VERIFY A CONTAINER IS IN THE LIST

docker ps

EXECUTE BASH OR ATTACH YOUR CONTAINER

docker exec -ti [name_of_the_container] bash

OR

docker attach [name_of_the_container]

Useful commands inside the container

ACTIVATE CONDA ENVIRONMENT

source activate neuro

LAUNCH JUPYTER NOTEBOOK

jupyter notebook --port=8888 --no-browser --ip=0.0.0.0

If you did not use your container for a while

Verify it still runs :

docker ps -l

If your container is in the list, run :

docker start [name_of_the_container]

Else, relaunch it with :

docker run 	-ti \
		-p 8888:8888 \
		-v /home/egermani:/home \
		[name_of_the_image]

To use SPM inside the container, use this command at the beginning of your script:

from nipype.interfaces import spm

matlab_cmd = '/opt/spm12-r7771/run_spm12.sh /opt/matlabmcr-2010a/v713/ script'

spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)