Adding Jupyter to Nipype or fmriprep docker image


#1

Hi all,

My first time posting here, but I’ve struggled with what seemed at first to be a simple problem for long enough that I thought it worth posting.

I’m trying to add Jupyter to the fmriprep docker image to ease the process of developing a new pipeline (borrowing the existing workflows and environments, but rearranging some steps when necessary). The goal is to install everything necessary to run a Jupyter notebook, where image will begin by providing a link to connect.

e.g.

This is already done in the tutorial image (satra/nih-workshop-2017) but I don’t know how regularly the image is maintained, so do not want to rely on it for active projects. The Dockerfile for the tutorial image is also unavailable, so it is not easy to replicate the build.

If I simply build the fmriprep image from a Jupyter notebook base image (e.g. https://github.com/jupyter/docker-stacks/tree/master/minimal-notebook) then I run into a lot of permissions issues. After struggling with this for a while, I thought I would just check if anyone has an existing Dockerfile set up to integrate Jupyter into either fmriprep or the nipype/nipype docker image.

Thanks!


Previously working Neurodocker image failing - IsADirectoryError
#2

Hi @jordan_theriault,

you should check neurodocker that can help you to build an image. It supports software used in neuroimaging as well as conda that can be used to install jupyter.


#3

Hi @jordan_theriault,

you can also check the updated Dockerfile from Nipype Tutorial and the script that was used to generate the file with neurodocker.


#4

Thank you! I hadn’t seen Michael Notter’s separate docker images, since the link on the Nipype site went to satra/nih-workshop-2017. This is perfect!


#5

We’ve just updated the Dockerfile on Nipype Tutorial today. Since I used neurodocker to create it, I just thought it can help you to create your own customized Dockerfile.