Since you are not planning on extending/modifying the current nipype docker image (it already contains AFNI, ANTs, FSL, FreeSurfer, etc), you are probably better off just pulling the docker image:
docker pull nipype/nipype
I am currently pushing a fresh new image for you (this will be automated as of next release).
In order to run your code, I suggest adding it as a mounted directory:
docker run --rm -it -v <path-to-your-code>:/root/workspace/code -v <path-to-your-data>:/data -v <path-to-a-workdir>:/scratch -w /scratch
In that piece of code three mount points are specified (-v arguments), you can play around them as you wish.
If you need any further help, please let us know.