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pnlbwh / pnlNipype

PNL pipeline for NIFTI images
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docker image with neurodocker #31

Closed kaczmarj closed 4 years ago

kaczmarj commented 5 years ago

hello, this project can use neurodocker to generate a docker image or singularity image with the required dependencies.

docker run --rm kaczmarj/neurodocker:0.6.0 generate docker \
  --base=neurodebian:stretch-non-free --pkg-manager=apt \
  --freesurfer version=6.0.1 \
  --ants version=2.3.0 \
  --install dcm2niix fsl \
  --miniconda use_env=base conda_install="python=3.7"

this does not install UKFTractography but i can add that. let me know if you would be interested in me adding this as a PR to this project.

tashrifbillah commented 5 years ago

Hi @kaczmarj , I have already developed docker image for our pnlpipe. It is being tested by our collaborators out of the country. Once we obtain feedback, I shall develop containers, docker and singularity, for pnlNipype as well.

When I started developing the containers, I didn't use neurodocker because, rather primitive Centos7 for having more control on building my virtual machine.

You may find a few of my containers here.

I can work around your idea in a few weeks.

kaczmarj commented 5 years ago

hi @tashrifbillah - that makes sense. thanks for the reply. for what it's worth, you can use neurodocker to build on centos:7 as well, but i do understand that you want more fine-grained control over your images.

tashrifbillah commented 4 years ago

Hi @kaczmarj , I forgot to reply here, I created a CentOS 7 based docker image about a year ago. https://hub.docker.com/r/tbillah/pnlpipe

kaczmarj commented 4 years ago

Thanks for the reply @tashrifbillah ! i'll close this