Neuroscience research
We are not expert in Neuroscience ourselves, please contact us if you see any improvements that could be made to this page, or if you need any help to get it working.
The Neurodocker project helps you to create a Docker image with the Neuroscience softwares you need, such as FSL, FreeSurfer, AFNI or ANTs.
Checkout the Neurodocker documentation for more details: https://github.com/ReproNim/neurodocker
In this page we will show you how to generate a Docker image with popular Neuroscience research softwares installed such as FreeSurfer and FSL. Feel free to check the Neurodocker documentation, and adapt the installation process to your needs.
FreeSurfer and FSL
Generate a Dockerfile with:
- FreeSurfer 6.0.1
- FSL 6.0.3
docker run --rm repronim/neurodocker:0.7.0 generate docker \
--base debian:stretch --pkg-manager apt \
--freesurfer version=6.0.1 --fsl version=6.0.3 > Dockerfile
FreeSurfer and AFNI
Generate a Dockerfile with:
- FreeSurfer 6.0.1
- AFNI, R and Python3
docker run --rm repronim/neurodocker:0.7.0 generate docker \
--base debian:stretch --pkg-manager apt \
--afni version=latest install_r=true install_r_pkgs=true install_python3=true \
--freesurfer version=6.0.1 > Dockerfile
Deploy the generated Dockerfile
Before deploying the Dockerfile to the DSRI you can open it, and add commands to install additional package you are interested in, such as nighres or nipype.
Checkout the documentation to deploy the Dockerfile on DSRI.
Running a UI with VNC (e.g. FSLeyes) is still a work in progress. See this issue for more details.
Use the GPUs
More details about using GPU with FSL: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GPU