diannepat/fsl5-core repository overview

This pulls from the BIDS fsl5 core base and adds SCIF, tree, apt-get updates as of 03/09/2020. There is also a shared directory containing MNI 1mm and 2mm brains, a 1mm MNI mask, and the Freesurfer defacing files. This assumes the Dockerfile is built in a directory containing the necessary files: see https://bitbucket.org/dpat/scif_fsl/src/master/⁠ for a copy of those files.

Dockerfile:

FROM bids/base_fsl

RUN apt-get update &&
apt-get install -y git python3-pip python3 tree

RUN pip3 install scif

RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

#Create local shared directory for tools and atlases

COPY shared/ /shared/ ENV SHARED=/shared ENV PATH=${SHARED}:${PATH}

ENTRYPOINT ["scif"]