Dockerfile

# docker build for distributing a base fs 7.2.0 container

FROM centos:7

# shell settings
WORKDIR /root

# install utils
RUN yum -y update
RUN yum -y install bc libgomp perl tar tcsh wget vim-common
RUN yum -y install mesa-libGL libXext libSM libXrender libXmu
RUN yum clean all

# install fs
RUN wget https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer-linux-centos7_x86_64-7.2.0.tar.gz -O fs.tar.gz && \
    tar --no-same-owner -xzvf fs.tar.gz && \
    mv freesurfer /usr/local && \
    rm fs.tar.gz

# setup fs env
ENV OS Linux
ENV PATH /usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
ENV FREESURFER_HOME /usr/local/freesurfer
ENV FREESURFER /usr/local/freesurfer
ENV SUBJECTS_DIR /usr/local/freesurfer/subjects
ENV LOCAL_DIR /usr/local/freesurfer/local
ENV FSFAST_HOME /usr/local/freesurfer/fsfast
ENV FMRI_ANALYSIS_DIR /usr/local/freesurfer/fsfast
ENV FUNCTIONALS_DIR /usr/local/freesurfer/sessions

# set default fs options
ENV FS_OVERRIDE 0
ENV FIX_VERTEX_AREA ""
ENV FSF_OUTPUT_FORMAT nii.gz

# mni env requirements
ENV MINC_BIN_DIR /usr/local/freesurfer/mni/bin
ENV MINC_LIB_DIR /usr/local/freesurfer/mni/lib
ENV MNI_DIR /usr/local/freesurfer/mni
ENV MNI_DATAPATH /usr/local/freesurfer/mni/data
ENV MNI_PERL5LIB /usr/local/freesurfer/mni/share/perl5
ENV PERL5LIB /usr/local/freesurfer/mni/share/perl5