Dockerfile

FROM neurodebian:xenial-non-free

# fsl: fsl used in script
# afni: afni used in script
# curl: to download freesurfer
# ca-certificates: necessary for curl
# libgdcm-tools: gdcmdump used in script
RUN apt-get update &&\
    apt-get install -y --no-install-recommends \
        fsl \
        afni \
        curl \
        ca-certificates \
        libgdcm-tools

# remove the fsl5.0 prefix
RUN ["/bin/bash", "-c", "for fil in /usr/bin/fsl5.0-*; do mv ${fil} ${fil/fsl5.0-/}; done"]

# add afni commands to PATH
ENV PATH=/usr/lib/afni/bin:${PATH}

# download freesurfer
RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \
    --exclude='freesurfer/diffusion' \
    --exclude='freesurfer/docs' \
    --exclude='freesurfer/fsfast' \
    --exclude='freesurfer/lib/cuda' \
    --exclude='freesurfer/lib/qt' \
    --exclude='freesurfer/matlab' \
    --exclude='freesurfer/mni/share/man' \
    --exclude='freesurfer/subjects/fsaverage_sym' \
    --exclude='freesurfer/subjects/fsaverage3' \
    --exclude='freesurfer/subjects/fsaverage4' \
    --exclude='freesurfer/subjects/cvs_avg35' \
    --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
    --exclude='freesurfer/subjects/bert' \
    --exclude='freesurfer/subjects/lh.EC_average' \
    --exclude='freesurfer/subjects/rh.EC_average' \
    --exclude='freesurfer/subjects/sample-*.mgz' \
    --exclude='freesurfer/subjects/V1_average' \
    --exclude='freesurfer/trctrain'

ENV FSL_DIR="/usr/share/fsl/5.0" \
    OS="Linux" \
    FS_OVERRIDE=0 \
    FIX_VERTEX_AREA="" \
    FSF_OUTPUT_FORMAT="nii.gz" \
    FREESURFER_HOME="/opt/freesurfer"
ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
    FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
    MNI_DIR="$FREESURFER_HOME/mni" \
    LOCAL_DIR="$FREESURFER_HOME/local" \
    MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
    MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
    MNI_DATAPATH="$FREESURFER_HOME/mni/data"
ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
    MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
    PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"

COPY GE_dcm_to_nii.sh /opt/

RUN chmod +x /opt/GE_dcm_to_nii.sh

ENTRYPOINT ["/opt/GE_dcm_to_nii.sh"]