Update Dockerfile

Dockerfile

@@ -61,6 +61,8 @@ RUN  pip install --no-cache-dir nipype nibabel niworkflows nilearn matplotlib
 RUN  rm -rf ~/.cache/pip/* && sync
 RUN  apt-get update
 
+ENV FSLDIR="/opt/fsl-5.0.10" \
+    PATH="/opt/fsl-5.0.10/bin:$PATH"
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
            bc \
@@ -83,29 +85,17 @@ RUN apt-get update -qq \
            libxt6 \
            wget \
     && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* 
-
-ENV FSLDIR="/opt/fsl-6.0.3" \
-      PATH="/opt/fsl-6.0.3/bin:$PATH"
-
-RUN echo "Downloading FSL ..." \
-      && mkdir -p /opt/fsl-6.0.3 \
-      && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.3-centos6_64.tar.gz \
-      | tar -xz -C /opt/fsl-6.0.3 --strip-components 1 \
-      --exclude='fsl/doc' \
-      --exclude='fsl/data/atlases' \
-      --exclude='fsl/data/possum' \
-      --exclude='fsl/src' \
-      --exclude='fsl/extras/src' \
-      --exclude='fsl/bin/fslview*' \
-      --exclude='fsl/bin/FSLeyes' \
-      && echo "Installing FSL conda environment ..." \
-      && sed -i -e "/fsleyes/d" -e "/wxpython/d" \
-         ${FSLDIR}/etc/fslconf/fslpython_environment.yml \
-      && bash /opt/fsl-6.0.3/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.3 \
-      && find ${FSLDIR}/fslpython/envs/fslpython/lib/python3.7/site-packages/ -type d -name "tests"  -print0 | xargs -0 rm -r \
-      && ${FSLDIR}/fslpython/bin/conda clean --all
-
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
+    && echo "Downloading FSL ..." \
+    && mkdir -p /opt/fsl-5.0.10 \
+    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.10-centos6_64.tar.gz \
+    | tar -xz -C /opt/fsl-5.0.10 --strip-components 1 \
+    && sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT \
+    && sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT \
+    && sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT \
+    && sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT \
+    && echo "Installing FSL conda environment ..." \
+    && bash /opt/fsl-5.0.10/etc/fslconf/fslpython_install.sh -f /opt/fsl-5.0.10
 
 ENV C3DPATH="/opt/convert3d-1.0.0" \
     PATH="/opt/convert3d-1.0.0/bin:$PATH"
@@ -239,7 +229,7 @@ RUN bash -c \
     && rm i30llenk6s37kv8nkqxgulwylaxp928g.xz'
 
 
-RUN bash -c 'BRAINATLAS=/xcpEngine/atlas BRAINSPACE=/xcpEngine/space XCPEDIR=/xcpEngine FSLDIR=/opt/fsl-6.0.3 AFNI_PATH=/opt/afni-latest C3D_PATH=/opt/convert3d-nightly/bin ANTSPATH=/opt/ants-latest/bin /xcpEngine/xcpReset \
+RUN bash -c 'BRAINATLAS=/xcpEngine/atlas BRAINSPACE=/xcpEngine/space XCPEDIR=/xcpEngine FSLDIR=/opt/fsl-5.0.10 AFNI_PATH=/opt/afni-latest C3D_PATH=/opt/convert3d-nightly/bin ANTSPATH=/opt/ants-latest/bin /xcpEngine/xcpReset \
     && BRAINATLAS=/xcpEngine/atlas BRAINSPACE=/xcpEngine/space XCPEDIR=/xcpEngine /xcpEngine/utils/repairMetadata'
 
 RUN bash -c 'echo R_ENVIRON_USER\="" >> /usr/lib/R/etc/Renviron \