diff --git a/.circle/codecov.sh b/.circle/codecov.sh
index 84df39c1c2..c71cf1c6f5 100644
--- a/.circle/codecov.sh
+++ b/.circle/codecov.sh
@@ -9,17 +9,17 @@ set -e         # Exit immediately if a command exits with a non-zero status.
 set -u         # Treat unset variables as an error when substituting.
 set -x         # Print command traces before executing command.
 
+mkdir -p ${CIRCLE_TEST_REPORTS}/
+for report in $( ls ~/scratch/*.xml ); do
+    rname=$( basename $report )
+    cp ${report} ${CIRCLE_TEST_REPORTS}/${rname:: -4}_${CIRCLE_NODE_INDEX}.xml
+done
+
 # Send coverage data to codecov.io
 curl -so codecov.io https://codecov.io/bash
 chmod 755 codecov.io
 
-find "${WORKDIR}/" -name 'coverage*.xml' -maxdepth 1 -print0 | \
+find "${CIRCLE_TEST_REPORTS}/" -name 'coverage*.xml' -print0 | \
   xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F unittests
-find "${WORKDIR}/" -name 'smoketest*.xml' -maxdepth 1 -print0 | \
+find "${CIRCLE_TEST_REPORTS}/" -name 'smoketests*.xml' -print0 | \
   xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F smoketests
-
-# Place test and coverage in the tests folder
-mkdir -p ${CIRCLE_TEST_REPORTS}/tests/
-cp ${WORKDIR}/pytest*.xml ${CIRCLE_TEST_REPORTS}/tests/ || true
-cp ${WORKDIR}/coverage*.xml ${CIRCLE_TEST_REPORTS}/tests/ || true
-cp ${WORKDIR}/smoketest*.xml ${CIRCLE_TEST_REPORTS}/tests/ || true
diff --git a/.circle/tests.sh b/.circle/tests.sh
index 51a7957259..602dddca8b 100644
--- a/.circle/tests.sh
+++ b/.circle/tests.sh
@@ -17,23 +17,23 @@ fi
 # They may need to be rebalanced in the future.
 case ${CIRCLE_NODE_INDEX} in
   0)
-    docker run --rm -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /src/nipype nipype/nipype:py27 /usr/bin/run_pytests.sh py27 && \
-    docker run --rm -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /src/nipype nipype/nipype:py35 /usr/bin/run_pytests.sh py35 && \
-    docker run --rm -it -v $WORKDIR:/work -w /src/nipype/doc nipype/nipype:py35 /usr/bin/run_builddocs.sh && \
-    docker run --rm -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow3d && \
-    docker run --rm -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d
+    docker run --rm -it -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_pytests.sh py27 && \
+    docker run --rm -it -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_pytests.sh py35 && \
+    docker run --rm -it -v $SCRATCH:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh && \
+    docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d && \
+    docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d
     ;;
   1)
-    docker run --rm -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ level1 && \
-    docker run --rm -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ l2pipeline
+    docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 && \
+    docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline
     ;;
   2)
-    docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
-    docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
+    docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1 && \
+    docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
     ;;
   3)
-    docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
-    docker run --rm -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /data/examples/ l1pipeline && \
-    docker run --rm -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /data/examples/ level1_workflow
+    docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1 && \
+    docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline && \
+    docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
     ;;
 esac
diff --git a/.coveragerc b/.coveragerc
index 80af6f0119..c69c0eef3c 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,5 +1,6 @@
 [run]
 branch = True
+source = nipype
 include = */nipype/*
 omit =
     */nipype/external/*
diff --git a/Dockerfile b/Dockerfile
index 3dd2a98ff9..bca876526b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -30,70 +30,191 @@
 #
 # Based on https://github.com/poldracklab/fmriprep/blob/9c92a3de9112f8ef1655b876de060a2ad336ffb0/Dockerfile
 #
-FROM nipype/base:latest
+FROM ubuntu:xenial-20161213
 MAINTAINER The nipype developers https://github.com/nipy/nipype
 
-ARG PYTHON_VERSION_MAJOR=3
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Pre-cache neurodebian key
+COPY docker/files/neurodebian.gpg /root/.neurodebian.gpg
+
+# Prepare environment
+RUN apt-key add /root/.neurodebian.gpg && \
+    apt-get update && \
+    apt-get install -y --no-install-recommends curl bzip2 ca-certificates xvfb && \
+    curl -sSL http://neuro.debian.net/lists/xenial.us-ca.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
+    apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true; \
+    apt-get update
+
+# Installing freesurfer
+RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar zxv -C /opt \
+    --exclude='freesurfer/trctrain' \
+    --exclude='freesurfer/subjects/fsaverage_sym' \
+    --exclude='freesurfer/subjects/fsaverage3' \
+    --exclude='freesurfer/subjects/fsaverage4' \
+    --exclude='freesurfer/subjects/fsaverage5' \
+    --exclude='freesurfer/subjects/fsaverage6' \
+    --exclude='freesurfer/subjects/cvs_avg35' \
+    --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
+    --exclude='freesurfer/subjects/bert' \
+    --exclude='freesurfer/subjects/V1_average' \
+    --exclude='freesurfer/average/mult-comp-cor' \
+    --exclude='freesurfer/lib/cuda' \
+    --exclude='freesurfer/lib/qt'
+
+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 \
+    FSFAST_HOME=$FREESURFER_HOME/fsfast \
+    MINC_BIN_DIR=$FREESURFER_HOME/mni/bin \
+    MINC_LIB_DIR=$FREESURFER_HOME/mni/lib \
+    MNI_DATAPATH=$FREESURFER_HOME/mni/data \
+    FMRI_ANALYSIS_DIR=$FREESURFER_HOME/fsfast
+ENV PERL5LIB=$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
+RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
+
+# Installing Neurodebian packages (FSL, AFNI, git)
+RUN apt-get install -y --no-install-recommends \
+                    fsl-core=5.0.9-1~nd+1+nd16.04+1 \
+                    fsl-mni152-templates=5.0.7-2 \
+                    afni=16.2.07~dfsg.1-2~nd16.04+1
+
+ENV FSLDIR=/usr/share/fsl/5.0 \
+    FSLOUTPUTTYPE=NIFTI_GZ \
+    FSLMULTIFILEQUIT=TRUE \
+    POSSUMDIR=/usr/share/fsl/5.0 \
+    LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH \
+    FSLTCLSH=/usr/bin/tclsh \
+    FSLWISH=/usr/bin/wish \
+    AFNI_MODELPATH=/usr/lib/afni/models \
+    AFNI_IMSAVE_WARNINGS=NO \
+    AFNI_TTATLAS_DATASET=/usr/share/afni/atlases \
+    AFNI_PLUGINPATH=/usr/lib/afni/plugins \
+    PATH=/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH
+
+# Installing and setting up ANTs
+RUN mkdir -p /opt/ants && \
+    curl -sSL "https://github.com/stnava/ANTs/releases/download/v2.1.0/Linux_Ubuntu14.04.tar.bz2" \
+    | tar -xjC /opt/ants --strip-components 1
+
+ENV ANTSPATH=/opt/ants \
+    PATH=$ANTSPATH:$PATH
+
+# Installing and setting up c3d
+RUN mkdir -p /opt/c3d && \
+    curl -sSL "http://downloads.sourceforge.net/project/c3d/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz" \
+    | tar -xzC /opt/c3d --strip-components 1
+
+ENV C3DPATH=/opt/c3d/ \
+    PATH=$C3DPATH/bin:$PATH
+
+# Install some other required tools
+RUN apt-get install -y --no-install-recommends \
+                    git=1:2.7.4-0ubuntu1 \
+                    graphviz=2.38.0-12ubuntu2 \
+                    unzip \
+                    apt-utils \
+                    fusefat \
+                    make \
+                    ruby=1:2.3.0+1 && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Install fake-S3
+ENV GEM_HOME /usr/lib/ruby/gems/2.3
+ENV BUNDLE_PATH="$GEM_HOME" \
+    BUNDLE_BIN="$GEM_HOME/bin" \
+    BUNDLE_SILENCE_ROOT_WARNING=1 \
+    BUNDLE_APP_CONFIG="$GEM_HOME"
+ENV PATH $BUNDLE_BIN:$PATH
+RUN mkdir -p "$GEM_HOME" "$BUNDLE_BIN" && \
+    chmod 777 "$GEM_HOME" "$BUNDLE_BIN"
+
+RUN gem install fakes3
+
+# Install Matlab MCR: from the good old install_spm_mcr.sh of @chrisfilo
+WORKDIR /opt
+RUN echo "destinationFolder=/opt/mcr" > mcr_options.txt && \
+    echo "agreeToLicense=yes" >> mcr_options.txt && \
+    echo "outputFile=/tmp/matlabinstall_log" >> mcr_options.txt && \
+    echo "mode=silent" >> mcr_options.txt && \
+    mkdir -p matlab_installer && \
+    curl -sSL http://www.mathworks.com/supportfiles/downloads/R2015a/deployment_files/R2015a/installers/glnxa64/MCR_R2015a_glnxa64_installer.zip \
+         -o matlab_installer/installer.zip && \
+    unzip matlab_installer/installer.zip -d matlab_installer/ && \
+    matlab_installer/install -inputFile mcr_options.txt && \
+    rm -rf matlab_installer mcr_options.txt
+
+# Install SPM
+RUN curl -sSL http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_r6472_Linux_R2015a.zip -o spm12.zip && \
+    unzip spm12.zip && \
+    rm -rf spm12.zip
+
+ENV MATLABCMD="/opt/mcr/v85/toolbox/matlab" \
+    SPMMCRCMD="/opt/spm12/run_spm12.sh /opt/mcr/v85/ script" \
+    FORCE_SPMMCR=1
+
 
 # Installing and setting up miniconda
-RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda${PYTHON_VERSION_MAJOR}-4.2.12-Linux-x86_64.sh && \
-    bash Miniconda${PYTHON_VERSION_MAJOR}-4.2.12-Linux-x86_64.sh -b -p /usr/local/miniconda && \
-    rm Miniconda${PYTHON_VERSION_MAJOR}-4.2.12-Linux-x86_64.sh
+RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh && \
+    bash Miniconda3-4.2.12-Linux-x86_64.sh -b -p /usr/local/miniconda && \
+    rm Miniconda3-4.2.12-Linux-x86_64.sh
 
 ENV PATH=/usr/local/miniconda/bin:$PATH \
     LANG=C.UTF-8 \
     LC_ALL=C.UTF-8 \
-    ACCEPT_INTEL_PYTHON_EULA=yes \
-    MKL_NUM_THREADS=1 \
-    OMP_NUM_THREADS=1
-# MKL/OMP_NUM_THREADS: unless otherwise specified, each process should
-# only use one thread - nipype will handle parallelization
+    ACCEPT_INTEL_PYTHON_EULA=yes
 
 # Installing precomputed python packages
-ARG PYTHON_VERSION_MINOR=5
-RUN conda config --add channels conda-forge; sync && \
-    conda config --set always_yes yes --set changeps1 no; sync && \
-    conda install -y python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR} \
-                     mkl \
-                     numpy \
-                     scipy \
-                     scikit-learn \
-                     matplotlib \
-                     pandas \
-                     libxml2 \
-                     libxslt \
+RUN conda config --add channels conda-forge --add channels intel && \
+    chmod +x /usr/local/miniconda/bin/* && \
+    conda config --set always_yes yes --set changeps1 no && \
+    conda update -q conda && \
+    chmod +x /usr/local/miniconda/bin/*; sync && \
+    conda install -y mkl=2017.0.1 \
+                     numpy=1.11.2 \
+                     scipy=0.18.1 \
+                     scikit-learn=0.17.1 \
+                     matplotlib=1.5.3 \
+                     pandas=0.19.0 \
+                     libxml2=2.9.4 \
+                     libxslt=1.1.29 \
                      traits=4.6.0 \
-                     psutil \
+                     psutil=5.0.1 \
                      icu=58.1 && \
-    sync;
+    find /usr/local/miniconda/ -exec chmod 775 {} +
 
 # matplotlib cleanups: set default backend, precaching fonts
-RUN sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages/matplotlib/mpl-data/matplotlibrc && \
+RUN sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python3.5/site-packages/matplotlib/mpl-data/matplotlibrc && \
     python -c "from matplotlib import font_manager"
 
+# Unless otherwise specified each process should only use one thread - nipype
+# will handle parallelization
+ENV MKL_NUM_THREADS=1 \
+    OMP_NUM_THREADS=1
+
 # Installing dev requirements (packages that are not in pypi)
-WORKDIR /src/
+WORKDIR /root/
 COPY requirements.txt requirements.txt
 RUN pip install -r requirements.txt && \
     rm -rf ~/.cache/pip
 
 # Installing nipype
-COPY . /src/nipype
-RUN cd /src/nipype && \
+COPY . /root/src/nipype
+RUN cd /root/src/nipype && \
     pip install -e .[all] && \
     rm -rf ~/.cache/pip
 
-# Install CI scripts
-COPY docker/files/run_* /usr/bin/
-RUN chmod +x /usr/bin/run_*
-
-# Replace imglob with a Python3 compatible version
-COPY nipype/external/fsl_imglob.py /usr/bin/fsl_imglob.py
-RUN rm -rf ${FSLDIR}/bin/imglob && \
-    chmod +x /usr/bin/fsl_imglob.py && \
-    ln -s /usr/bin/fsl_imglob.py ${FSLDIR}/bin/imglob
-
-WORKDIR /work/
+WORKDIR /root/
 
 ARG BUILD_DATE
 ARG VCS_REF
diff --git a/circle.yml b/circle.yml
index 24eaed8e2d..ac27d71a56 100644
--- a/circle.yml
+++ b/circle.yml
@@ -7,7 +7,7 @@ machine:
     DATA_NIPYPE_TUTORIAL_URL: "${OSF_NIPYPE_URL}/57f4739cb83f6901ed94bf21"
     DATA_NIPYPE_FSL_COURSE: "${OSF_NIPYPE_URL}/57f472cf9ad5a101f977ecfe"
     DATA_NIPYPE_FSL_FEEDS: "${OSF_NIPYPE_URL}/57f473066c613b01f113e7af"
-    WORKDIR: "$HOME/work"
+    SCRATCH: "$HOME/scratch"
     CODECOV_TOKEN: "ac172a50-8e66-42e5-8822-5373fcf54686"
   services:
     - docker
@@ -22,25 +22,24 @@ dependencies:
     # Let CircleCI cache the apt archive
     - mkdir -p ~/.apt-cache/partial && sudo rm -rf /var/cache/apt/archives && sudo ln -s ~/.apt-cache /var/cache/apt/archives
     - sudo apt-get -y update && sudo apt-get install -y wget bzip2
-    # Create work folder and force group permissions
-    - mkdir -p $WORKDIR && sudo setfacl -d -m group:ubuntu:rwx $WORKDIR && sudo setfacl -m group:ubuntu:rwx $WORKDIR
-    - mkdir -p $HOME/docker $HOME/examples $WORKDIR/pytest $WORKDIR/logs
+    # Create scratch folder and force group permissions
+    - mkdir -p $SCRATCH && sudo setfacl -d -m group:ubuntu:rwx $SCRATCH && sudo setfacl -m group:ubuntu:rwx $SCRATCH
+    - mkdir -p $HOME/docker $HOME/examples $SCRATCH/pytest $SCRATCH/logs
   override:
-    - if [[ -e $HOME/docker/cache.tar ]]; then docker load --input $HOME/docker/cache.tar; fi :
+    - if [[ -e $HOME/docker/cache.tar ]]; then docker load --input $HOME/docker/cache.tar; else echo 'No docker image found in cache'; fi :
         timeout: 6000
-    - docker images
-    - docker pull nipype/base:latest
     - if [[ ! -d ~/examples/nipype-tutorial ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-tutorial.tar.bz2 "${DATA_NIPYPE_TUTORIAL_URL}" && tar xjf nipype-tutorial.tar.bz2 -C ~/examples/; fi
     - if [[ ! -d ~/examples/nipype-fsl_course_data ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-fsl_course_data.tar.gz "${DATA_NIPYPE_FSL_COURSE}" && tar xzf nipype-fsl_course_data.tar.gz -C ~/examples/; fi
     - if [[ ! -d ~/examples/feeds ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O fsl-5.0.9-feeds.tar.gz "${DATA_NIPYPE_FSL_FEEDS}" && tar xzf fsl-5.0.9-feeds.tar.gz -C ~/examples/; fi
-    - if [ "$CIRCLE_TAG" != "" ]; then sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'$CIRCLE_TAG'/" nipype/info.py; fi
-#     - e=1 && for i in {1..5}; do docker build -f docker/base.Dockerfile --rm=false -t nipype/base:latest . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
-#         timeout: 21600
-    - e=1 && for i in {1..5}; do docker build --rm=false -t nipype/nipype:latest -t nipype/nipype:py35 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION=$CIRCLE_TAG . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
-        timeout: 6000
-    - e=1 && for i in {1..5}; do docker build --rm=false -t nipype/nipype:py27 --build-arg PYTHON_VERSION_MAJOR=2 --build-arg PYTHON_VERSION_MINOR=7 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION=$CIRCLE_TAG-py27 . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
-        timeout: 6000
-    - docker save -o $HOME/docker/cache.tar nipype/base:latest nipype/nipype:py35 nipype/nipype:py27 :
+    - docker images
+    - sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'$CIRCLE_TAG'/" nipype/info.py
+    - e=1 && for i in {1..5}; do docker build --rm=false -t nipype/nipype:latest --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION=$CIRCLE_TAG . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
+        timeout: 21600
+    - e=1 && for i in {1..5}; do docker build --rm=false -f docker/Dockerfile_py27 -t nipype/nipype_test:py27 . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
+        timeout: 1600
+    - e=1 && for i in {1..5}; do docker build --rm=false -f docker/Dockerfile_py35 -t nipype/nipype_test:py35 . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
+        timeout: 1600
+    - docker save -o $HOME/docker/cache.tar nipype/nipype:latest nipype/nipype_test:py27 nipype/nipype_test:py35 :
         timeout: 6000
 
 test:
@@ -54,14 +53,14 @@ test:
 
 general:
   artifacts:
-    - "~/work/docs"
-    - "~/work/logs"
+    - "~/scratch/docs"
+    - "~/scratch/logs"
 
 deployment:
   production:
     tag: /.*/
     commands:
-      # Deploy to docker hub
+      # Deploy to docker hub      
       - if [[ -n "$DOCKER_PASS" ]]; then docker login -e $DOCKER_EMAIL -u $DOCKER_USER -p $DOCKER_PASS && docker push nipype/nipype:latest; fi :
           timeout: 21600
       - if [[ -n "$DOCKER_PASS" ]]; then docker login -e $DOCKER_EMAIL -u $DOCKER_USER -p $DOCKER_PASS && docker tag nipype/nipype nipype/nipype:$CIRCLE_TAG && docker push nipype/nipype:$CIRCLE_TAG; fi :
diff --git a/docker/Dockerfile_py27 b/docker/Dockerfile_py27
new file mode 100644
index 0000000000..b1264294c3
--- /dev/null
+++ b/docker/Dockerfile_py27
@@ -0,0 +1,47 @@
+# Copyright (c) 2016, The developers of nipype
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
+#
+# * Neither the name of crn_base nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+FROM nipype/nipype:latest
+MAINTAINER The nipype developers https://github.com/nipy/nipype
+
+COPY docker/files/run_* /usr/bin/
+RUN chmod +x /usr/bin/run_*
+
+# Downgrade python to 2.7
+# matplotlib cleanups: set default backend, precaching fonts
+RUN conda install python=2.7 && \
+    find /usr/local/miniconda/ -exec chmod 775 {} + && \
+    sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc && \
+    python -c "from matplotlib import font_manager"
+
+# Re-install nipype
+COPY . /root/src/nipype
+RUN cd /root/src/nipype && \
+    pip install -e .[all]
+
+CMD ["/bin/bash"]
diff --git a/docker/Dockerfile_py34 b/docker/Dockerfile_py34
new file mode 100644
index 0000000000..88e84841e6
--- /dev/null
+++ b/docker/Dockerfile_py34
@@ -0,0 +1,54 @@
+# Copyright (c) 2016, The developers of nipype
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
+#
+# * Neither the name of crn_base nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+FROM nipype/nipype:latest
+MAINTAINER The nipype developers https://github.com/nipy/nipype
+
+# Downgrade python to 3.4
+RUN conda install python=3.4 && \
+    conda update --all -y python=3.4
+
+COPY docker/files/run_* /usr/bin/
+RUN chmod +x /usr/bin/run_*
+
+# Replace imglob with a Python3 compatible version
+COPY nipype/external/fsl_imglob.py /usr/bin/fsl_imglob.py
+RUN rm -r ${FSLDIR}/bin/imglob && \
+    chmod +x /usr/bin/fsl_imglob.py && \
+    ln -s /usr/bin/fsl_imglob.py ${FSLDIR}/bin/imglob
+
+# matplotlib cleanups: set default backend, precaching fonts
+RUN sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python3.4/site-packages/matplotlib/mpl-data/matplotlibrc && \
+    python -c "from matplotlib import font_manager"
+
+# Re-install nipype
+COPY . /root/src/nipype
+RUN cd /root/src/nipype && \
+    pip install -e .[all]
+
+CMD ["/bin/bash"]
\ No newline at end of file
diff --git a/docker/Dockerfile_py35 b/docker/Dockerfile_py35
new file mode 100644
index 0000000000..f08c655941
--- /dev/null
+++ b/docker/Dockerfile_py35
@@ -0,0 +1,42 @@
+# Copyright (c) 2016, The developers of nipype
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
+#
+# * Neither the name of crn_base nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+FROM nipype/nipype:latest
+MAINTAINER The nipype developers https://github.com/nipy/nipype
+
+# Replace imglob with a Python3 compatible version
+COPY nipype/external/fsl_imglob.py /usr/bin/fsl_imglob.py
+RUN rm -r ${FSLDIR}/bin/imglob && \
+    chmod +x /usr/bin/fsl_imglob.py && \
+    ln -s /usr/bin/fsl_imglob.py ${FSLDIR}/bin/imglob
+COPY docker/files/run_* /usr/bin/
+RUN chmod +x /usr/bin/run_*
+
+WORKDIR /root
+
+CMD ["/bin/bash"]
diff --git a/docker/base.Dockerfile b/docker/base.Dockerfile
deleted file mode 100644
index e21385e44c..0000000000
--- a/docker/base.Dockerfile
+++ /dev/null
@@ -1,170 +0,0 @@
-# Copyright (c) 2016, The developers of the Stanford CRN
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-#
-# * Redistributions of source code must retain the above copyright notice, this
-#   list of conditions and the following disclaimer.
-#
-# * Redistributions in binary form must reproduce the above copyright notice,
-#   this list of conditions and the following disclaimer in the documentation
-#   and/or other materials provided with the distribution.
-#
-# * Neither the name of crn_base nor the names of its
-#   contributors may be used to endorse or promote products derived from
-#   this software without specific prior written permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-#
-# Based on https://github.com/poldracklab/fmriprep/blob/9c92a3de9112f8ef1655b876de060a2ad336ffb0/Dockerfile
-#
-FROM ubuntu:xenial-20161213
-MAINTAINER The nipype developers https://github.com/nipy/nipype
-
-# Set noninteractive
-ENV DEBIAN_FRONTEND=noninteractive
-
-# Installing requirements for freesurfer installation
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends curl ca-certificates && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
-WORKDIR /opt
-# Installing freesurfer -- do it first so that it is cached early
-RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar zxv -C /opt \
-    --exclude='freesurfer/trctrain' \
-    --exclude='freesurfer/subjects/fsaverage_sym' \
-    --exclude='freesurfer/subjects/fsaverage3' \
-    --exclude='freesurfer/subjects/fsaverage4' \
-    --exclude='freesurfer/subjects/fsaverage5' \
-    --exclude='freesurfer/subjects/fsaverage6' \
-    --exclude='freesurfer/subjects/cvs_avg35' \
-    --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
-    --exclude='freesurfer/subjects/bert' \
-    --exclude='freesurfer/subjects/V1_average' \
-    --exclude='freesurfer/average/mult-comp-cor' \
-    --exclude='freesurfer/lib/cuda' \
-    --exclude='freesurfer/lib/qt'
-
-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=$FREESURFER_HOME/local \
-    FSFAST_HOME=$FREESURFER_HOME/fsfast \
-    MINC_BIN_DIR=$FREESURFER_HOME/mni/bin \
-    MINC_LIB_DIR=$FREESURFER_HOME/mni/lib \
-    MNI_DATAPATH=$FREESURFER_HOME/mni/data \
-    FMRI_ANALYSIS_DIR=$FREESURFER_HOME/fsfast
-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:$PATH
-RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
-
-# Enable neurodebian
-COPY docker/files/neurodebian.gpg /etc/apt/neurodebian.gpg
-RUN curl -sSL http://neuro.debian.net/lists/xenial.us-ca.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
-    apt-key add /etc/apt/neurodebian.gpg && \
-    apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true
-
-# Installing general Debian utilities and Neurodebian packages (FSL, AFNI, git)
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends \
-                    fsl-core=5.0.9-1~nd+1+nd16.04+1 \
-                    fsl-mni152-templates=5.0.7-2 \
-                    afni=16.2.07~dfsg.1-2~nd16.04+1 \
-                    bzip2 \
-                    ca-certificates \
-                    xvfb \
-                    git=1:2.7.4-0ubuntu1 \
-                    graphviz=2.38.0-12ubuntu2 \
-                    unzip \
-                    apt-utils \
-                    fusefat \
-                    make \
-                    ruby=1:2.3.0+1 && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
-ENV FSLDIR=/usr/share/fsl/5.0 \
-    FSLOUTPUTTYPE=NIFTI_GZ \
-    FSLMULTIFILEQUIT=TRUE \
-    POSSUMDIR=/usr/share/fsl/5.0 \
-    LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH \
-    FSLTCLSH=/usr/bin/tclsh \
-    FSLWISH=/usr/bin/wish \
-    AFNI_MODELPATH=/usr/lib/afni/models \
-    AFNI_IMSAVE_WARNINGS=NO \
-    AFNI_TTATLAS_DATASET=/usr/share/afni/atlases \
-    AFNI_PLUGINPATH=/usr/lib/afni/plugins \
-    PATH=/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH
-
-# Installing and setting up ANTs
-RUN mkdir -p /opt/ants && \
-    curl -sSL "https://github.com/stnava/ANTs/releases/download/v2.1.0/Linux_Ubuntu14.04.tar.bz2" \
-    | tar -xjC /opt/ants --strip-components 1
-
-ENV ANTSPATH=/opt/ants \
-    PATH=$ANTSPATH:$PATH
-
-# Installing and setting up c3d
-RUN mkdir -p /opt/c3d && \
-    curl -sSL "http://downloads.sourceforge.net/project/c3d/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz" \
-    | tar -xzC /opt/c3d --strip-components 1
-
-ENV C3DPATH=/opt/c3d/ \
-    PATH=$C3DPATH/bin:$PATH
-
-# Install fake-S3
-ENV GEM_HOME /usr/lib/ruby/gems/2.3
-ENV BUNDLE_PATH="$GEM_HOME" \
-    BUNDLE_BIN="$GEM_HOME/bin" \
-    BUNDLE_SILENCE_ROOT_WARNING=1 \
-    BUNDLE_APP_CONFIG="$GEM_HOME"
-ENV PATH $BUNDLE_BIN:$PATH
-RUN mkdir -p "$GEM_HOME" "$BUNDLE_BIN" && \
-    chmod 777 "$GEM_HOME" "$BUNDLE_BIN"
-
-RUN gem install fakes3
-
-# Install Matlab MCR: from the good old install_spm_mcr.sh of @chrisfilo
-RUN echo "destinationFolder=/opt/mcr" > mcr_options.txt && \
-    echo "agreeToLicense=yes" >> mcr_options.txt && \
-    echo "outputFile=/tmp/matlabinstall_log" >> mcr_options.txt && \
-    echo "mode=silent" >> mcr_options.txt && \
-    mkdir -p matlab_installer && \
-    curl -sSL http://www.mathworks.com/supportfiles/downloads/R2015a/deployment_files/R2015a/installers/glnxa64/MCR_R2015a_glnxa64_installer.zip \
-         -o matlab_installer/installer.zip && \
-    unzip matlab_installer/installer.zip -d matlab_installer/ && \
-    matlab_installer/install -inputFile mcr_options.txt && \
-    rm -rf matlab_installer mcr_options.txt
-
-# Install SPM
-RUN curl -sSL http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_r6472_Linux_R2015a.zip -o spm12.zip && \
-    unzip spm12.zip && \
-    rm -rf spm12.zip
-
-ENV MATLABCMD="/opt/mcr/v85/toolbox/matlab" \
-    SPMMCRCMD="/opt/spm12/run_spm12.sh /opt/mcr/v85/ script" \
-    FORCE_SPMMCR=1
-
-WORKDIR /work
-
diff --git a/docker/files/run_builddocs.sh b/docker/files/run_builddocs.sh
index fb6111c9ea..ce289206d8 100644
--- a/docker/files/run_builddocs.sh
+++ b/docker/files/run_builddocs.sh
@@ -3,9 +3,7 @@ set -e
 set -x
 set -u
 
-WORKDIR=${WORK:-/work}
-
-mkdir -p ${WORKDIR}/docs
-make html 2>&1 | tee ${WORKDIR}/builddocs.log
-cp -r /src/nipype/doc/_build/html/* ${WORKDIR}/docs/
-cat ${WORKDIR}/builddocs.log && if grep -q "ERROR" ${WORKDIR}/builddocs.log; then false; else true; fi
+mkdir -p /scratch/docs
+make html 2>&1 | tee /scratch/builddocs.log
+cp -r /root/src/nipype/doc/_build/html/* /scratch/docs/
+cat /scratch/builddocs.log && if grep -q "ERROR" /scratch/builddocs.log; then false; else true; fi
diff --git a/docker/files/run_examples.sh b/docker/files/run_examples.sh
index e30ca221c6..43a94a2649 100644
--- a/docker/files/run_examples.sh
+++ b/docker/files/run_examples.sh
@@ -3,37 +3,15 @@ set -e
 set -x
 set -u
 
-WORKDIR=${WORK:-/work}
+mkdir -p /root/.nipype
+echo '[logging]' > /root/.nipype/nipype.cfg
+echo 'workflow_level = DEBUG' >> /root/.nipype/nipype.cfg
+echo 'interface_level = DEBUG' >> /root/.nipype/nipype.cfg
+echo 'filemanip_level = DEBUG' >> /root/.nipype/nipype.cfg
+echo 'log_to_file = true' >> /root/.nipype/nipype.cfg
+echo 'log_directory = /scratch/logs/' >> /root/.nipype/nipype.cfg
+
+coverage run /root/src/nipype/tools/run_examples.py $@
 arr=$@
 tmp_var=$( IFS=$' '; echo "${arr[*]}" )
-example_id=${tmp_var//[^A-Za-z0-9_-]/_}
-
-mkdir -p ${HOME}/.nipype ${WORKDIR}/logs/example_${example_id}
-echo "[logging]" > ${HOME}/.nipype/nipype.cfg
-echo "workflow_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg
-echo "interface_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg
-echo "filemanip_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg
-echo "log_to_file = true" >> ${HOME}/.nipype/nipype.cfg
-echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> ${HOME}/.nipype/nipype.cfg
-
-# Set up coverage
-echo "[run]" >> .coveragerc
-echo "branch = True" >> .coveragerc
-echo "source = /src/nipype" >> .coveragerc
-echo "include = */nipype/*" >> .coveragerc
-echo "omit =" >> .coveragerc
-echo "    */nipype/external/*" >> .coveragerc
-echo "    */nipype/fixes/*" >> .coveragerc
-echo "    */setup.py" >> .coveragerc
-
-
-parallel=""
-if [ "$2" == "MultiProc" ]; then
-	parallel="--concurrency=multiprocessing"
-fi
-
-coverage run ${parallel} /src/nipype/tools/run_examples.py $@
-test_exit=$?
-coverage xml -o "${WORKDIR}/smoketest_${example_id}.xml"
-
-exit $test_exit
\ No newline at end of file
+coverage xml -o "/scratch/smoketest_${tmp_var//[^A-Za-z0-9_-]/_}.xml"
diff --git a/docker/files/run_pytests.sh b/docker/files/run_pytests.sh
index 3b4b99786f..3ad4cfd28c 100644
--- a/docker/files/run_pytests.sh
+++ b/docker/files/run_pytests.sh
@@ -3,37 +3,36 @@ set -e
 set -x
 set -u
 
-WORKDIR=${WORK:-/work}
 PYTHON_VERSION=$( python -c "import sys; print('{}{}'.format(sys.version_info[0], sys.version_info[1]))" )
 
 # Create necessary directories
-mkdir -p ${WORKDIR}/crashfiles ${WORKDIR}/logs/py${PYTHON_VERSION}
+mkdir -p /scratch/pytest /scratch/crashfiles /scratch/logs/py${PYTHON_VERSION}
 
 # Create a nipype config file
-mkdir -p ${HOME}/.nipype
-echo '[logging]' > ${HOME}/.nipype/nipype.cfg
-echo 'log_to_file = true' >> ${HOME}/.nipype/nipype.cfg
-echo "log_directory = ${WORKDIR}/logs/py${PYTHON_VERSION}" >> ${HOME}/.nipype/nipype.cfg
+mkdir -p /root/.nipype
+echo '[logging]' > /root/.nipype/nipype.cfg
+echo 'log_to_file = true' >> /root/.nipype/nipype.cfg
+echo "log_directory = /scratch/logs/py${PYTHON_VERSION}" >> /root/.nipype/nipype.cfg
 
 # Enable profile_runtime tests only for python 2.7
 if [[ "${PYTHON_VERSION}" -lt "30" ]]; then
-    echo '[execution]' >> ${HOME}/.nipype/nipype.cfg
-    echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg
+    echo '[execution]' >> /root/.nipype/nipype.cfg
+    echo 'profile_runtime = true' >> /root/.nipype/nipype.cfg
 fi
 
-cd /src/nipype/
-make clean
 # Run tests using pytest
-py.test -n ${CIRCLE_NCPUS:-4} --doctest-modules --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}.xml --cov=nipype nipype
+cd /root/src/nipype/
+make clean
+py.test --doctest-modules --cov-report xml:/scratch/coverage_py${PYTHON_VERSION}.xml --cov=nipype nipype
 
 
 # Workaround: run here the profiler tests in python 3
 if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
-    echo '[execution]' >> ${HOME}/.nipype/nipype.cfg
-    echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg
-    py.test -n ${CIRCLE_NCPUS:-4} --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_profiler.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_profiler.xml --cov=nipype nipype/interfaces/tests/test_runtime_profiler.py
-    py.test -n ${CIRCLE_NCPUS:-4} --junitxml=${WORKDIR}/pytests_py${PYTHON_VERSION}_multiproc.xml --cov-report xml:${WORKDIR}/coverage_py${PYTHON_VERSION}_multiproc.xml --cov=nipype nipype/pipeline/plugins/tests/test_multiproc*.py
+    echo '[execution]' >> /root/.nipype/nipype.cfg
+    echo 'profile_runtime = true' >> /root/.nipype/nipype.cfg
+    py.test --cov-report xml:/scratch/coverage_py${PYTHON_VERSION}_profiler.xml --cov=nipype nipype/interfaces/tests/test_runtime_profiler.py 
+    py.test --cov-report xml:/scratch/coverage_py${PYTHON_VERSION}_multiproc.xml --cov=nipype nipype/pipeline/plugins/tests/test_multiproc*.py 
 fi
 
 # Copy crashfiles to scratch
-find /src/nipype/ -name "crash-*" -exec cp {} ${WORKDIR}/crashfiles/ \;
+for i in $(find /root/src/nipype/ -name "crash-*" ); do cp $i /scratch/crashfiles/; done
diff --git a/nipype/info.py b/nipype/info.py
index c170d3800c..b990d67a05 100644
--- a/nipype/info.py
+++ b/nipype/info.py
@@ -5,11 +5,13 @@
 from __future__ import print_function, division, unicode_literals, absolute_import
 
 
-# nipype version information.  An empty version_extra corresponds to a
-# full release.  '.dev' as a version_extra string means this is a development
+# nipype version information.  An empty _version_extra corresponds to a
+# full release.  '.dev' as a _version_extra string means this is a development
 # version
-# Remove -dev for release
-__version__ = '0.13.0-dev'
+_version_major = 0
+_version_minor = 13
+_version_micro = 0
+_version_extra = '-dev'  # Remove -dev for release
 
 
 def get_nipype_gitversion():
@@ -41,10 +43,16 @@ def get_nipype_gitversion():
         ver = o.decode().strip().split('-')[-1]
     return ver
 
-if __version__.endswith('-dev'):
+if '-dev' in _version_extra:
     gitversion = get_nipype_gitversion()
     if gitversion:
-        __version__ = __version__.replace('-dev', '-' + gitversion + '.dev')
+        _version_extra = '-' + gitversion + '.dev'
+
+# Format expected by setup.py and doc/source/conf.py: string of form 'X.Y.Z'
+__version__ = '%s.%s.%s%s' % (_version_major,
+                              _version_minor,
+                              _version_micro,
+                              _version_extra)
 
 CLASSIFIERS = ['Development Status :: 5 - Production/Stable',
                'Environment :: Console',
@@ -118,11 +126,10 @@ def get_nipype_gitversion():
 AUTHOR = 'nipype developers'
 AUTHOR_EMAIL = 'neuroimaging@python.org'
 PLATFORMS = 'OS Independent'
-MAJOR = __version__.split('.')[0]
-MINOR = __version__.split('.')[1]
-MICRO = __version__.replace('-', '.').split('.')[2]
-ISRELEASE = (len(__version__.replace('-', '.').split('.')) == 3 or
-             'post' in __version__.replace('-', '.').split('.')[-1])
+MAJOR = _version_major
+MINOR = _version_minor
+MICRO = _version_micro
+ISRELEASE = _version_extra == ''
 VERSION = __version__
 PROVIDES = ['nipype']
 REQUIRES = [
@@ -144,7 +151,6 @@ def get_nipype_gitversion():
 TESTS_REQUIRES = [
     'pytest>=%s' % PYTEST_MIN_VERSION,
     'pytest-cov',
-    'pytest-xdist',
     'mock',
     'codecov',
     'dipy',