diff --git a/docker/generate_dockerfiles.sh b/docker/generate_dockerfiles.sh
index bd1fcb637e..9c281f8bbc 100755
--- a/docker/generate_dockerfiles.sh
+++ b/docker/generate_dockerfiles.sh
@@ -52,77 +52,71 @@ do
   esac
 done
 
-
-# neurodocker version 0.3.1-22-gb0ee069
-NEURODOCKER_IMAGE="kaczmarj/neurodocker@sha256:f15ca90803f4b89acfca55cd1c7269bf2ec2dfd95b3de1118b08afa34b87d9d1"
-
-# neurodebian:stretch-non-free pulled on November 3, 2017
-BASE_IMAGE="neurodebian@sha256:7590552afd0e7a481a33314724ae27f76ccedd05ffd7ac06ec38638872427b9b"
+# neurodocker version 0.4.1-22-g7c44e01
+NEURODOCKER_IMAGE="kaczmarj/neurodocker:master@sha256:858632a7533cac100f70932749b4cfc77fc40f667f41fca208f406215cff8a27"
+# neurodebian:stretch-non-free pulled on September 19, 2018
+BASE_IMAGE="neurodebian:stretch-non-free@sha256:7cd978427d7ad215834fee221d0536ed7825b3cddebc481eba2d792dfc2f7332"
 
 NIPYPE_BASE_IMAGE="nipype/nipype:base"
 PKG_MANAGER="apt"
 DIR="$(dirname "$0")"
 
 function generate_base_dockerfile() {
-  docker run --rm "$NEURODOCKER_IMAGE" generate \
-  --base "$BASE_IMAGE" --pkg-manager "$PKG_MANAGER" \
-  --label maintainer="The nipype developers https://github.com/nipy/nipype" \
-  --spm version=12 matlab_version=R2017a \
-  --afni version=latest install_python2=true \
-  --freesurfer version=6.0.0 min=true \
-  --run 'echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh' \
-  --install ants apt-utils bzip2 convert3d file fsl-core fsl-mni152-templates \
-            fusefat g++ git graphviz make ruby unzip xvfb \
-  --add-to-entrypoint "source /etc/fsl/fsl.sh" \
-  --env ANTSPATH='/usr/lib/ants' PATH='/usr/lib/ants:$PATH' \
-  --run "gem install fakes3" \
-  --no-check-urls > "$DIR/Dockerfile.base"
+  docker run --rm "$NEURODOCKER_IMAGE" generate docker \
+    --base "$BASE_IMAGE" --pkg-manager "$PKG_MANAGER" \
+    --label maintainer="The nipype developers https://github.com/nipy/nipype" \
+    --spm12 version=r7219 \
+    --env 'LD_LIBRARY_PATH=/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH' \
+    --freesurfer version=6.0.0-min \
+    --run 'echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tCjUxNzIKICpDdnVtdkVWM3pUZmcKRlM1Si8yYzFhZ2c0RQoiID4gL29wdC9mcmVlc3VyZmVyLTYuMC4wLW1pbi9saWNlbnNlLnR4dA==" | base64 -d | sh' \
+    --install afni ants apt-utils bzip2 convert3d file fsl-core \
+              fsl-mni152-templates fusefat g++ git graphviz make python ruby \
+              unzip xvfb \
+    --add-to-entrypoint "source /etc/fsl/fsl.sh && source /etc/afni/afni.sh" \
+    --env ANTSPATH='/usr/lib/ants' \
+          PATH='/usr/lib/ants:$PATH' \
+    --run "gem install fakes3" \
+    > "$DIR/Dockerfile.base"
 }
 
 
 function generate_main_dockerfile() {
-  docker run --rm "$NEURODOCKER_IMAGE" generate \
-  --base "$NIPYPE_BASE_IMAGE" --pkg-manager "$PKG_MANAGER" \
-  --label maintainer="The nipype developers https://github.com/nipy/nipype" \
-  --env MKL_NUM_THREADS=1 OMP_NUM_THREADS=1 \
-  --user neuro \
-  --miniconda env_name=neuro \
-              activate=true \
-  --copy docker/files/run_builddocs.sh docker/files/run_examples.sh \
-         docker/files/run_pytests.sh nipype/external/fsl_imglob.py /usr/bin/ \
-  --copy . /src/nipype \
-  --user root \
-  --run 'chown -R neuro /src
-&& chmod +x /usr/bin/fsl_imglob.py /usr/bin/run_*.sh
-&& . /etc/fsl/fsl.sh
-&& ln -sf /usr/bin/fsl_imglob.py ${FSLDIR}/bin/imglob
-&& mkdir /work
-&& chown neuro /work' \
-  --user neuro \
-  --arg PYTHON_VERSION_MAJOR=3 PYTHON_VERSION_MINOR=6 BUILD_DATE VCS_REF VERSION \
-  --miniconda env_name=neuro \
-              conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
-                             icu=58.1 libxml2 libxslt matplotlib mkl numpy paramiko
-                             pandas psutil scikit-learn scipy traits=4.6.0' \
-              pip_opts="-e" \
-              pip_install="/src/nipype[all]" \
-  --miniconda env_name=neuro \
-              pip_install="grabbit==0.1.2" \
-  --run-bash "mkdir -p /src/pybids
-         && curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/0.5.1
-         | tar -xz -C /src/pybids --strip-components 1
-         && source activate neuro
-         && pip install --no-cache-dir -e /src/pybids" \
-  --workdir /work \
-  --label org.label-schema.build-date='$BUILD_DATE' \
-          org.label-schema.name="NIPYPE" \
-          org.label-schema.description="NIPYPE - Neuroimaging in Python: Pipelines and Interfaces" \
-          org.label-schema.url="http://nipype.readthedocs.io" \
-          org.label-schema.vcs-ref='$VCS_REF' \
-          org.label-schema.vcs-url="https://github.com/nipy/nipype" \
-          org.label-schema.version='$VERSION' \
-          org.label-schema.schema-version="1.0" \
-  --no-check-urls
+  docker run --rm "$NEURODOCKER_IMAGE" generate docker \
+    --base "$NIPYPE_BASE_IMAGE" --pkg-manager "$PKG_MANAGER" \
+    --label maintainer="The nipype developers https://github.com/nipy/nipype" \
+    --env MKL_NUM_THREADS=1 \
+          OMP_NUM_THREADS=1 \
+    --arg PYTHON_VERSION_MAJOR=3 PYTHON_VERSION_MINOR=6 BUILD_DATE VCS_REF VERSION \
+    --user neuro \
+    --miniconda create_env=neuro \
+                conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
+                               icu=58.1 libxml2 libxslt matplotlib mkl numpy paramiko
+                               pandas psutil scikit-learn scipy traits=4.6.0' \
+                pip_install="grabbit==0.1.2 https://github.com/INCF/pybids/tarball/0.6.5" \
+                activate=true \
+    --copy docker/files/run_builddocs.sh docker/files/run_examples.sh \
+           docker/files/run_pytests.sh nipype/external/fsl_imglob.py /usr/bin/ \
+    --copy . /src/nipype \
+    --user root \
+    --run 'chown -R neuro /src
+  && chmod +x /usr/bin/fsl_imglob.py /usr/bin/run_*.sh
+  && . /etc/fsl/fsl.sh
+  && ln -sf /usr/bin/fsl_imglob.py ${FSLDIR}/bin/imglob
+  && mkdir /work
+  && chown neuro /work' \
+    --user neuro \
+    --miniconda use_env=neuro \
+                pip_opts="-e" \
+                pip_install="/src/nipype[all]" \
+    --workdir /work \
+    --label org.label-schema.build-date='$BUILD_DATE' \
+            org.label-schema.name="NIPYPE" \
+            org.label-schema.description="NIPYPE - Neuroimaging in Python: Pipelines and Interfaces" \
+            org.label-schema.url="http://nipype.readthedocs.io" \
+            org.label-schema.vcs-ref='$VCS_REF' \
+            org.label-schema.vcs-url="https://github.com/nipy/nipype" \
+            org.label-schema.version='$VERSION' \
+            org.label-schema.schema-version="1.0"
 }