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Dockerfile
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Dockerfile
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# sMRIPrep Docker Container Image distribution
#
# MIT License
#
# Copyright (c) 2022 The NiPreps Developers
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
# Use Ubuntu 20.04 LTS
FROM ubuntu:focal-20210416
# Prepare environment
RUN apt-get update && \
apt-get install -y --no-install-recommends \
apt-utils \
autoconf \
build-essential \
bzip2 \
ca-certificates \
curl \
git \
libtool \
lsb-release \
netbase \
pkg-config \
unzip \
xvfb && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
ENV DEBIAN_FRONTEND="noninteractive" \
LANG="en_US.UTF-8" \
LC_ALL="en_US.UTF-8"
# Installing freesurfer
COPY docker/files/freesurfer7.2-exclude.txt /usr/local/etc/freesurfer7.2-exclude.txt
RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz \
 | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.2-exclude.txt
# Simulate SetUpFreeSurfer.sh
ENV FSL_DIR="/opt/fsl-6.0.5.1" \
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:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
# FSL 6.0.5.1
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
bc \
dc \
file \
libfontconfig1 \
libfreetype6 \
libgl1-mesa-dev \
libgl1-mesa-dri \
libglu1-mesa-dev \
libgomp1 \
libice6 \
libxcursor1 \
libxft2 \
libxinerama1 \
libxrandr2 \
libxrender1 \
libxt6 \
sudo \
wget \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Downloading FSL ..." \
&& mkdir -p /opt/fsl-6.0.5.1 \
&& curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-centos7_64.tar.gz \
| tar -xz -C /opt/fsl-6.0.5.1 --strip-components 1 \
--exclude "fsl/config" \
--exclude "fsl/data/atlases" \
--exclude "fsl/data/first" \
--exclude "fsl/data/mist" \
--exclude "fsl/data/possum" \
--exclude "fsl/data/standard/bianca" \
--exclude "fsl/data/standard/tissuepriors" \
--exclude "fsl/doc" \
--exclude "fsl/etc/default_flobs.flobs" \
--exclude "fsl/etc/fslconf" \
--exclude "fsl/etc/js" \
--exclude "fsl/etc/luts" \
--exclude "fsl/etc/matlab" \
--exclude "fsl/extras" \
--exclude "fsl/include" \
--exclude "fsl/python" \
--exclude "fsl/refdoc" \
--exclude "fsl/src" \
--exclude "fsl/tcl" \
--exclude "fsl/bin/FSLeyes" \
&& find /opt/fsl-6.0.5.1/bin -type f -not \( \
-name "applywarp" -or \
-name "bet" -or \
-name "bet2" -or \
-name "convert_xfm" -or \
-name "fast" -or \
-name "flirt" -or \
-name "fsl_regfilt" -or \
-name "fslhd" -or \
-name "fslinfo" -or \
-name "fslmaths" -or \
-name "fslmerge" -or \
-name "fslroi" -or \
-name "fslsplit" -or \
-name "fslstats" -or \
-name "imtest" -or \
-name "mcflirt" -or \
-name "melodic" -or \
-name "prelude" -or \
-name "remove_ext" -or \
-name "susan" -or \
-name "topup" -or \
-name "zeropad" \) -delete \
&& find /opt/fsl-6.0.5.1/data/standard -type f -not -name "MNI152_T1_2mm_brain.nii.gz" -delete
ENV FSLDIR="/opt/fsl-6.0.5.1" \
PATH="/opt/fsl-6.0.5.1/bin:$PATH" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
FSLLOCKDIR="" \
FSLMACHINELIST="" \
FSLREMOTECALL="" \
FSLGECUDAQ="cuda.q" \
LD_LIBRARY_PATH="/opt/fsl-6.0.5.1/lib:$LD_LIBRARY_PATH"
# Convert3D (neurodocker build)
RUN echo "Downloading Convert3D ..." \
&& mkdir -p /opt/convert3d-1.0.0 \
&& curl -fsSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download \
| tar -xz -C /opt/convert3d-1.0.0 --strip-components 1 \
--exclude "c3d-1.0.0-Linux-x86_64/lib" \
--exclude "c3d-1.0.0-Linux-x86_64/share" \
--exclude "c3d-1.0.0-Linux-x86_64/bin/c3d_gui"
ENV C3DPATH="/opt/convert3d-1.0.0" \
PATH="/opt/convert3d-1.0.0/bin:$PATH"
# AFNI latest (neurodocker build)
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
apt-utils \
ed \
gsl-bin \
libglib2.0-0 \
libglu1-mesa-dev \
libglw1-mesa \
libgomp1 \
libjpeg62 \
libxm4 \
netpbm \
tcsh \
xfonts-base \
xvfb \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& curl -sSL --retry 5 -o /tmp/multiarch.deb http://archive.ubuntu.com/ubuntu/pool/main/g/glibc/multiarch-support_2.27-3ubuntu1.5_amd64.deb \
&& dpkg -i /tmp/multiarch.deb \
&& rm /tmp/multiarch.deb \
&& curl -sSL --retry 5 -o /tmp/libxp6.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
&& dpkg -i /tmp/libxp6.deb \
&& rm /tmp/libxp6.deb \
&& curl -sSL --retry 5 -o /tmp/libpng.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
&& dpkg -i /tmp/libpng.deb \
&& rm /tmp/libpng.deb \
&& apt-get install -f \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \
&& if [ -n "$gsl2_path" ]; then \
ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
fi \
&& ldconfig \
&& echo "Downloading AFNI ..." \
&& mkdir -p /opt/afni-latest \
&& curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
| tar -xz -C /opt/afni-latest --strip-components 1 \
--exclude "linux_openmp_64/*.gz" \
--exclude "linux_openmp_64/funstuff" \
--exclude "linux_openmp_64/shiny" \
--exclude "linux_openmp_64/afnipy" \
--exclude "linux_openmp_64/lib/RetroTS" \
--exclude "linux_openmp_64/meica.libs" \
# Keep only what we use
&& find /opt/afni-latest -type f -not \( \
-name "3dTshift" -or \
-name "3dUnifize" -or \
-name "3dAutomask" -or \
-name "3dvolreg" \) -delete
ENV PATH="/opt/afni-latest:$PATH" \
AFNI_IMSAVE_WARNINGS="NO" \
AFNI_PLUGINPATH="/opt/afni-latest"
# Installing ANTs 2.3.3 (NeuroDocker build)
# Note: the URL says 2.3.4 but it is actually 2.3.3
ENV ANTSPATH="/opt/ants" \
PATH="/opt/ants:$PATH"
WORKDIR $ANTSPATH
RUN curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
| tar -xzC $ANTSPATH --strip-components 1
# nipreps/miniconda:py39_0525.0
COPY --from=nipreps/miniconda@sha256:40fffd37963502dcd8549773559fc21182f52460e59e0ad6398a84faf6055641 /opt/conda /opt/conda
RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
echo "conda activate base" >> ~/.bashrc
# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
ENV PATH="/opt/conda/bin:$PATH" \
CPATH="/opt/conda/include:$CPATH" \
LD_LIBRARY_PATH="/opt/conda/lib:$LD_LIBRARY_PATH" \
LANG="C.UTF-8" \
LC_ALL="C.UTF-8" \
PYTHONNOUSERSITE=1
# Unless otherwise specified each process should only use one thread - nipype
# will handle parallelization
ENV MKL_NUM_THREADS=1 \
OMP_NUM_THREADS=1
# Create a shared $HOME directory
RUN useradd -m -s /bin/bash -G users smriprep
WORKDIR /home/smriprep
ENV HOME="/home/smriprep" \
LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> $HOME/.bashrc && \
echo "conda activate base" >> $HOME/.bashrc
# Precaching atlases
COPY scripts/fetch_templates.py fetch_templates.py
RUN /opt/conda/bin/python fetch_templates.py && \
rm fetch_templates.py && \
find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && \
find $HOME/.cache/templateflow -type f -exec chmod go=u {} +
# Installing sMRIPREP
COPY . /src/smriprep
ARG VERSION
# Force static versioning within container
RUN echo "${VERSION}" > /src/smriprep/smriprep/VERSION && \
echo "include smriprep/VERSION" >> /src/smriprep/MANIFEST.in && \
/opt/conda/bin/python -m pip install --no-cache-dir "/src/smriprep[all]"
RUN find $HOME -type d -exec chmod go=u {} + && \
find $HOME -type f -exec chmod go=u {} + && \
rm -rf $HOME/.npm $HOME/.conda $HOME/.empty
# HACK for FreeSurfer 7.2.0
# Fixed in https://github.com/freesurfer/freesurfer/pull/886, so remove on release
ENV FREESURFER="/opt/freesurfer"
ENV IS_DOCKER_8395080871=1
RUN ldconfig
WORKDIR /tmp
ENTRYPOINT ["/opt/conda/bin/smriprep"]
ARG BUILD_DATE
ARG VCS_REF
ARG VERSION
LABEL org.label-schema.build-date=$BUILD_DATE \
org.label-schema.name="sMRIPrep" \
org.label-schema.description="sMRIPrep - robust structural MRI preprocessing tool" \
org.label-schema.url="http://smriprep.org" \
org.label-schema.vcs-ref=$VCS_REF \
org.label-schema.vcs-url="https://github.com/nipreps/smriprep" \
org.label-schema.version=$VERSION \
org.label-schema.schema-version="1.0"