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Singularity
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Singularity
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Bootstrap: debootstrap
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
OSVersion: bionic
Include: apt file gnupg
%labels
MAINTAINER Robert E. Smith <robert.smith@florey.edu.au>
%files
mrtrix3_connectome.py /mrtrix3_connectome.py
neurodebian.gpg /neurodebian.gpg
version /version
%environment
# ANTs
ANTSPATH=/usr/lib/ants
export ANTSPATH
# FreeSurfer
OS=Linux
SUBJECTS_DIR=/opt/freesurfer/subjects
FSF_OUTPUT_FORMAT=nii.gz
MNI_DIR=/opt/freesurfer/mni
LOCAL_DIR=/opt/freesurfer/local
FREESURFER_HOME=/opt/freesurfer
FSFAST_HOME=/opt/freesurfer/fsfast
MINC_BIN_DIR=/opt/freesurfer/mni/bin
MINC_LIB_DIR=/opt/freesurfer/mni/lib
MNI_DATAPATH=/opt/freesurfer/mni/data
FMRI_ANALYSIS_DIR=/opt/freesurfer/fsfast
PERL5LIB=/opt/freesurfer/mni/lib/perl5/5.8.5
MNI_PERL5LIB=/opt/freesurfer/mni/lib/perl5/5.8.5
export OS SUBJECTS_DIR FSF_OUTPUT_FORMAT MNI_DIR LOCAL_DIR FREESURFER_HOME FSFAST_HOME MINC_BIN_DIR MINC_LIB_DIR MNI_DATAPATH FMRI_ANALYSIS_DIR PERL5LIB MNI_PERL5LIB
# FSL
FSLDIR=/opt/fsl
FSLOUTPUTTYPE=NIFTI
FSLMULTIFILEQUIT=TRUE
FSLTCLSH=/opt/fsl/bin/fsltclsh
FSLWISH=/opt/fsl/bin/fslwish
export FSLDIR FSLOUTPUTTYPE FSLMULTIFILEQUIT FSLTCLSH FSLWISH
# MRtrix3
PYTHONPATH=/opt/mrtrix3/lib:$PYTHONPATH
export PYTHONPATH
# All
LD_LIBRARY_PATH=/usr/local/cuda/lib64:/usr/local/cuda/bin:/.singularity.d/libs:/usr/lib:/opt/fsl/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH
PATH=/opt/mrtrix3/bin:/usr/local/cuda/bin:/usr/lib/ants:/opt/freesurfer/bin:/opt/freesurfer/mni/bin:/opt/fsl/bin:/opt/ROBEX:$PATH
export PATH
%post
# Non-interactive installation of packages
export DEBIAN_FRONTEND=noninteractive
# Grab additional repositories
sed -i 's/main/main restricted universe multiverse/g' /etc/apt/sources.list
apt-get update && apt-get upgrade -y
# Base requirements
apt-get update && apt-get install -y bc build-essential curl dc git libegl1-mesa-dev libopenblas-dev nano perl-modules-5.26 python python3 tar tcsh tzdata unzip wget
# PPA for newer version of nodejs, which is required for bids-validator
curl -sL https://deb.nodesource.com/setup_12.x -o nodesource_setup.sh && bash nodesource_setup.sh && rm -f nodesource_setup.sh
apt-get update && apt-get install -y nodejs
# NeuroDebian setup
wget -qO- http://neuro.debian.net/lists/bionic.au.full | tee -a /etc/apt/sources.list
apt-key add /neurodebian.gpg && apt-get update
# Additional dependencies for MRtrix3 compilation
apt-get install -y libeigen3-dev libfftw3-dev libpng-dev libtiff5-dev zlib1g-dev
# Neuroimaging software / data dependencies
wget -qO- https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-linux-centos8_x86_64-7.1.1.tar.gz | tar zx -C /opt --exclude='freesurfer/trctrain' --exclude='freesurfer/subjects/fsaverage_sym' --exclude='freesurfer/subjects/fsaverage3' --exclude='freesurfer/subjects/fsaverage4' --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/qt'
echo "cHJpbnRmICJyb2JlcnQuc21pdGhAZmxvcmV5LmVkdS5hdVxuMjg1NjdcbiAqQ3FLLjFwTXY4ZE5rXG4gRlNvbGRZRXRDUFZqNlxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
FREESURFER_HOME=/opt/freesurfer /bin/bash -c 'source /opt/freesurfer/SetUpFreeSurfer.sh'
apt-get install -y ants=2.2.0-1ubuntu1
wget -q http://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py
chmod 775 fslinstaller.py
python2 /fslinstaller.py -d /opt/fsl -V 6.0.4 -q
rm /fslinstaller.py
which immv || ( echo "FSLPython not properly configured; re-running" && rm -rf /opt/fsl/fslpython && /opt/fsl/etc/fslconf/fslpython_install.sh -f /opt/fsl || ( cat /tmp/fslpython*/fslpython_miniconda_installer.log && exit 1 ) )
wget -qO- "https://www.nitrc.org/frs/download.php/5994/ROBEXv12.linux64.tar.gz//?i_agree=1&download_now=1" | tar zx -C /opt
npm install -gq bids-validator@1.5.3
# apt cleanup to recover as much space as possible
apt-get remove libegl1-mesa-dev -y && apt-get autoremove -y
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
# Download additional data for neuroimaging software, e.g. templates / atlases
wget -q https://object.cscs.ch/v1/AUTH_4791e0a3b3de43e2840fe46d9dc2b334/ext-d000035_AAL1Atlas_pub/Release2018_SPM12/aal_for_SPM12.zip && unzip aal_for_SPM12.zip -d /opt && rm -f aal_for_SPM12.zip
wget -qO- http://www.gin.cnrs.fr/wp-content/uploads/aal2_for_SPM12.tar.gz | tar zx -C /opt
wget -q https://github.com/AlistairPerry/CCA/raw/master/parcellations/512inMNI.nii -O /opt/512inMNI.nii
wget -qO- http://www.nitrc.org/frs/download.php/5906/ADHD200_parcellations.tar.gz | tar zx -C /opt
wget -q "https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/5528816/lh.HCPMMP1.annot" -O /opt/freesurfer/subjects/fsaverage/label/lh.HCPMMP1.annot
wget -q "https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/5528819/rh.HCPMMP1.annot" -O /opt/freesurfer/subjects/fsaverage/label/rh.HCPMMP1.annot
mkdir /opt/brainnetome
wget -q "http://ddl.escience.cn/f/IiyU?func=download&rid=8135438" -O /opt/freesurfer/average/rh.BN_Atlas.gcs || wget -q "https://osf.io/e6zkg/download" -O /opt/freesurfer/average/rh.BN_Atlas.gcs
wget -q "http://ddl.escience.cn/f/IiyP?func=download&rid=8135433" -O /opt/freesurfer/average/lh.BN_Atlas.gcs || wget -q "https://osf.io/af9ut/download" -O /opt/freesurfer/average/lh.BN_Atlas.gcs
wget -q "http://ddl.escience.cn/f/PC7Q?func=download&rid=9882718" -O /opt/freesurfer/average/BN_Atlas_subcortex.gca || wget -q "https://osf.io/k2cd8/download" -O /opt/freesurfer/average/BN_Atlas_subcortex.gca
wget -q "http://ddl.escience.cn/f/PC7O?func=download&rid=9882716" -O /opt/brainnetome/BN_Atlas_246_LUT.txt || wget -q "https://osf.io/eb7pm/download" -O /opt/brainnetome/BN_Atlas_246_LUT.txt
wget -q "http://ddl.escience.cn/f/Bvhg?func=download&rid=6516020" -O /opt/brainnetome/BNA_MPM_thr25_1.25mm.nii.gz || wget -q "https://osf.io/dbqep/download" -O /opt/brainnetome/BNA_MPM_thr25_1.25mm.nii.gz
cp /opt/brainnetome/BN_Atlas_246_LUT.txt /opt/freesurfer/
wget -qO- "https://github.com/ThomasYeoLab/CBIG/archive/v0.11.1-Wu2017_RegistrationFusion.tar.gz" | tar zx -C /opt
cp /opt/CBIG-0.11.1-Wu2017_RegistrationFusion/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/*h.Yeo2011_*Networks_N1000.split_components.annot /opt/freesurfer/subjects/fsaverage5/label/
cp /opt/CBIG-0.11.1-Wu2017_RegistrationFusion/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/project_to_individual/Yeo2011_*networks_Split_Components_LUT.txt /opt/freesurfer/
mkdir /opt/Yeo2011
cp /opt/CBIG-0.11.1-Wu2017_RegistrationFusion/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/Yeo2011_*Networks_N1000.split_components.FSL_MNI152_*mm.nii.gz /opt/Yeo2011/
cp /opt/CBIG-0.11.1-Wu2017_RegistrationFusion/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/*Networks_ColorLUT_freeview.txt /opt/Yeo2011/
rm -rf /opt/CBIG-0.11.1-Wu2017_RegistrationFusion
# MRtrix3 setup
# Commitish is 3.0.3 plus relevant hotfix
git clone https://github.com/MRtrix3/mrtrix3.git /opt/mrtrix3 && cd /opt/mrtrix3 && git checkout d3941f44318112cf64ca1afd0f960f8f641da9e5 && python3 configure -nogui && python3 build -persistent -nopaginate && git describe --tags > /mrtrix3_version && rm -rf .git/ cmd/ core/ src/ testing/ tmp/ && cd ../../
wget -q "https://osf.io/v8n5g/download" -O /opt/mrtrix3/share/mrtrix3/labelconvert/Yeo2011_7N_split.txt
wget -q "https://osf.io/ug2ef/download" -O /opt/mrtrix3/share/mrtrix3/labelconvert/Yeo2011_17N_split.txt
# MRtrix3_connectome script
chmod 775 /mrtrix3_connectome.py
%runscript
exec /usr/bin/python /mrtrix3_connectome.py "$@"