Singularity

Bootstrap: docker
From: ubuntu:18.04


%files

    #/home-local/kimm58/AtlasToDiffusionReg/code/get_transforms.sh /
    
    #The following should run as long as you ran git pull for the repository

    FILES/JHUEVE3/Labels_JHU_MNI_SS_WMPM_Type-III.txt /FILES/JHUEVE3/Labels_JHU_MNI_SS_WMPM_Type-III.txt
    FILES/JHUEVE3/Atlas_JHU_MNI_SS_WMPM_Type-III.nii.gz /FILES/JHUEVE3/Atlas_JHU_MNI_SS_WMPM_Type-III.nii.gz
    FILES/JHUEVE3/template.nii.gz /FILES/JHUEVE3/template.nii.gz
    FILES/MNI152/template.nii.gz /FILES/MNI152/template.nii.gz
    FILES/T1_seg.txt /FILES/T1_seg.txt

%help

https://github.com/MASILab/AtlasToDiffusionReg

%post -c /bin/bash

    cd /

    # Prepare directories for installing applications
    mkdir -p APPS
    mkdir -p INSTALLERS

    # Update all libraries
    apt-get -y update

    # Install xvfb
    apt-get -y install xvfb

    # Install ghostscript for pdf management
    apt-get -y install ghostscript
#####
    # Install MRTrix3
    apt-get -y install git g++ python python-numpy libeigen3-dev zlib1g-dev libqt4-opengl-dev libgl1-mesa-dev libfftw3-dev libtiff5-dev python3-distutils
    cd APPS
    git clone https://github.com/MRtrix3/mrtrix3.git
    cd mrtrix3
    git checkout 3.0.3
    ./configure
    ./build
    cd /

    # Install FSL
    apt-get -y install python wget ca-certificates libglu1-mesa libgl1-mesa-glx libsm6 libice6 libxt6 libpng16-16 libxrender1 libxcursor1 libxinerama1 libfreetype6 libxft2 libxrandr2 libgtk2.0-0 libpulse0 libasound2 libcaca0 libopenblas-base bzip2 dc bc 
    #wget -O /INSTALLERS/fslinstaller.py "https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py"
    #wget -O /INSTALLERS/fslinstaller.py "https://git.fmrib.ox.ac.uk/fsl/installer/-/raw/3.3.0/fslinstaller.py?inline=false"
    wget -O /INSTALLERS/fslinstaller.py "https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py"
    cd /INSTALLERS
    chmod +x fslinstaller.py
    python fslinstaller.py -d /APPS/fsl -V 6.0.6 -o 2>&1 | tee /tmp/fslinstaller_build.log
    cat /tmp/fslinstaller_build.log
    cd /

    # Install Convert3D (stable build 1.0.0)
    apt-get -y install wget tar
    wget -O /INSTALLERS/c3d-1.0.0-Linux-x86_64.tar.gz "https://downloads.sourceforge.net/project/c3d/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fc3d%2Ffiles%2Fc3d%2F1.0.0%2Fc3d-1.0.0-Linux-x86_64.tar.gz%2Fdownload&ts=1571934949"
    tar -xf /INSTALLERS/c3d-1.0.0-Linux-x86_64.tar.gz -C /APPS/
    cd /

    # Install ANTs (and compatible CMake)
    apt-get -y install build-essential libssl-dev
    # CMake: The latest ANTs requires newer version of cmake than can be installed
    # through apt-get, so we need to build higher version of cmake from source
    cd /INSTALLERS
    mkdir cmake_install
    cd cmake_install
    wget https://github.com/Kitware/CMake/releases/download/v3.23.0-rc2/cmake-3.23.0-rc2.tar.gz
    tar -xf cmake-3.23.0-rc2.tar.gz
    cd cmake-3.23.0-rc2/
    ./bootstrap
    make
    make install
    cd /
    # ANTS
    cd /INSTALLERS
    mkdir ants_installer
    cd ants_installer
    git clone https://github.com/ANTsX/ANTs.git
    cd ANTs/
    git checkout efa80e3f582d78733724c29847b18f3311a66b54
    mkdir ants_build
    cd ants_build
    cmake /INSTALLERS/ants_installer/ANTs -DCMAKE_INSTALL_PREFIX=/APPS/ants
    make 2>&1 | tee build.log
    cd ANTS-build
    make install 2>&1 | tee install.log
    cd /

    # ##new commands
    # cd /INSTALLERS
    # wget https://github.com/Kitware/CMake/releases/download/v3.23.0/cmake-3.23.0.tar.gz
    # tar -xf cmake-3.23.0.tar.gz
    # cd cmake-3.23.0
    # ./bootstrap
    # make
    # make install
    # cd /
    # cd /INSTALLERS

    # apt-get update && apt-get install -y \
    #     zlib1g-dev \
    #     libbz2-dev \
    #     liblzma-dev \
    #     libpng-dev \
    #     libtiff-dev \
    #     libjpeg-dev \
    #     libexpat1-dev \
    #     libssl-dev \
    #     libcurl4-openssl-dev \
    #     build-essential \
    #     git \
    #     wget
    # git clone https://github.com/ANTsX/ANTs.git
    # cd ANTs
    # git checkout efa80e3f582d78733724c29847b18f3311a66b54
    # mkdir build
    # cd build
    # cmake .. \
    # -DCMAKE_INSTALL_PREFIX=/APPS/ants \
    # -DBUILD_SHARED_LIBS=ON \
    # -DZLIB_INCLUDE_DIR=/usr/include \
    # -DZLIB_LIBRARY=/usr/lib/x86_64-linux-gnu/libz.so
    # make 2>&1 | tee build.log
    # #cd ANTS-build
    # make install 2>&1 | tee install.log
    # cd /

########
    # Install FreeSurfer
    #apt-get -y install bc binutils libgomp1 perl psmisc sudo tar tcsh unzip uuid-dev vim-common libjpeg62-dev
    #wget -O /INSTALLERS/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz "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 -C /APPS -xzvf /INSTALLERS/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
    #echo "This is a dummy license file. Please bind your freesurfer license file to this file." > /APPS/freesurfer/license.txt
    #cd /
    
    # Make custom folders
    mkdir -p INPUTS
    mkdir -p SUPPLEMENTAL
    mkdir -p OUTPUTS
    mkdir -p CODE

    # Set Permissions
    chmod 755 /INPUTS
    chmod 755 /SUPPLEMENTAL
    chmod 755 /APPS
    chmod 775 /OUTPUTS
    chmod 755 /CODE
    
    # Install source code
    cd /
    apt-get -y install git gcc libpq-dev python-dev python-pip python3 python3-dev python3-pip python3-venv python3-wheel
    cd /INSTALLERS
    #git clone https://github.com/MASILab/PreQual.git
    git clone https://github.com/MASILab/AtlasToDiffusionReg.git
    cd AtlasToDiffusionReg
    #git checkout main
    
	#Write all your scripts in a folder on github repo and then move them into the corresponding folders in this singularity
	

    #mv src/APPS/* /APPS
    mv src/CODE/* /CODE
    #mv src/SUPPLEMENTAL/* /SUPPLEMENTAL
    #cd /APPS/synb0
    #python3.6 -m venv pytorch
    #source pytorch/bin/activate
    #pip3 install wheel
    #pip install -r /INSTALLERS/PreQual/venv/pip_install_synb0.txt
    #deactivate
    cd /CODE
    python3 -m venv venv
    source venv/bin/activate
    pip3 install wheel
    pip install -r /INSTALLERS/AtlasToDiffusionReg/venv/pip_install.txt
    deactivate
    cd /

    # Clean up
    rm -r /INSTALLERS

%environment

    # MRTrix3
    export PATH="/APPS/mrtrix3/bin:$PATH"

    # FSL
    FSLDIR=/APPS/fsl
    . ${FSLDIR}/etc/fslconf/fsl.sh
    PATH=${FSLDIR}/bin:${PATH}
    export FSLDIR PATH

    # Convert3D
    export PATH="/APPS/c3d-1.0.0-Linux-x86_64/bin:$PATH"

    # ANTs
    export ANTSPATH=/APPS/ants/bin/
    export PATH=${ANTSPATH}:$PATH

    # FreeSurfer
    #export FREESURFER_HOME=/APPS/freesurfer
    #source $FREESURFER_HOME/SetUpFreeSurfer.sh # For us, only synb0 needs it so will put in that script.

    # CUDA
    #export CPATH="/usr/local/cuda/include:$CPATH"
    #export PATH="/usr/local/cuda/bin:$PATH"
    #export LD_LIBRARY_PATH="/usr/local/cuda/lib64:$LD_LIBRARY_PATH"
    #export CUDA_HOME="/usr/local/cuda"

%runscript
	#everything below this will run when you call singularity run xxx.simg
	#this creates the PDF, figure out later
    #xvfb-run -a --server-num=$((65536+$$)) --server-args="-screen 0 1600x1280x24 -ac" bash /CODE/run_dtiQA.sh /INPUTS /OUTPUTS "$@"

    #v1.5: added the low/high for the bval threshold instead of hard coding it in
    low=0
    high=1500
    atlastype=""

    # Loop through all arguments
    while [ "$#" -gt 0 ]; do
    case "$1" in
        --low)
        low=$(echo "$2" | cut -d '.' -f 1)
        shift 2
        ;;
        --high)
        high=$(echo "$2" | cut -d '.' -f 1)
        shift 2
        ;;
        --EVE3|--MNI|--custom)
        atlas_type="$1"  # Capture the atlas type instead of relying on $1 later
        shift
        ;;
        --) # End of options
        shift
        break
        ;;
        -*)
        echo "Unknown option: $1" >&2
        exit 1
        ;;
    esac
    done

    case "$atlas_type" in
        --EVE3)
            echo "Registering to EVE3 Atlas."
            ln -s /FILES/JHUEVE3/template.nii.gz /INPUTS/template.nii.gz
            ln -s /FILES/JHUEVE3/Atlas_JHU_MNI_SS_WMPM_Type-III.nii.gz /INPUTS/Atlas_JHU_MNI_SS_WMPM_Type-III.nii.gz
            ln -s /FILES/JHUEVE3/Labels_JHU_MNI_SS_WMPM_Type-III.txt /INPUTS/Labels_JHU_MNI_SS_WMPM_Type-III.txt
            ;;
        --MNI)
            echo "Registering to MNI152 Atlas."
            ln -s /FILES/MNI152/template.nii.gz /INPUTS/template.nii.gz
            ;;
        --custom)
            echo "Registering to custom template. Ensure that there is a file named 'template.nii.gz' in the inputs directory."
            echo "Also, if you want to register Atlases, make sure there are corresponding Atlas* and Labels* files in the inputs directory."
            ;;
        *)
            echo "Invalid arguments."
            echo "USAGE: singularity run <BINDS> <SIMG> [--EVE3|--MNI|--custom] [--low <val>] [--high <val>]"
            exit 1
            ;;
    esac

    #if [ ! -f /INPUTS/template.nii.gz ]; then
    #    ln -s /FILES/template.nii.gz /INPUTS/template.nii.gz
    #    ln -s /FILES/Atlas_JHU_MNI_SS_WMPM_Type-III.nii.gz /INPUTS/Atlas_JHU_MNI_SS_WMPM_Type-III.nii.gz
    #    ln -s /FILES/Labels_JHU_MNI_SS_WMPM_Type-III.txt /INPUTS/Labels_JHU_MNI_SS_WMPM_Type-III.txt
    #fi
    seglink="False"
    if [ ! -e /INPUTS/T1_seg.txt ]; then
        ln -s /FILES/T1_seg.txt /INPUTS/T1_seg.txt
        seglink="True"
    fi
    cd /CODE
    bash get_transforms.sh
    bash apply_transforms.sh
    #bash activate_venv.sh
    python3 extract_single_shell.py --u_thresh $high --l_thresh $low
    bash calc_scalars.sh
    python3 calc_metrics_per_roi.py
    python3 create_QA_png.py
    deactivate
    case "$atlas_type" in
        --EVE3)
            echo "Registering to EVE3 Atlas."
            rm /INPUTS/template.nii.gz
            rm /INPUTS/Atlas_JHU_MNI_SS_WMPM_Type-III.nii.gz
            rm /INPUTS/Labels_JHU_MNI_SS_WMPM_Type-III.txt
            ;;
        --MNI)
            echo "Registering to MNI152 Atlas."
            rm /INPUTS/template.nii.gz
            ;;
    esac
    if [ "$seglink" = "True" ]; then
        rm /INPUTS/T1_seg.txt
    fi