Add VBG

[stebo85]

No description provided.

[stebo85]

https://github.com/KUL-Radneuron/KUL_VBG

These would be the building blocks we need for the dependencies:

--ants method=source version=2.3.1 make_opts='-j2'\

--fsl version=6.0 \
   --env FSLOUTPUTTYPE=NIFTI_GZ \
   --install locales \
   --run="sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && locale-gen" \
   --env LANG=en_US.UTF-8 \
   --env LANGUAGE=en_US:en \
   --env LC_ALL=en_US.UTF-8 \

   --mrtrix3 version=3.0.2 method="source" build_processes=1 \
   --workdir /opt/mrtrix3 \
   --install dbus-x11 less python3-distutils mesa-common-dev libglu1-mesa qt5-default libqt5svg5-dev wget libqt5opengl5-dev libqt5opengl5 libqt5gui5 libqt5core5a libtiff5-dev libtiff5 libfftw3-dev \
   --run "python3 configure" \
   --run "python3 build" \
   --run "ln -s /usr/bin/python3 /usr/bin/python" \


--install git \
   --miniconda version=4.7.12.1 \
         conda_install='python=3.6' \
   --workdir /opt \
   --run="git clone https://github.com/MIC-DKFZ/HD-BET" \
   --workdir /opt/HD-BET \
   --run="echo 'import os' > /opt/HD-BET/HD_BET/paths.py" \
   --run="echo 'folder_with_parameter_files = \"/opt/HD-BET/hd-bet_params\"' >> /opt/HD-BET/HD_BET/paths.py" \
   --run="mkdir -p /opt/HD-BET/hd-bet_params" \
   --run="curl -o /opt/HD-BET/hd-bet_params/0.model https://zenodo.org/record/2540695/files/0.model?download=1" \
   --run="curl -o /opt/HD-BET/hd-bet_params/1.model https://zenodo.org/record/2540695/files/1.model?download=1" \
   --run="curl -o /opt/HD-BET/hd-bet_params/2.model https://zenodo.org/record/2540695/files/2.model?download=1" \
   --run="curl -o /opt/HD-BET/hd-bet_params/3.model https://zenodo.org/record/2540695/files/3.model?download=1" \
   --run="curl -o /opt/HD-BET/hd-bet_params/4.model https://zenodo.org/record/2540695/files/4.model?download=1" \
   --run="pip install -e ." \
   --env DEPLOY_BINS=hd-bet \

--freesurfer version=6.0 \

--run="git clone --depth 1 --branch v1.1.1 https://github.com/Deep-MI/FastSurfer.git /opt/FastSurfer \
       && sed -i 's/cu113/cpu/g' /opt/FastSurfer/requirements.txt \
       && pip install -r /opt/FastSurfer/requirements.txt" \
   --env FASTSURFER_HOME="/opt/FastSurfer" \
   --env PATH="\${PATH}:/opt/FastSurfer" \

@dkp

[dkp]

Cool! It seems like a great use for Neurodesk, and would make their software much more accessible!