├── .codacy.yml ├── .gitattributes ├── .github ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── GHA_increase_disk_space.sh │ ├── c-cpp.yml │ ├── cffconvert.yml │ ├── docker.yml │ ├── install_docker.sh │ └── test_cil.sh ├── .gitignore ├── .gitmodules ├── .mailmap ├── CHANGES.md ├── CITATION.cff ├── CMake ├── ExternalProjectDependency.cmake ├── FindCython.cmake ├── FindFFTW3.cmake ├── FindNiftyPET.cmake ├── FindSPM.cmake ├── RenameVariable.cmake ├── SetCanonicalDirectoryNames.cmake ├── SetExternalProjectFlags.cmake ├── SetGitTagAndRepo.cmake ├── append_to_file.cmake └── install_NiftyPET.cmake ├── CMakeLists.txt ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE.txt ├── NOTICE.txt ├── README.md ├── SuperBuild.cmake ├── SuperBuild ├── External_Armadillo.cmake ├── External_Boost.cmake ├── External_Boost_buildboost.cmake ├── External_Boost_configureboost.cmake ├── External_CCPi-Regularisation-Toolkit.cmake ├── External_CIL.cmake ├── External_Date.cmake ├── External_FFTW3.cmake ├── External_FFTW3double.cmake ├── External_GTest.cmake ├── External_Gadgetron.cmake ├── External_HDF5.cmake ├── External_ISMRMRD.cmake ├── External_ITK.cmake ├── External_JSON.cmake ├── External_NIFTYREG.cmake ├── External_NiftyPET.cmake ├── External_ROOT.cmake ├── External_RocksDB.cmake ├── External_SIRF-Contribs.cmake ├── External_SIRF.cmake ├── External_SPM.cmake ├── External_STIR.cmake ├── External_SWIG.cmake ├── External_SWIG_build.cmake ├── External_SWIG_configure.cmake ├── External_TomoPhantom.cmake ├── External_astra-python-wrapper.cmake ├── External_astra-toolbox.cmake ├── External_glog.cmake ├── External_mrd-storage-server.cmake ├── External_parallelproj.cmake ├── External_pet_rd_tools.cmake ├── External_pugixml.cmake ├── External_range-v3.cmake └── External_siemens_to_ismrmrd.cmake ├── VirtualBox ├── CHANGES.md ├── INSTALL.md ├── README.md ├── Using_VM_as_server.md ├── VM_version.txt ├── documentation │ ├── Basic-usage.md │ ├── Creating-a-Base-Box-for-Vagrant.md │ ├── Extending-the-VM-to-full-STIR.md │ ├── Getting-started-with-SIRF.md │ ├── README.md │ └── Using-VM-as-a-Gadgetron-server.md ├── requirements-jupyter.txt ├── scripts │ ├── INSTALL_CMake.sh │ ├── INSTALL_prerequisites_with_apt-get.sh │ ├── INSTALL_python_packages.sh │ ├── README.md │ ├── UPDATE.sh │ ├── UPDATE_functions.sh │ ├── bootstrap_ubuntu.sh │ ├── clean_before_VM_export.sh │ ├── configure_gnome.sh │ ├── configure_jupyter.sh │ ├── configure_matplotlib.sh │ ├── first_run.sh │ ├── rm_build_files.sh │ ├── update_VGA.sh │ ├── update_VM.sh │ ├── update_VM_to_full_CIL.sh │ ├── update_VM_to_full_STIR.sh │ ├── update_with_backup_for_exercises.sh │ └── zero_fill.sh └── vagrant │ ├── .gitignore │ ├── README.md │ └── Vagrantfile ├── cloud └── terraform │ └── azure │ ├── README.md │ ├── configure_azure.sh │ ├── creds.json.skeleton │ ├── main.tf │ ├── modules │ └── sirf-gpu-offset │ │ ├── install_gpu_rdp.sh │ │ ├── main.tf │ │ └── variables.tf │ ├── packer │ ├── scripts │ │ ├── data_disk_config.sh │ │ ├── install_cuda.sh │ │ ├── install_prerequisites.sh │ │ ├── install_rdp.sh │ │ ├── jupyter.service │ │ ├── jupyter_config.sh │ │ ├── jupyter_set_pwd.sh │ │ ├── launch.sh │ │ └── provision.sh │ ├── sirf-cpu.json │ └── sirf-gpu.json │ ├── scripts │ └── ssh_all.sh │ └── variables.tf ├── docker-compose.yml ├── docker ├── .bashrc ├── .dockerignore ├── .gitignore ├── .profile ├── README.md ├── build_essential-ubuntu.sh ├── build_gadgetron-ubuntu.sh ├── build_python-ubuntu.sh ├── build_system-ubuntu.sh ├── compose.sh ├── ctest_sirf.sh ├── devel │ ├── .ccache │ │ └── .gitignore │ ├── shared.txt │ └── test.sh ├── docker-compose.devel-gpu.yml ├── docker-compose.devel.yml ├── docker-compose.gpu.yml ├── docker-compose.nix.yml ├── download_data.sh ├── get_pip_download_link.py ├── install-sirf-exercises-dep.py ├── raw-ubuntu.sh ├── requirements.txt ├── requirements.yml ├── start-gadgetron-notebook.sh ├── update_nvidia_keys.sh ├── user_demos.sh ├── user_python-ubuntu.sh └── 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