├── .editorconfig ├── .gitchangelog.rc ├── .gitchangelog.tpl ├── .gitignore ├── .travis.yml ├── CHANGELOG.rst ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.rst ├── containers ├── Dockerfile.intel ├── Dockerfile.nvidia ├── Singularity.intel └── silent.cfg ├── debian ├── copyright └── menu.ex ├── docs ├── Makefile ├── _dynamic_modules │ ├── batch_profiles.rst │ ├── compartment_models.rst │ ├── composite_models.rst │ ├── library_functions.rst │ └── parameters.rst ├── _static │ ├── custom.css │ ├── figures │ │ ├── mdt_additional_problem_data.png │ │ ├── mdt_compilation_flow.png │ │ ├── mdt_gui_generate_protocol.png │ │ ├── mdt_gui_generate_protocol_filled.png │ │ ├── mdt_gui_intro_screenshot.png │ │ ├── mdt_gui_runtime_settings.png │ │ ├── mdt_maps_visualizer_control_panel.png │ │ ├── mdt_maps_visualizer_intro.png │ │ ├── mdt_model_building.png │ │ ├── mdt_optimization_options.png │ │ └── mdt_view_maps_gui.png │ ├── html_favicon.ico │ └── noddi_comparison │ │ ├── noddi_comparison.conf │ │ ├── noddi_comparison.png │ │ └── noddi_comparison_script.py ├── _templates │ └── navigation.html ├── adding_components.rst ├── auto_gen_cli_index.rst ├── changelog.rst ├── cli_index.rst ├── concepts.rst ├── conf.py ├── configuration.rst ├── credits.rst ├── developer_guidelines.rst ├── development_ideas.rst ├── faq.rst ├── index.rst ├── index_latex.rst ├── index_man.rst ├── install.rst ├── make.bat ├── maps_visualizer.rst ├── mcmc_sampling.rst ├── mdt.cli_scripts.rst ├── mdt.component_templates.rst ├── mdt.gui.maps_visualizer.config_tabs.rst ├── mdt.gui.maps_visualizer.design.rst ├── mdt.gui.maps_visualizer.renderers.rst ├── mdt.gui.maps_visualizer.rst ├── mdt.gui.model_fit.design.rst ├── mdt.gui.model_fit.rst ├── mdt.gui.model_fit.tabs.rst ├── mdt.gui.rst ├── mdt.gui.widgets.design.rst ├── mdt.gui.widgets.rst ├── mdt.lib.file_conversions.rst ├── mdt.lib.rst ├── mdt.model_building.parameter_functions.rst ├── mdt.model_building.rst ├── mdt.models.rst ├── mdt.rst ├── mdt.visualization.maps.rst ├── mdt.visualization.rst ├── mle_fitting.rst ├── modules.rst ├── readme_latex.rst ├── readme_man.rst ├── references.bib ├── scientific_articles.rst └── using_mdt.rst ├── mdt ├── __init__.py ├── __version__.py ├── cli_scripts │ ├── MDT.py │ ├── __init__.py │ ├── mdt_apply_mask.py │ ├── mdt_batch_fit.py │ ├── mdt_create_bvec_bval.py │ ├── mdt_create_mask.py │ ├── mdt_create_protocol.py │ ├── mdt_create_roi_slice.py │ ├── mdt_estimate_noise_std.py │ ├── mdt_get_example_data.py │ ├── mdt_gui.py │ ├── mdt_info_img.py │ ├── mdt_info_protocol.py │ ├── mdt_init_user_settings.py │ ├── mdt_list_devices.py │ ├── mdt_list_models.py │ ├── mdt_math_img.py │ ├── mdt_math_protocol.py │ ├── mdt_model_fit.py │ ├── mdt_view_maps.py │ └── mdt_volume_merge.py ├── component_templates │ ├── __init__.py │ ├── base.py │ ├── batch_profiles.py │ ├── compartment_models.py │ ├── composite_models.py │ ├── library_functions.py │ ├── parameters.py │ └── utils.py ├── configuration.py ├── data │ ├── components │ │ └── standard │ │ │ ├── batch_profiles │ │ │ ├── general.py │ │ │ └── hcp.py │ │ │ ├── compartment_models │ │ │ ├── AstroCylinders.py │ │ │ ├── AstroSticks.py │ │ │ ├── Ball.py │ │ │ ├── CHARMEDRestricted.py │ │ │ ├── CylinderGPD.py │ │ │ ├── Dot.py │ │ │ ├── GDRCylinders.py │ │ │ ├── KurtosisTensor.py │ │ │ ├── NODDI.py │ │ │ ├── PDRCylinders.py │ │ │ ├── Racket.py │ │ │ ├── S0.py │ │ │ ├── SSFP.py │ │ │ ├── SphereGPD.py │ │ │ ├── Stick.py │ │ │ ├── SymmetricNonParametricTensor.py │ │ │ ├── Tensor.py │ │ │ ├── TimeDependentZeppelin.py │ │ │ ├── Weights.py │ │ │ ├── Zeppelin.py │ │ │ └── relaxometry.py │ │ │ ├── composite_models │ │ │ ├── ActiveAx.py │ │ │ ├── AxCaliber.py │ │ │ ├── BallRackets.py │ │ │ ├── BallSticks.py │ │ │ ├── CHARMED.py │ │ │ ├── Kurtosis.py │ │ │ ├── NODDI.py │ │ │ ├── SSFP.py │ │ │ ├── Tensor.py │ │ │ ├── VERDICT.py │ │ │ ├── ivim.py │ │ │ ├── qmt.py │ │ │ ├── relaxometry.py │ │ │ └── s0s.py │ │ │ ├── library_functions │ │ │ ├── MRIConstants.py │ │ │ ├── SSFP.py │ │ │ ├── bessel_roots.py │ │ │ ├── distributions.py │ │ │ ├── linear_algebra.py │ │ │ ├── noddi.py │ │ │ ├── physical_diffusion_models.py │ │ │ └── tensor_kurtosis.py │ │ │ └── parameters │ │ │ ├── free.py │ │ │ └── protocol.py │ ├── logo.svg │ ├── logo_docs.png │ ├── logo_gui.png │ ├── mdt.conf │ ├── mdt_example_data │ │ ├── b1k_b2k │ │ │ ├── b1k_b2k.bval │ │ │ ├── b1k_b2k.bvec │ │ │ ├── b1k_b2k.prtcl │ │ │ ├── b1k_b2k_example_slices_24_38.nii.gz │ │ │ └── b1k_b2k_example_slices_24_38_mask.nii.gz │ │ └── multishell_b6k_max │ │ │ ├── multishell_b6k_max.bval │ │ │ ├── multishell_b6k_max.bvec │ │ │ ├── multishell_b6k_max.prtcl │ │ │ ├── multishell_b6k_max_example_slices_24_38.nii.gz │ │ │ └── multishell_b6k_max_example_slices_24_38_mask.nii.gz │ └── qt_designs │ │ ├── Makefile │ │ ├── maps_visualizer │ │ ├── MainWindow.ui │ │ ├── Makefile │ │ ├── MapSpecificOptions.ui │ │ ├── TabGeneral.ui │ │ ├── TabMapSpecific.ui │ │ ├── TabTextual.ui │ │ ├── arrow_redo.png │ │ ├── arrow_undo.png │ │ ├── main.qrc │ │ └── save_image_dialog.ui │ │ ├── model_fit │ │ ├── Makefile │ │ ├── about_dialog.ui │ │ ├── dialog_get_example_data.ui │ │ ├── fit_model_tab.ui │ │ ├── generate_brain_mask_tab.ui │ │ ├── generate_protocol_load_gb_dialog.ui │ │ ├── generate_protocol_tab.ui │ │ ├── generate_protocol_update_dialog.ui │ │ ├── generate_roi_mask_tab.ui │ │ ├── icon_status_green.png │ │ ├── icon_status_red.png │ │ ├── main_gui.qrc │ │ ├── main_gui.ui │ │ ├── optimization_extra_data_add_protocol_map_dialog.ui │ │ ├── optimization_extra_data_dialog.ui │ │ ├── optimization_options_dialog.ui │ │ └── runtime_settings_dialog.ui │ │ └── widgets │ │ ├── Makefile │ │ └── scientific_number_scroller_widget.ui ├── gui │ ├── __init__.py │ ├── maps_visualizer │ │ ├── __init__.py │ │ ├── actions.py │ │ ├── base.py │ │ ├── config_tabs │ │ │ ├── __init__.py │ │ │ ├── tab_general.py │ │ │ ├── tab_map_specific.py │ │ │ └── tab_textual.py │ │ ├── design │ │ │ ├── __init__.py │ │ │ ├── main_rc.py │ │ │ ├── ui_MainWindow.py │ │ │ ├── ui_MapSpecificOptions.py │ │ │ ├── ui_TabGeneral.py │ │ │ ├── ui_TabMapSpecific.py │ │ │ ├── ui_TabTextual.py │ │ │ └── ui_save_image_dialog.py │ │ ├── main.py │ │ ├── renderers │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ └── matplotlib_renderer.py │ │ └── widgets.py │ ├── model_fit │ │ ├── __init__.py │ │ ├── design │ │ │ ├── __init__.py │ │ │ ├── main_gui_rc.py │ │ │ ├── ui_about_dialog.py │ │ │ ├── ui_dialog_get_example_data.py │ │ │ ├── ui_fit_model_tab.py │ │ │ ├── ui_generate_brain_mask_tab.py │ │ │ ├── ui_generate_protocol_load_gb_dialog.py │ │ │ ├── ui_generate_protocol_tab.py │ │ │ ├── ui_generate_protocol_update_dialog.py │ │ │ ├── ui_generate_roi_mask_tab.py │ │ │ ├── ui_main_gui.py │ │ │ ├── ui_optimization_extra_data_add_protocol_map_dialog.py │ │ │ ├── ui_optimization_extra_data_dialog.py │ │ │ ├── ui_optimization_options_dialog.py │ │ │ └── ui_runtime_settings_dialog.py │ │ ├── qt_main.py │ │ ├── tabs │ │ │ ├── __init__.py │ │ │ ├── fit_model_tab.py │ │ │ ├── generate_brain_mask_tab.py │ │ │ ├── generate_protocol_tab.py │ │ │ └── generate_roi_mask_tab.py │ │ └── utils.py │ ├── utils.py │ └── widgets │ │ ├── __init__.py │ │ ├── composite_widgets.py │ │ ├── decorator_widgets.py │ │ └── design │ │ ├── __init__.py │ │ └── ui_scientific_number_scroller_widget.py ├── lib │ ├── __init__.py │ ├── batch_utils.py │ ├── components.py │ ├── deferred_mappings.py │ ├── exceptions.py │ ├── file_conversions │ │ ├── __init__.py │ │ └── npy.py │ ├── fsl_sampling_routine.py │ ├── input_data.py │ ├── log_handlers.py │ ├── masking.py │ ├── nifti.py │ ├── post_processing.py │ ├── processing │ │ ├── __init__.py │ │ ├── model_bootstrapping.py │ │ ├── model_fitting.py │ │ ├── model_sampling.py │ │ └── processing_strategies.py │ ├── shell_utils.py │ └── sorting.py ├── model_building │ ├── __init__.py │ ├── likelihood_functions.py │ ├── model_functions.py │ ├── parameter_functions │ │ ├── __init__.py │ │ ├── dependencies.py │ │ ├── numdiff_info.py │ │ ├── priors.py │ │ └── transformations.py │ ├── parameters.py │ ├── signal_noise_models.py │ ├── trees.py │ └── utils.py ├── models │ ├── __init__.py │ ├── base.py │ ├── compartments.py │ └── composite.py ├── protocols.py ├── simulations.py ├── utils.py └── visualization │ ├── __init__.py │ ├── dict_conversion.py │ ├── layouts.py │ ├── maps │ ├── __init__.py │ ├── base.py │ ├── matplotlib_renderer.py │ └── utils.py │ ├── samples.py │ └── utils.py ├── requirements.txt ├── requirements_documentation.txt ├── requirements_tests.txt ├── setup.cfg ├── setup.py ├── tests ├── __init__.py ├── data │ ├── __init__.py │ └── components │ │ ├── __init__.py │ │ └── library_functions │ │ ├── SSFP.py │ │ ├── VanGelderenCylindricalRestrictedSignal.py │ │ └── __init__.py └── test_example_data.py └── tox.ini /.editorconfig: -------------------------------------------------------------------------------- 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