LICENSE
MANIFEST.in
README.rst
requirements.txt
requirements_tests.txt
setup.cfg
setup.py
docs/Makefile
docs/adding_models.rst
docs/advanced_usage.rst
docs/auto_gen_cli_index.rst
docs/changelog.rst
docs/cli_index.rst
docs/concepts.rst
docs/conf.py
docs/configuration.rst
docs/developers.rst
docs/faq.rst
docs/getting_started.rst
docs/index.rst
docs/index_latex.rst
docs/index_man.rst
docs/install.rst
docs/make.bat
docs/mdt.cli_scripts.rst
docs/mdt.component_templates.rst
docs/mdt.file_conversions.rst
docs/mdt.gui.maps_visualizer.config_tabs.rst
docs/mdt.gui.maps_visualizer.design.rst
docs/mdt.gui.maps_visualizer.renderers.rst
docs/mdt.gui.maps_visualizer.rst
docs/mdt.gui.model_fit.design.rst
docs/mdt.gui.model_fit.rst
docs/mdt.gui.model_fit.tabs.rst
docs/mdt.gui.rst
docs/mdt.gui.widgets.design.rst
docs/mdt.gui.widgets.rst
docs/mdt.lib.rst
docs/mdt.model_building.parameter_functions.rst
docs/mdt.model_building.rst
docs/mdt.models.rst
docs/mdt.rst
docs/mdt.visualization.maps.rst
docs/mdt.visualization.rst
docs/modules.rst
docs/readme_latex.rst
docs/readme_man.rst
docs/scientific_articles.rst
docs/_dynamic_modules/batch_profiles.rst
docs/_dynamic_modules/cascade_models.rst
docs/_dynamic_modules/compartment_models.rst
docs/_dynamic_modules/composite_models.rst
docs/_dynamic_modules/library_functions.rst
docs/_dynamic_modules/parameters.rst
mdt/__init__.py
mdt/__version__.py
mdt/configuration.py
mdt/protocols.py
mdt/simulations.py
mdt/utils.py
mdt.egg-info/PKG-INFO
mdt.egg-info/SOURCES.txt
mdt.egg-info/dependency_links.txt
mdt.egg-info/entry_points.txt
mdt.egg-info/not-zip-safe
mdt.egg-info/requires.txt
mdt.egg-info/top_level.txt
mdt/cli_scripts/MDT.py
mdt/cli_scripts/__init__.py
mdt/cli_scripts/mdt_apply_mask.py
mdt/cli_scripts/mdt_batch_fit.py
mdt/cli_scripts/mdt_create_bvec_bval.py
mdt/cli_scripts/mdt_create_mask.py
mdt/cli_scripts/mdt_create_protocol.py
mdt/cli_scripts/mdt_create_roi_slice.py
mdt/cli_scripts/mdt_estimate_noise_std.py
mdt/cli_scripts/mdt_get_example_data.py
mdt/cli_scripts/mdt_gui.py
mdt/cli_scripts/mdt_info_img.py
mdt/cli_scripts/mdt_info_protocol.py
mdt/cli_scripts/mdt_init_user_settings.py
mdt/cli_scripts/mdt_list_devices.py
mdt/cli_scripts/mdt_list_models.py
mdt/cli_scripts/mdt_math_img.py
mdt/cli_scripts/mdt_math_protocol.py
mdt/cli_scripts/mdt_model_fit.py
mdt/cli_scripts/mdt_view_maps.py
mdt/cli_scripts/mdt_volume_merge.py
mdt/component_templates/__init__.py
mdt/component_templates/base.py
mdt/component_templates/batch_profiles.py
mdt/component_templates/cascade_models.py
mdt/component_templates/compartment_models.py
mdt/component_templates/composite_models.py
mdt/component_templates/library_functions.py
mdt/component_templates/parameters.py
mdt/component_templates/utils.py
mdt/data/logo.svg
mdt/data/logo_docs.png
mdt/data/logo_gui.png
mdt/data/mdt.conf
mdt/data/components/standard/batch_profiles/general.py
mdt/data/components/standard/batch_profiles/hcp.py
mdt/data/components/standard/cascade_models/ActiveAx.py
mdt/data/components/standard/cascade_models/BallRackets.py
mdt/data/components/standard/cascade_models/BallSticks.py
mdt/data/components/standard/cascade_models/CHARMED.py
mdt/data/components/standard/cascade_models/Kurtosis.py
mdt/data/components/standard/cascade_models/NODDI.py
mdt/data/components/standard/cascade_models/Tensor.py
mdt/data/components/standard/cascade_models/relaxometry.py
mdt/data/components/standard/compartment_models/AstroCylinders.py
mdt/data/components/standard/compartment_models/AstroSticks.py
mdt/data/components/standard/compartment_models/Ball.py
mdt/data/components/standard/compartment_models/CHARMEDRestricted.py
mdt/data/components/standard/compartment_models/CylinderGPD.py
mdt/data/components/standard/compartment_models/Dot.py
mdt/data/components/standard/compartment_models/KurtosisTensor.py
mdt/data/components/standard/compartment_models/NODDI_EC.py
mdt/data/components/standard/compartment_models/NODDI_IC.py
mdt/data/components/standard/compartment_models/Racket.py
mdt/data/components/standard/compartment_models/S0.py
mdt/data/components/standard/compartment_models/SSFP.py
mdt/data/components/standard/compartment_models/Stick.py
mdt/data/components/standard/compartment_models/SymmetricNonParametricTensor.py
mdt/data/components/standard/compartment_models/Tensor.py
mdt/data/components/standard/compartment_models/TimeDependentZeppelin.py
mdt/data/components/standard/compartment_models/Weights.py
mdt/data/components/standard/compartment_models/Zeppelin.py
mdt/data/components/standard/compartment_models/relaxometry.py
mdt/data/components/standard/composite_models/ActiveAx.py
mdt/data/components/standard/composite_models/BallRackets.py
mdt/data/components/standard/composite_models/BallSticks.py
mdt/data/components/standard/composite_models/CHARMED.py
mdt/data/components/standard/composite_models/Kurtosis.py
mdt/data/components/standard/composite_models/NODDI.py
mdt/data/components/standard/composite_models/SSFP.py
mdt/data/components/standard/composite_models/Tensor.py
mdt/data/components/standard/composite_models/relaxometry.py
mdt/data/components/standard/composite_models/s0s.py
mdt/data/components/standard/library_functions/KurtosisMultiplication.py
mdt/data/components/standard/library_functions/MRIConstants.py
mdt/data/components/standard/library_functions/SSFP.py
mdt/data/components/standard/library_functions/TensorApparentDiffusion.py
mdt/data/components/standard/library_functions/bessel_roots.py
mdt/data/components/standard/library_functions/distributions.py
mdt/data/components/standard/library_functions/linear_algebra.py
mdt/data/components/standard/library_functions/physical_diffusion_models.py
mdt/data/components/standard/parameters/free.py
mdt/data/components/standard/parameters/protocol.py
mdt/data/mdt_example_data/b1k_b2k/b1k_b2k.bval
mdt/data/mdt_example_data/b1k_b2k/b1k_b2k.bvec
mdt/data/mdt_example_data/b1k_b2k/b1k_b2k.prtcl
mdt/data/mdt_example_data/b1k_b2k/b1k_b2k_example_slices_24_38.nii.gz
mdt/data/mdt_example_data/b1k_b2k/b1k_b2k_example_slices_24_38_mask.nii.gz
mdt/data/mdt_example_data/multishell_b6k_max/multishell_b6k_max.bval
mdt/data/mdt_example_data/multishell_b6k_max/multishell_b6k_max.bvec
mdt/data/mdt_example_data/multishell_b6k_max/multishell_b6k_max.prtcl
mdt/data/mdt_example_data/multishell_b6k_max/multishell_b6k_max_example_slices_24_38.nii.gz
mdt/data/mdt_example_data/multishell_b6k_max/multishell_b6k_max_example_slices_24_38_mask.nii.gz
mdt/data/qt_designs/Makefile
mdt/data/qt_designs/maps_visualizer/MainWindow.ui
mdt/data/qt_designs/maps_visualizer/Makefile
mdt/data/qt_designs/maps_visualizer/MapSpecificOptions.ui
mdt/data/qt_designs/maps_visualizer/TabGeneral.ui
mdt/data/qt_designs/maps_visualizer/TabMapSpecific.ui
mdt/data/qt_designs/maps_visualizer/TabTextual.ui
mdt/data/qt_designs/maps_visualizer/arrow_redo.png
mdt/data/qt_designs/maps_visualizer/arrow_undo.png
mdt/data/qt_designs/maps_visualizer/main.qrc
mdt/data/qt_designs/maps_visualizer/save_image_dialog.ui
mdt/data/qt_designs/model_fit/Makefile
mdt/data/qt_designs/model_fit/about_dialog.ui
mdt/data/qt_designs/model_fit/dialog_get_example_data.ui
mdt/data/qt_designs/model_fit/fit_model_tab.ui
mdt/data/qt_designs/model_fit/generate_brain_mask_tab.ui
mdt/data/qt_designs/model_fit/generate_protocol_load_gb_dialog.ui
mdt/data/qt_designs/model_fit/generate_protocol_tab.ui
mdt/data/qt_designs/model_fit/generate_protocol_update_dialog.ui
mdt/data/qt_designs/model_fit/generate_roi_mask_tab.ui
mdt/data/qt_designs/model_fit/icon_status_green.png
mdt/data/qt_designs/model_fit/icon_status_red.png
mdt/data/qt_designs/model_fit/main_gui.qrc
mdt/data/qt_designs/model_fit/main_gui.ui
mdt/data/qt_designs/model_fit/optimization_extra_data_add_protocol_map_dialog.ui
mdt/data/qt_designs/model_fit/optimization_extra_data_dialog.ui
mdt/data/qt_designs/model_fit/optimization_options_dialog.ui
mdt/data/qt_designs/model_fit/runtime_settings_dialog.ui
mdt/data/qt_designs/model_fit/view_results_tab.ui
mdt/data/qt_designs/widgets/Makefile
mdt/data/qt_designs/widgets/scientific_number_scroller_widget.ui
mdt/file_conversions/__init__.py
mdt/file_conversions/npy.py
mdt/gui/__init__.py
mdt/gui/utils.py
mdt/gui/maps_visualizer/__init__.py
mdt/gui/maps_visualizer/actions.py
mdt/gui/maps_visualizer/base.py
mdt/gui/maps_visualizer/main.py
mdt/gui/maps_visualizer/widgets.py
mdt/gui/maps_visualizer/config_tabs/__init__.py
mdt/gui/maps_visualizer/config_tabs/tab_general.py
mdt/gui/maps_visualizer/config_tabs/tab_map_specific.py
mdt/gui/maps_visualizer/config_tabs/tab_textual.py
mdt/gui/maps_visualizer/design/__init__.py
mdt/gui/maps_visualizer/design/main_rc.py
mdt/gui/maps_visualizer/design/ui_MainWindow.py
mdt/gui/maps_visualizer/design/ui_MapSpecificOptions.py
mdt/gui/maps_visualizer/design/ui_TabGeneral.py
mdt/gui/maps_visualizer/design/ui_TabMapSpecific.py
mdt/gui/maps_visualizer/design/ui_TabTextual.py
mdt/gui/maps_visualizer/design/ui_save_image_dialog.py
mdt/gui/maps_visualizer/renderers/__init__.py
mdt/gui/maps_visualizer/renderers/base.py
mdt/gui/maps_visualizer/renderers/matplotlib_renderer.py
mdt/gui/model_fit/__init__.py
mdt/gui/model_fit/qt_main.py
mdt/gui/model_fit/utils.py
mdt/gui/model_fit/design/__init__.py
mdt/gui/model_fit/design/main_gui_rc.py
mdt/gui/model_fit/design/ui_about_dialog.py
mdt/gui/model_fit/design/ui_dialog_get_example_data.py
mdt/gui/model_fit/design/ui_fit_model_tab.py
mdt/gui/model_fit/design/ui_generate_brain_mask_tab.py
mdt/gui/model_fit/design/ui_generate_protocol_load_gb_dialog.py
mdt/gui/model_fit/design/ui_generate_protocol_tab.py
mdt/gui/model_fit/design/ui_generate_protocol_update_dialog.py
mdt/gui/model_fit/design/ui_generate_roi_mask_tab.py
mdt/gui/model_fit/design/ui_main_gui.py
mdt/gui/model_fit/design/ui_optimization_extra_data_add_protocol_map_dialog.py
mdt/gui/model_fit/design/ui_optimization_extra_data_dialog.py
mdt/gui/model_fit/design/ui_optimization_options_dialog.py
mdt/gui/model_fit/design/ui_runtime_settings_dialog.py
mdt/gui/model_fit/design/ui_view_results_tab.py
mdt/gui/model_fit/tabs/__init__.py
mdt/gui/model_fit/tabs/fit_model_tab.py
mdt/gui/model_fit/tabs/generate_brain_mask_tab.py
mdt/gui/model_fit/tabs/generate_protocol_tab.py
mdt/gui/model_fit/tabs/generate_roi_mask_tab.py
mdt/gui/model_fit/tabs/view_results_tab.py
mdt/gui/widgets/__init__.py
mdt/gui/widgets/composite_widgets.py
mdt/gui/widgets/decorator_widgets.py
mdt/gui/widgets/design/__init__.py
mdt/gui/widgets/design/ui_scientific_number_scroller_widget.py
mdt/lib/__init__.py
mdt/lib/batch_utils.py
mdt/lib/components.py
mdt/lib/deferred_mappings.py
mdt/lib/exceptions.py
mdt/lib/fsl_sampling_routine.py
mdt/lib/log_handlers.py
mdt/lib/masking.py
mdt/lib/model_fitting.py
mdt/lib/model_sampling.py
mdt/lib/nifti.py
mdt/lib/post_processing.py
mdt/lib/processing_strategies.py
mdt/lib/shell_utils.py
mdt/lib/sorting.py
mdt/model_building/__init__.py
mdt/model_building/likelihood_functions.py
mdt/model_building/model_functions.py
mdt/model_building/parameters.py
mdt/model_building/signal_noise_models.py
mdt/model_building/trees.py
mdt/model_building/utils.py
mdt/model_building/parameter_functions/__init__.py
mdt/model_building/parameter_functions/dependencies.py
mdt/model_building/parameter_functions/numdiff_info.py
mdt/model_building/parameter_functions/priors.py
mdt/model_building/parameter_functions/transformations.py
mdt/models/__init__.py
mdt/models/base.py
mdt/models/cascade.py
mdt/models/compartments.py
mdt/models/composite.py
mdt/visualization/__init__.py
mdt/visualization/dict_conversion.py
mdt/visualization/layouts.py
mdt/visualization/samples.py
mdt/visualization/utils.py
mdt/visualization/maps/__init__.py
mdt/visualization/maps/base.py
mdt/visualization/maps/matplotlib_renderer.py
mdt/visualization/maps/utils.py
tests/__init__.py
tests/test_example_data.py
tests/data/__init__.py
tests/data/components/__init__.py
tests/data/components/library_functions/SSFP.py
tests/data/components/library_functions/VanGelderenCylindricalRestrictedSignal.py
tests/data/components/library_functions/__init__.py