LICENSE
MANIFEST.in
README.rst
requirements.txt
requirements_tests.txt
setup.cfg
setup.py
docs/Makefile
docs/concepts.rst
docs/conf.py
docs/configuration.rst
docs/credits.rst
docs/developers.rst
docs/dynamic_modules.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.cl_routines.mapping.rst
docs/mdt.cl_routines.rst
docs/mdt.cli_scripts.rst
docs/mdt.data_loaders.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.models.parsers.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/_build/latex/Makefile
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/noise_std_estimators.rst
docs/_dynamic_modules/parameters.rst
docs/_dynamic_modules/processing_strategies.rst
docs/_getting_started/analysis.rst
docs/_getting_started/model_building.rst
mdt/__init__.py
mdt/__version__.py
mdt/batch_utils.py
mdt/components_loader.py
mdt/configuration.py
mdt/deferred_mappings.py
mdt/exceptions.py
mdt/log_handlers.py
mdt/masking.py
mdt/model_fitting.py
mdt/model_protocol_problem.py
mdt/model_sampling.py
mdt/nifti.py
mdt/processing_strategies.py
mdt/protocols.py
mdt/shell_utils.py
mdt/simulations.py
mdt/user_script_info.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/cl_routines/__init__.py
mdt/cl_routines/mapping/__init__.py
mdt/cl_routines/mapping/calculate_eigenvectors.py
mdt/cl_routines/mapping/dti_measures.py
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_generate_bvec_bval.py
mdt/cli_scripts/mdt_generate_mask.py
mdt/cli_scripts/mdt_generate_protocol.py
mdt/cli_scripts/mdt_generate_roi_slice.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/data/logo.svg
mdt/data/logo_docs.png
mdt/data/logo_gui.png
mdt/data/mdt.conf
mdt/data/components/standard/batch_profiles/DirPerSubject.py
mdt/data/components/standard/batch_profiles/HCP_MGH.py
mdt/data/components/standard/batch_profiles/HCP_WUMINN.py
mdt/data/components/standard/batch_profiles/SingleDir.py
mdt/data/components/standard/cascade_models/BallSticks.py
mdt/data/components/standard/cascade_models/CHARMED.py
mdt/data/components/standard/cascade_models/NODDI.py
mdt/data/components/standard/cascade_models/Tensor.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.cl
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/ExpT1DecGRE.py
mdt/data/components/standard/compartment_models/ExpT1DecTM.py
mdt/data/components/standard/compartment_models/ExpT1DecTR.py
mdt/data/components/standard/compartment_models/ExpT1ExpT2GRE.py
mdt/data/components/standard/compartment_models/ExpT1ExpT2STEAM.py
mdt/data/components/standard/compartment_models/ExpT1ExpT2sGRE.py
mdt/data/components/standard/compartment_models/ExpT2Dec.py
mdt/data/components/standard/compartment_models/ExpT2DecSTEAM.py
mdt/data/components/standard/compartment_models/GDRCylinders.cl
mdt/data/components/standard/compartment_models/GDRCylinders.py
mdt/data/components/standard/compartment_models/GDRCylindersFixedRadii.cl
mdt/data/components/standard/compartment_models/GDRCylindersFixedRadii.py
mdt/data/components/standard/compartment_models/LinMPM_Fit.py
mdt/data/components/standard/compartment_models/LinT1GRE.py
mdt/data/components/standard/compartment_models/LinT2Dec.py
mdt/data/components/standard/compartment_models/MPM_Fit.py
mdt/data/components/standard/compartment_models/NODDI_EC.cl
mdt/data/components/standard/compartment_models/NODDI_EC.py
mdt/data/components/standard/compartment_models/NODDI_IC.cl
mdt/data/components/standard/compartment_models/NODDI_IC.py
mdt/data/components/standard/compartment_models/S0.py
mdt/data/components/standard/compartment_models/SphereGPD.cl
mdt/data/components/standard/compartment_models/SphereGPD.py
mdt/data/components/standard/compartment_models/Stick.py
mdt/data/components/standard/compartment_models/Tensor.cl
mdt/data/components/standard/compartment_models/Tensor.py
mdt/data/components/standard/compartment_models/Zeppelin.py
mdt/data/components/standard/composite_models/ActiveAx.py
mdt/data/components/standard/composite_models/BallSticks.py
mdt/data/components/standard/composite_models/CHARMED.py
mdt/data/components/standard/composite_models/NODDI.py
mdt/data/components/standard/composite_models/Tensor.py
mdt/data/components/standard/composite_models/s0s.py
mdt/data/components/standard/library_functions/MRIConstants.cl
mdt/data/components/standard/library_functions/MRIConstants.h
mdt/data/components/standard/library_functions/MRIConstants.py
mdt/data/components/standard/library_functions/NeumannCylPerpPGSESum.cl
mdt/data/components/standard/library_functions/NeumannCylPerpPGSESum.h
mdt/data/components/standard/library_functions/NeumannCylPerpPGSESum.py
mdt/data/components/standard/noise_std_estimators/AllUnweightedVolumes.py
mdt/data/components/standard/noise_std_estimators/AverageOfAir_DilatedMask.py
mdt/data/components/standard/noise_std_estimators/AverageOfAir_ExtendedMask.py
mdt/data/components/standard/noise_std_estimators/TwoUnweightedVolumes.py
mdt/data/components/standard/parameters/free.py
mdt/data/components/standard/parameters/model_data.py
mdt/data/components/standard/parameters/protocol.py
mdt/data/components/standard/parameters/static_maps.py
mdt/data/components/standard/processing_strategies/AllVoxelsAtOnce.py
mdt/data/components/standard/processing_strategies/ProtocolDependent.py
mdt/data/components/standard/processing_strategies/VoxelRange.py
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/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_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_loaders/__init__.py
mdt/data_loaders/brain_mask.py
mdt/data_loaders/noise_std.py
mdt/data_loaders/protocol.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/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_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_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/models/__init__.py
mdt/models/base.py
mdt/models/cascade.py
mdt/models/compartments.py
mdt/models/composite.py
mdt/models/parameters.py
mdt/models/parsers/CompositeModelExpression.py
mdt/models/parsers/CompositeModelExpressionParser.py
mdt/models/parsers/__init__.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
tests/__init__.py