CAT12

Module contents

Input and output specifications for CAT12 functions.

Submodules

django_mri.analysis.specifications.spm.cat12.segmentation module

Input and output specification dictionaries for CAT12 segmentation interface.

See also

• CAT12 segmentation interface

django_mri.analysis.specifications.spm.cat12.segmentation.CAT12_SEGMENTATION_INPUT_SPECIFICATION = {'accuracy': {'choices': ['average', 'high', 'ultra high'], 'default': 'average', 'description': '', 'is_configuration': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'affine_preprocessing': {'choices': ['none', 'light', 'full', 'rough'], 'default': 'rough', 'description': '', 'is_configuration': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'affine_regularisation': {'choices': ['mni', 'eastern', 'none'], 'default': 'mni', 'description': '', 'is_configuration': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'bias_strength': {'choices': ['light', 'medium', 'strong'], 'default': 'medium', 'description': '', 'is_configuration': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'cobra': {'default': False, 'description': '', 'is_configuration': False, 'is_output_switch': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'dartel_grey_matter': {'default': False, 'description': '', 'is_configuration': False, 'is_output_switch': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'dartel_white_matter': {'default': False, 'description': '', 'is_configuration': False, 'is_output_switch': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'deformation_fields': {'choices': ['none', 'forward', 'inverse', 'both'], 'default': 'none', 'description': '', 'is_configuration': False, 'is_output_switch': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'destination': {'description': 'Where to output the results.', 'is_configuration': False, 'is_output_directory': True, 'run_method_input': True, 'type': <class 'django_analyses.models.input.definitions.directory_input_definition.DirectoryInputDefinition'>}, 'hammers': {'default': False, 'description': '', 'is_configuration': False, 'is_output_switch': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'internal_resampling': {'default': 1.5, 'description': '', 'is_configuration': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.float_input_definition.FloatInputDefinition'>}, 'jacobian_determinant': {'default': False, 'description': '', 'is_configuration': False, 'is_output_switch': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'local_adaptive_segmentation_strength': {'choices': ['none', 'light', 'medium', 'strong'], 'default': 'medium', 'description': '', 'is_configuration': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'lpba40': {'default': False, 'description': '', 'is_configuration': False, 'is_output_switch': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'modulated_grey_matter': {'default': True, 'description': '', 'is_configuration': False, 'is_output_switch': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'modulated_white_matter': {'default': True, 'description': '', 'is_configuration': False, 'is_output_switch': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'n_processes': {'default': 4, 'description': 'Whether to implement multi-threading and with how many processes.', 'is_configuration': False, 'required': False, 'type': <class 'django_analyses.models.input.definitions.integer_input_definition.IntegerInputDefinition'>}, 'native_grey_matter': {'default': False, 'description': '', 'is_configuration': False, 'is_output_switch': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'native_pve': {'default': True, 'description': '', 'is_configuration': False, 'is_output_switch': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'native_white_matter': {'default': False, 'description': '', 'is_configuration': False, 'is_output_switch': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'neuromorphometrics': {'default': True, 'description': '', 'is_configuration': False, 'is_output_switch': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'normalized_image_voxel_size': {'default': 1.5, 'description': '', 'is_configuration': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.float_input_definition.FloatInputDefinition'>}, 'path': {'description': 'Anatomical high resolution raw data to be segmented.', 'is_configuration': False, 'required': True, 'run_method_input': True, 'type': <class 'django_analyses.models.input.definitions.file_input_definition.FileInputDefinition'>}, 'skull_stripping': {'choices': ['none', 'spm', 'gcut', 'aprg'], 'default': 'aprg', 'description': '', 'is_configuration': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.string_input_definition.StringInputDefinition'>}, 'surface_estimation': {'default': False, 'description': '', 'is_configuration': False, 'is_output_switch': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}, 'tpm_path': {'description': 'Tissue probability map to be used.', 'is_configuration': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.file_input_definition.FileInputDefinition'>}, 'warped_image': {'default': True, 'description': '', 'is_configuration': False, 'is_output_switch': True, 'required': False, 'type': <class 'django_analyses.models.input.definitions.boolean_input_definition.BooleanInputDefinition'>}}

CAT12 segmentation interface input specification dictionary.

django_mri.analysis.specifications.spm.cat12.segmentation.CAT12_SEGMENTATION_OUTPUT_SPECIFICATION = {'batch_file': {'description': 'The MATLAB .m file used to run the CAT12 segmentation.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'dartel_grey_matter': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'dartel_white_matter': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'forward_deformation_field': {'description': 'The deformation field from the image to the template.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'inverse_deformation_field': {'description': 'The deformation field from the template to the image.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'jacobian_determinant': {'description': 'A value representing local volume changes.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'labels_mat': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'labels_xml': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'left_hemisphere_central_surface': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'left_hemisphere_cortical_thickness': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'left_hemisphere_spherical_registered_surface': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'left_hemisphere_spherical_surface': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'modulated_grey_matter': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'modulated_white_matter': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'native_grey_matter': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'native_pve': {'description': 'Labeled version of the segmentation in native space.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'native_white_matter': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'report_jpg': {'description': 'JPG log of the run.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'report_mat': {'description': "MATLAB format .mat file containing the run's log.", 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'report_pdf': {'description': 'PDF log of the run.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'report_txt': {'description': 'Text format log file.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'report_xml': {'description': 'XML log of the run.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'right_hemisphere_central_surface': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'right_hemisphere_cortical_thickness': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'right_hemisphere_spherical_registered_surface': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'right_hemisphere_spherical_surface': {'description': '', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}, 'warped_image': {'description': 'The image in normalised space without any modulation.', 'type': <class 'django_analyses.models.output.definitions.file_output_definition.FileOutputDefinition'>}}

CAT12 segmentation interface output specification dictionary.