morphologist.capsul.morphologist.Morphologist¶
Morphologist¶
Note
- Type ‘Morphologist.help()’ for a full description of this process parameters.
- Type ‘<Morphologist>.get_input_spec()’ for a full description of this process input trait types.
- Type ‘<Morphologist>.get_output_spec()’ for a full description of this process output trait types.
Inputs¶
[Mandatory]
- t1mri: a file name ([‘File’] - mandatory)
- No description.
- select_Talairach: a legal value ([‘Enum’] - mandatory)
- No description.
- anterior_commissure: a legal value ([‘List_Float’] - mandatory)
- No description.
- posterior_commissure: a legal value ([‘List_Float’] - mandatory)
- No description.
- interhemispheric_point: a legal value ([‘List_Float’] - mandatory)
- No description.
- left_hemisphere_point: a legal value ([‘List_Float’] - mandatory)
- No description.
- nodes_activation: a legal value ([‘ControllerTrait’] - mandatory)
- No description.
- CorticalFoldsGraph_graph_version: a legal value ([‘Enum’] - mandatory)
- No description.
- allow_flip_initial_MRI: a boolean ([‘Bool’] - mandatory)
- No description.
- normalization_allow_retry_initialization: a boolean ([‘Bool’] - mandatory)
- No description.
- perform_skull_stripped_renormalization: a legal value ([‘Enum’] - mandatory)
- No description.
- fix_random_seed: a boolean ([‘Bool’] - mandatory)
- No description.
- grey_white_topology_version: a legal value ([‘Enum’] - mandatory)
- No description.
- pial_mesh_version: a legal value ([‘Enum’] - mandatory)
- No description.
- sulci_skeleton_version: a legal value ([‘Enum’] - mandatory)
- No description.
- compute_fold_meshes: a boolean ([‘Bool’] - mandatory)
- No description.
- allow_multithreading: a boolean ([‘Bool’] - mandatory)
- No description.
- CorticalFoldsGraph_write_cortex_mid_interface: a boolean ([‘Bool’] - mandatory)
- No description.
- select_sulci_recognition: a legal value ([‘Enum’] - mandatory)
- No description.
- sulcal_morphometry_sulci_file: a file name ([‘File’] - mandatory)
- No description.
- pipeline_steps: a legal value ([‘ControllerTrait’] - mandatory)
Steps are groups of pipeline nodes, which may be disabled at runtime. They are normally defined in a logical order regarding the workflow streams. They are different from sub-pipelines in that steps are purely virtual groups, they do not have parameters. To activate or diasable a step, just do: pipeline.steps.my_step = False
To get the nodes list in a step: pipeline.get_step_nodes(“my_step”)
- visible_groups: a legal value ([‘Set_Any’] - mandatory)
- No description.
[Optional]
- Normalization_select_Normalization_pipeline: a legal value ([‘Enum’] - optional)
- No description.
- PrepareSubject_TalairachFromNormalization_normalized_referential: a file name ([‘File’] - optional)
- No description.
- PrepareSubject_TalairachFromNormalization_acpc_referential: a file name ([‘File’] - optional)
- No description.
- PrepareSubject_TalairachFromNormalization_transform_chain_ACPC_to_Normalized: a file name ([‘File’] - optional)
- No description.
- SPAM_recognition_labels_translation_map: a file name ([‘File’] - optional)
- No description.
- sulci_recognition2000_forbid_unknown_label: a boolean ([‘Bool’] - optional)
- No description.
- sulci_recognition2000_model_hint: a legal value ([‘Enum’] - optional)
- No description.
- sulci_recognition2000_rate: a float ([‘Float’] - optional)
- No description.
- sulci_recognition2000_stop_rate: a float ([‘Float’] - optional)
- No description.
- sulci_recognition2000_niter_below_stop_prop: an integer (int or long) ([‘Int’] - optional)
- No description.
- sulci_recognition_spam_local_or_markovian: a legal value ([‘Enum’] - optional)
- No description.
- sulci_recognition_spam_global_model_type: a legal value ([‘Enum’] - optional)
- No description.
- rebuild_graph_attributes_after_split: a boolean ([‘Bool’] - optional)
- No description.
- spm_normalization_version: a legal value ([‘Enum’] - optional)
- No description.
- importation_output_database: a legal value ([‘Enum’] - optional)
- No description.
- importation_attributes_merging: a legal value ([‘Enum’] - optional)
- No description.
- importation_selected_attributes_from_header: a legal value ([‘List_Any’] - optional)
- No description.
- PrepareSubject_StandardACPC_Normalised: a legal value ([‘Enum’] - optional)
- No description.
- PrepareSubject_StandardACPC_remove_older_MNI_normalization: a boolean ([‘Bool’] - optional)
- No description.
- PrepareSubject_StandardACPC_older_MNI_normalization: a file name ([‘File’] - optional)
- No description.
- PrepareSubject_Normalization_commissures_coordinates: a file name ([‘File’] - optional)
- No description.
- PrepareSubject_Normalization_init_translation_origin: a legal value ([‘Enum’] - optional)
- No description.
- PrepareSubject_Normalization_NormalizeFSL_template: a file name ([‘File’] - optional)
- No description.
- PrepareSubject_Normalization_NormalizeFSL_alignment: a legal value ([‘Enum’] - optional)
- No description.
- PrepareSubject_Normalization_NormalizeFSL_set_transformation_in_source_volume: a boolean ([‘Bool’] - optional)
- No description.
- PrepareSubject_Normalization_NormalizeFSL_NormalizeFSL_cost_function: a legal value ([‘Enum’] - optional)
- No description.
- PrepareSubject_Normalization_NormalizeFSL_NormalizeFSL_search_cost_function: a legal value ([‘Enum’] - optional)
- No description.
- PrepareSubject_Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template: a legal value ([‘Enum’] - optional)
- No description.
- PrepareSubject_Normalization_NormalizeSPM_template: a file name ([‘File’] - optional)
- No description.
- PrepareSubject_Normalization_NormalizeSPM_voxel_size: a legal value ([‘Enum’] - optional)
- No description.
- PrepareSubject_Normalization_NormalizeSPM_cutoff_option: an integer (int or long) ([‘Int’] - optional)
- No description.
- PrepareSubject_Normalization_NormalizeSPM_nbiteration: an integer (int or long) ([‘Int’] - optional)
- No description.
- PrepareSubject_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_target: a legal value ([‘Enum’] - optional)
- No description.
- PrepareSubject_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_normalized_volume: a file name ([‘File’] - optional)
- No description.
- PrepareSubject_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_removeSource: a boolean ([‘Bool’] - optional)
- No description.
- PrepareSubject_Normalization_NormalizeBaladin_template: a file name ([‘File’] - optional)
- No description.
- PrepareSubject_Normalization_NormalizeBaladin_set_transformation_in_source_volume: a boolean ([‘Bool’] - optional)
- No description.
- PrepareSubject_Normalization_Normalization_AimsMIRegister_anatomical_template: a file name ([‘File’] - optional)
- No description.
- PrepareSubject_Normalization_Normalization_AimsMIRegister_mni_to_acpc: a file name ([‘File’] - optional)
- No description.
- PrepareSubject_Normalization_Normalization_AimsMIRegister_smoothing: a float ([‘Float’] - optional)
- No description.
- BiasCorrection_sampling: a float ([‘Float’] - optional)
- No description.
- BiasCorrection_field_rigidity: a float ([‘Float’] - optional)
- No description.
- BiasCorrection_zdir_multiply_regul: a float ([‘Float’] - optional)
- No description.
- BiasCorrection_wridges_weight: a float ([‘Float’] - optional)
- No description.
- BiasCorrection_ngrid: an integer (int or long) ([‘Int’] - optional)
- No description.
- BiasCorrection_delete_last_n_slices: a unicode string ([‘Str’] - optional)
- No description.
- BiasCorrection_mode: a legal value ([‘Enum’] - optional)
- No description.
- BiasCorrection_write_field: a legal value ([‘Enum’] - optional)
- No description.
- BiasCorrection_write_hfiltered: a legal value ([‘Enum’] - optional)
- No description.
- BiasCorrection_write_wridges: a legal value ([‘Enum’] - optional)
- No description.
- BiasCorrection_variance_fraction: an integer (int or long) ([‘Int’] - optional)
- No description.
- BiasCorrection_write_variance: a legal value ([‘Enum’] - optional)
- No description.
- BiasCorrection_edge_mask: a legal value ([‘Enum’] - optional)
- No description.
- BiasCorrection_write_edges: a legal value ([‘Enum’] - optional)
- No description.
- BiasCorrection_write_meancurvature: a legal value ([‘Enum’] - optional)
- No description.
- BiasCorrection_modality: a legal value ([‘Enum’] - optional)
- No description.
- BiasCorrection_use_existing_ridges: a boolean ([‘Bool’] - optional)
- No description.
- HistoAnalysis_use_hfiltered: a boolean ([‘Bool’] - optional)
- No description.
- HistoAnalysis_use_wridges: a boolean ([‘Bool’] - optional)
- No description.
- HistoAnalysis_undersampling: a legal value ([‘Enum’] - optional)
- No description.
- BrainSegmentation_lesion_mask: a file name ([‘File’] - optional)
- No description.
- BrainSegmentation_lesion_mask_mode: a legal value ([‘Enum’] - optional)
- No description.
- BrainSegmentation_variant: a legal value ([‘Enum’] - optional)
- No description.
- BrainSegmentation_erosion_size: a float ([‘Float’] - optional)
- No description.
- BrainSegmentation_visu: a legal value ([‘Enum’] - optional)
- No description.
- BrainSegmentation_layer: a legal value ([‘Enum’] - optional)
- No description.
- BrainSegmentation_first_slice: an integer (int or long) ([‘Int’] - optional)
- No description.
- BrainSegmentation_last_slice: an integer (int or long) ([‘Int’] - optional)
- No description.
- Renorm_template: a file name ([‘File’] - optional)
- No description.
- Renorm_Normalization_init_translation_origin: a legal value ([‘Enum’] - optional)
- No description.
- Renorm_Normalization_NormalizeFSL_alignment: a legal value ([‘Enum’] - optional)
- No description.
- Renorm_Normalization_NormalizeFSL_set_transformation_in_source_volume: a boolean ([‘Bool’] - optional)
- No description.
- Renorm_Normalization_NormalizeFSL_NormalizeFSL_cost_function: a legal value ([‘Enum’] - optional)
- No description.
- Renorm_Normalization_NormalizeFSL_NormalizeFSL_search_cost_function: a legal value ([‘Enum’] - optional)
- No description.
- Renorm_Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template: a legal value ([‘Enum’] - optional)
- No description.
- Renorm_Normalization_NormalizeSPM_voxel_size: a legal value ([‘Enum’] - optional)
- No description.
- Renorm_Normalization_NormalizeSPM_cutoff_option: an integer (int or long) ([‘Int’] - optional)
- No description.
- Renorm_Normalization_NormalizeSPM_nbiteration: an integer (int or long) ([‘Int’] - optional)
- No description.
- Renorm_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_target: a legal value ([‘Enum’] - optional)
- No description.
- Renorm_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_normalized_volume: a file name ([‘File’] - optional)
- No description.
- Renorm_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_removeSource: a boolean ([‘Bool’] - optional)
- No description.
- Renorm_Normalization_NormalizeBaladin_set_transformation_in_source_volume: a boolean ([‘Bool’] - optional)
- No description.
- Renorm_Normalization_Normalization_AimsMIRegister_mni_to_acpc: a file name ([‘File’] - optional)
- No description.
- Renorm_Normalization_Normalization_AimsMIRegister_smoothing: a float ([‘Float’] - optional)
- No description.
- SplitBrain_use_ridges: a boolean ([‘Bool’] - optional)
- No description.
- SplitBrain_use_template: a boolean ([‘Bool’] - optional)
- No description.
- SplitBrain_split_template: a file name ([‘File’] - optional)
- No description.
- SplitBrain_mode: a legal value ([‘Enum’] - optional)
- No description.
- SplitBrain_variant: a legal value ([‘Enum’] - optional)
- No description.
- SplitBrain_bary_factor: a legal value ([‘Enum’] - optional)
- No description.
- SplitBrain_mult_factor: a legal value ([‘Enum’] - optional)
- No description.
- SplitBrain_initial_erosion: a float ([‘Float’] - optional)
- No description.
- SplitBrain_cc_min_size: an integer (int or long) ([‘Int’] - optional)
- No description.
- HeadMesh_keep_head_mask: a boolean ([‘Bool’] - optional)
- No description.
- HeadMesh_remove_mask: a file name ([‘File’] - optional)
- No description.
- HeadMesh_first_slice: an integer (int or long) ([‘Int’] - optional)
- No description.
- HeadMesh_threshold: an integer (int or long) ([‘Int’] - optional)
- No description.
- HeadMesh_closing: a float ([‘Float’] - optional)
- No description.
- HeadMesh_threshold_mode: a legal value ([‘Enum’] - optional)
- No description.
- SulcalMorphometry_use_attribute: a legal value ([‘Enum’] - optional)
- No description.
- GreyWhiteClassification_lesion_mask: a file name ([‘File’] - optional)
- No description.
- GreyWhiteClassification_lesion_mask_mode: a legal value ([‘Enum’] - optional)
- No description.
- SulciRecognition_recognition2000_model: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_global_recognition_initial_transformation: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_global_recognition_labels_priors: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_global_recognition_model: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_local_recognition_model: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_local_recognition_local_referentials: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_local_recognition_direction_priors: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_local_recognition_angle_priors: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_local_recognition_translation_priors: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_markovian_recognition_model: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_markovian_recognition_segments_relations_model: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_CNN_recognition19_model_file: a file name ([‘File’] - optional)
- file (.mdsm) storing neural network parameters
- SulciRecognition_CNN_recognition19_param_file: a file name ([‘File’] - optional)
- file (.json) storing the hyperparameters (cutting threshold)
- SulciRecognition_CNN_recognition19_cuda: an integer (int or long) ([‘Int’] - optional)
- device on which to run the training(-1 for cpu, i>=0 for the i-th gpu)
- GreyWhiteClassification_1_lesion_mask: a file name ([‘File’] - optional)
- No description.
- GreyWhiteClassification_1_lesion_mask_mode: a legal value ([‘Enum’] - optional)
- No description.
- SulciRecognition_1_recognition2000_model: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_global_recognition_initial_transformation: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_global_recognition_labels_priors: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_global_recognition_model: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_local_recognition_model: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_local_recognition_local_referentials: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_local_recognition_direction_priors: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_local_recognition_angle_priors: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_local_recognition_translation_priors: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_markovian_recognition_model: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_markovian_recognition_segments_relations_model: a file name ([‘File’] - optional)
- No description.
- SulciRecognition_1_CNN_recognition19_model_file: a file name ([‘File’] - optional)
- file (.mdsm) storing neural network parameters
- SulciRecognition_1_CNN_recognition19_param_file: a file name ([‘File’] - optional)
- file (.json) storing the hyperparameters (cutting threshold)
- SulciRecognition_1_CNN_recognition19_cuda: an integer (int or long) ([‘Int’] - optional)
- device on which to run the training(-1 for cpu, i>=0 for the i-th gpu)
Outputs¶
- imported_t1mri: a file name ([‘File (filename: input)’] - mandatory)
- No description.
- commissure_coordinates: a file name ([‘File (filename: input)’] - mandatory)
- No description.
- normalized_t1mri: a file name ([‘File (filename: input)’] - optional)
- No description.
- Talairach_transform: a file name ([‘File (filename: input)’] - mandatory)
- No description.
- t1mri_nobias: a file name ([‘File (filename: input)’] - mandatory)
- No description.
- histo_analysis: a file name ([‘File (filename: input)’] - mandatory)
- No description.
- BrainSegmentation_brain_mask: a file name ([‘File (filename: input)’] - optional)
- No description.
- split_brain: a file name ([‘File (filename: input)’] - mandatory)
- No description.
- HeadMesh_head_mesh: a file name ([‘File (filename: input)’] - optional)
- No description.
- GreyWhiteClassification_grey_white: a file name ([‘File (filename: input)’] - optional)
- No description.
- GreyWhiteClassification_1_grey_white: a file name ([‘File (filename: input)’] - optional)
- No description.
- GreyWhiteTopology_hemi_cortex: a file name ([‘File (filename: input)’] - optional)
- No description.
- GreyWhiteTopology_1_hemi_cortex: a file name ([‘File (filename: input)’] - optional)
- No description.
- GreyWhiteMesh_white_mesh: a file name ([‘File (filename: input)’] - optional)
- No description.
- GreyWhiteMesh_1_white_mesh: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciSkeleton_skeleton: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciSkeleton_1_skeleton: a file name ([‘File (filename: input)’] - optional)
- No description.
- PialMesh_pial_mesh: a file name ([‘File (filename: input)’] - optional)
- No description.
- PialMesh_1_pial_mesh: a file name ([‘File (filename: input)’] - optional)
- No description.
- left_graph: a file name ([‘File (filename: input)’] - mandatory)
- No description.
- right_graph: a file name ([‘File (filename: input)’] - mandatory)
- No description.
- left_labelled_graph: a file name ([‘File (filename: input)’] - mandatory)
- No description.
- right_labelled_graph: a file name ([‘File (filename: input)’] - mandatory)
- No description.
- sulcal_morpho_measures: a file name ([‘File (filename: input)’] - mandatory)
- No description.
- t1mri_referential: a file name ([‘File (filename: input)’] - optional)
- No description.
- MNI_transform: a file name ([‘File (filename: input)’] - mandatory)
- No description.
- reoriented_t1mri: a file name ([‘File (filename: input)’] - optional)
- No description.
- normalization_spm_native_transformation_pass1: a file name ([‘File (filename: input)’] - optional)
- No description.
- normalization_spm_native_transformation: a file name ([‘File (filename: input)’] - optional)
- No description.
- normalization_fsl_native_transformation_pass1: a file name ([‘File (filename: input)’] - optional)
- No description.
- normalization_fsl_native_transformation: a file name ([‘File (filename: input)’] - optional)
- No description.
- normalization_baladin_native_transformation_pass1: a file name ([‘File (filename: input)’] - optional)
- No description.
- normalization_baladin_native_transformation: a file name ([‘File (filename: input)’] - optional)
- No description.
- BiasCorrection_field: a file name ([‘File (filename: input)’] - optional)
- No description.
- BiasCorrection_hfiltered: a file name ([‘File (filename: input)’] - optional)
- No description.
- BiasCorrection_white_ridges: a file name ([‘File (filename: input)’] - optional)
- No description.
- BiasCorrection_variance: a file name ([‘File (filename: input)’] - optional)
- No description.
- BiasCorrection_edges: a file name ([‘File (filename: input)’] - optional)
- No description.
- BiasCorrection_meancurvature: a file name ([‘File (filename: input)’] - optional)
- No description.
- HistoAnalysis_histo: a file name ([‘File (filename: input)’] - optional)
- No description.
- Renorm_skull_stripped: a file name ([‘File (filename: input)’] - optional)
- No description.
- HeadMesh_head_mask: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciSkeleton_roots: a file name ([‘File (filename: input)’] - optional)
- No description.
- CorticalFoldsGraph_sulci_voronoi: a file name ([‘File (filename: input)’] - optional)
- No description.
- CorticalFoldsGraph_cortex_mid_interface: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciRecognition_recognition2000_energy_plot_file: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_global_recognition_posterior_probabilities: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_global_recognition_output_transformation: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_global_recognition_output_t1_to_global_transformation: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_local_recognition_posterior_probabilities: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_local_recognition_output_local_transformations: a directory name ([‘Directory (filename: input)’] - optional)
- No description.
- SulciRecognition_SPAM_recognition09_markovian_recognition_posterior_probabilities: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciSkeleton_1_roots: a file name ([‘File (filename: input)’] - optional)
- No description.
- CorticalFoldsGraph_1_sulci_voronoi: a file name ([‘File (filename: input)’] - optional)
- No description.
- CorticalFoldsGraph_1_cortex_mid_interface: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciRecognition_1_recognition2000_energy_plot_file: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_global_recognition_posterior_probabilities: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_global_recognition_output_transformation: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_global_recognition_output_t1_to_global_transformation: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_local_recognition_posterior_probabilities: a file name ([‘File (filename: input)’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_local_recognition_output_local_transformations: a directory name ([‘Directory (filename: input)’] - optional)
- No description.
- SulciRecognition_1_SPAM_recognition09_markovian_recognition_posterior_probabilities: a file name ([‘File (filename: input)’] - optional)
- No description.
Pipeline schema¶
