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]

compute_fold_meshes: a boolean ([‘Bool’] - mandatory)
No description.
CorticalFoldsGraph_graph_version: a legal value ([‘Enum’] - mandatory)
No description.
t1mri: a file name ([‘File’] - mandatory)
No description.
allow_multithreading: a boolean ([‘Bool’] - mandatory)
No description.
sulcal_morphometry_sulci_file: a file name ([‘File’] - mandatory)
No description.
select_Talairach: a legal value ([‘Enum’] - 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.
nodes_activation: a legal value ([‘ControllerTrait’] - mandatory)
No description.
CorticalFoldsGraph_write_cortex_mid_interface: a boolean ([‘Bool’] -
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”)
allow_flip_initial_MRI: a boolean ([‘Bool’] - mandatory)
No description.

[Optional]

SulciRecognition_1_recognition2000_stopRate: a float ([‘Float’] -
optional)
No description.
PrepareSubject_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_target: a
legal value ([‘Enum’] - optional)
No description.
PrepareSubject_Normalization_NormalizeFSL_NormalizeFSL_init_translation_origin: a
legal value ([‘Enum’] - optional)
No description.
SulciRecognition_1_recognition2000_niterBelowStopProp: an integer
([‘Int’] - optional)
No description.
SulciRecognition_recognition2000_stopRate: a float ([‘Float’] -
optional)
No description.
BiasCorrection_mode: a legal value ([‘Enum’] - optional)
No description.
PialMesh_1_version: a legal value ([‘Enum’] - optional)
No description.
HeadMesh_keep_head_mask: a boolean ([‘Bool’] - optional)
No description.
SulciSkeleton_1_version: a legal value ([‘Enum’] - optional)
No description.
Renorm_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_target: a
legal value ([‘Enum’] - optional)
No description.
PrepareSubject_StandardACPC_Normalised: a legal value ([‘Enum’] -
optional)
No description.
BiasCorrection_delete_last_n_slices: a string ([‘Str’] - optional)
No description.
SulciRecognition_1_recognition2000_rate: a float ([‘Float’] -
optional)
No description.
SulciRecognition_1_SPAM_recognition09_global_recognition_model_type: a
legal value ([‘Enum’] - optional)
No description.
SulciRecognition_1_SPAM_recognition09_markovian_recognition_segments_relations_model: a
file name ([‘File’] - optional)
No description.
PrepareSubject_TalairachFromNormalization_source_referential: a file
name ([‘File’] - optional)
No description.
SulciRecognition_1_recognition2000_model: a file name ([‘File’] -
optional)
No description.
BiasCorrection_field_rigidity: a float ([‘Float’] - optional)
No description.
SulciRecognition_1_SPAM_recognition09_local_or_markovian: a legal
value ([‘Enum’] - optional)
No description.
BiasCorrection_write_field: a legal value ([‘Enum’] - optional)
No description.
Renorm_Normalization_NormalizeSPM_NormalizeSPM_nbiteration: an integer
([‘Int’] - optional)
No description.
HistoAnalysis_use_wridges: a boolean ([‘Bool’] - optional)
No description.
PrepareSubject_Normalization_NormalizeSPM_NormalizeSPM_nbiteration: an
integer ([‘Int’] - optional)
No description.
GreyWhiteTopology_1_version: a legal value ([‘Enum’] - optional)
No description.
SulcalMorphometry_use_attribute: a legal value ([‘Enum’] - optional)
No description.
SulciRecognition_SPAM_recognition09_markovian_recognition_model: a
file name ([‘File’] - optional)
No description.
BiasCorrection_use_existing_ridges: a boolean ([‘Bool’] - optional)
No description.
Renorm_Normalization_NormalizeSPM_NormalizeSPM_cutoff_option: an
integer ([‘Int’] - optional)
No description.
PrepareSubject_Normalization_NormalizeSPM_NormalizeSPM_voxel_size: a l
egal value ([‘Enum’] - optional)
No description.
SulciRecognition_1_SPAM_recognition09_markovian_recognition_model: a f
ile name ([‘File’] - optional)
No description.
PrepareSubject_Normalization_Normalization_AimsMIRegister_smoothing: a
float ([‘Float’] - optional)
No description.
SulciRecognition_1_recognition2000_model_hint: a legal value ([‘Enum’]
- optional)
No description.
PrepareSubject_Normalization_NormalizeFSL_NormalizeFSL_search_cost_function: a
legal value ([‘Enum’] - optional)
No description.
Renorm_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_removeSource: a
boolean ([‘Bool’] - optional)
No description.
HeadMesh_closing: a float ([‘Float’] - optional)
No description.
SulciRecognition_SPAM_recognition09_global_recognition_model: a file
name ([‘File’] - optional)
No description.
PrepareSubject_Normalization_Normalization_AimsMIRegister_mni_to_acpc: a
file name ([‘File’] - optional)
No description.
PrepareSubject_Normalization_NormalizeFSL_NormalizeFSL_cost_function: a
legal value ([‘Enum’] - optional)
No description.
PrepareSubject_Normalization_NormalizeSPM_NormalizeSPM_init_translation_origin: a
legal value ([‘Enum’] - optional)
No description.
interhemispheric_point: a legal value ([‘List_Float’] - optional)
No description.
PrepareSubject_StandardACPC_remove_older_MNI_normalization: a boolean
([‘Bool’] - optional)
No description.
SulciRecognition_1_recognition2000_forbid_unknown_label: a boolean
([‘Bool’] - optional)
No description.
SplitBrain_variant: a legal value ([‘Enum’] - optional)
No description.
SulciRecognition_SPAM_recognition09_global_recognition_labels_priors: a
file name ([‘File’] - optional)
No description.
SulciRecognition_SPAM_recognition09_global_recognition_initial_transformation: a
file name ([‘File’] - optional)
No description.
SulciRecognition_1_SPAM_recognition09_local_recognition_model: a file
name ([‘File’] - optional)
No description.
HeadMesh_remove_mask: a file name ([‘File’] - optional)
No description.
PrepareSubject_Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template: a
legal value ([‘Enum’] - optional)
No description.
PrepareSubject_TalairachFromNormalization_transform_chain_ACPC_to_Normalized: a
file name ([‘File’] - optional)
No description.
Renorm_Normalization_NormalizeFSL_NormalizeFSL_search_cost_function: a
legal value ([‘Enum’] - optional)
No description.
SulciRecognition_SPAM_recognition09_markovian_recognition_segments_relations_model: a
file name ([‘File’] - optional)
No description.
PrepareSubject_StandardACPC_older_MNI_normalization: a file name
([‘File’] - optional)
No description.
Renorm_Normalization_NormalizeFSL_NormalizeFSL_init_translation_origin: a
legal value ([‘Enum’] - optional)
No description.
SulciRecognition_SPAM_recognition09_local_recognition_model: a file
name ([‘File’] - optional)
No description.
BrainSegmentation_visu: a legal value ([‘Enum’] - optional)
No description.
Renorm_Normalization_NormalizeBaladin_set_transformation_in_source_volume: a
boolean ([‘Bool’] - optional)
No description.
Renorm_Normalization_NormalizeFSL_alignment: a legal value ([‘Enum’] -
optional)
No description.
BiasCorrection_write_variance: a legal value ([‘Enum’] - optional)
No description.
Renorm_Normalization_Normalization_AimsMIRegister_smoothing: a float (
[‘Float’] - optional)
No description.
SulciRecognition_SPAM_recognition09_local_or_markovian: a legal value
([‘Enum’] - optional)
No description.
SulciRecognition_recognition2000_model: a file name ([‘File’] -
optional)
No description.
PrepareSubject_Normalization_NormalizeFSL_set_transformation_in_source_volume: a
boolean ([‘Bool’] - optional)
No description.
HeadMesh_threshold: an integer ([‘Int’] - optional)
No description.
SulciRecognition_SPAM_recognition09_local_recognition_angle_priors: a
file name ([‘File’] - optional)
No description.
BiasCorrection_modality: a legal value ([‘Enum’] - optional)
No description.
PrepareSubject_Normalization_NormalizeFSL_alignment: a legal value
([‘Enum’] - optional)
No description.
SulciRecognition_SPAM_recognition09_global_recognition_model_type: a l
egal value ([‘Enum’] - optional)
No description.
Renorm_Normalization_NormalizeSPM_NormalizeSPM_voxel_size: a legal
value ([‘Enum’] - optional)
No description.
SplitBrain_initial_erosion: a float ([‘Float’] - optional)
No description.
PrepareSubject_Normalization_NormalizeSPM_template: a file name
([‘File’] - optional)
No description.
SulciRecognition_SPAM_recognition09_local_recognition_local_referentials: a
file name ([‘File’] - optional)
No description.
SulciRecognition_1_SPAM_recognition09_local_recognition_angle_priors: a
file name ([‘File’] - optional)
No description.
SplitBrain_split_template: a file name ([‘File’] - optional)
No description.
BiasCorrection_write_edges: a legal value ([‘Enum’] - optional)
No description.
SulciSkeleton_version: a legal value ([‘Enum’] - optional)
No description.
SulciRecognition_SPAM_recognition09_local_recognition_direction_priors: a
file name ([‘File’] - optional)
No description.
PialMesh_version: a legal value ([‘Enum’] - optional)
No description.
SulciRecognition_1_select_Sulci_Recognition: a legal value ([‘Enum’] -
optional)
No description.
SulciRecognition_1_SPAM_recognition09_local_recognition_local_referentials: a
file name ([‘File’] - optional)
No description.
SulciRecognition_1_SPAM_recognition09_global_recognition_labels_priors: a
file name ([‘File’] - optional)
No description.
PrepareSubject_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_normalized_volume: a
file name ([‘File’] - optional)
No description.
BrainSegmentation_erosion_size: a float ([‘Float’] - optional)
No description.
SplitBrain_bary_factor: a legal value ([‘Enum’] - optional)
No description.
SulciRecognition_select_Sulci_Recognition: a legal value ([‘Enum’] -
optional)
No description.
Normalization_select_Normalization_pipeline: a legal value ([‘Enum’] -
optional)
No description.
BiasCorrection_variance_fraction: an integer ([‘Int’] - optional)
No description.
HistoAnalysis_undersampling: a legal value ([‘Enum’] - optional)
No description.
SulciRecognition_1_SPAM_recognition09_local_recognition_direction_priors: a
file name ([‘File’] - optional)
No description.
BrainSegmentation_lesion_mask: a file name ([‘File’] - optional)
No description.
SplitBrain_mode: a legal value ([‘Enum’] - optional)
No description.
BiasCorrection_zdir_multiply_regul: a float ([‘Float’] - optional)
No description.
GreyWhiteTopology_version: a legal value ([‘Enum’] - optional)
No description.
Renorm_Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template: a
legal value ([‘Enum’] - optional)
No description.
PrepareSubject_Normalization_commissures_coordinates: a file name
([‘File’] - optional)
No description.
BrainSegmentation_first_slice: an integer ([‘Int’] - optional)
No description.
SulciRecognition_1_SPAM_recognition09_local_recognition_translation_priors: a
file name ([‘File’] - optional)
No description.
Renorm_Normalization_Normalization_AimsMIRegister_mni_to_acpc: a file
name ([‘File’] - optional)
No description.
BiasCorrection_ngrid: an integer ([‘Int’] - optional)
No description.
PrepareSubject_Normalization_NormalizeFSL_template: a file name
([‘File’] - optional)
No description.
BiasCorrection_edge_mask: a legal value ([‘Enum’] - optional)
No description.
Renorm_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_normalized_volume: a
file name ([‘File’] - optional)
No description.
BiasCorrection_write_hfiltered: a legal value ([‘Enum’] - optional)
No description.
PrepareSubject_Normalization_NormalizeSPM_NormalizeSPM_cutoff_option: a
n integer ([‘Int’] - optional)
No description.
BiasCorrection_write_wridges: a legal value ([‘Enum’] - optional)
No description.
SulciRecognition_recognition2000_rate: a float ([‘Float’] - optional)
No description.
BrainSegmentation_last_slice: an integer ([‘Int’] - optional)
No description.
left_hemisphere_point: a legal value ([‘List_Float’] - optional)
No description.
BrainSegmentation_layer: a legal value ([‘Enum’] - optional)
No description.
SulciRecognition_SPAM_recognition09_local_recognition_translation_priors: a
file name ([‘File’] - optional)
No description.
Renorm_template: a file name ([‘File’] - optional)
No description.
SulciRecognition_1_SPAM_recognition09_global_recognition_initial_transformation: a
file name ([‘File’] - optional)
No description.
BrainSegmentation_variant: a legal value ([‘Enum’] - optional)
No description.
BiasCorrection_write_meancurvature: a legal value ([‘Enum’] -
optional)
No description.
SulciRecognition_recognition2000_model_hint: a legal value ([‘Enum’] -
optional)
No description.
SulciRecognition_recognition2000_niterBelowStopProp: an integer
([‘Int’] - optional)
No description.
Renorm_Normalization_NormalizeFSL_NormalizeFSL_cost_function: a legal
value ([‘Enum’] - optional)
No description.
SplitBrain_cc_min_size: an integer ([‘Int’] - optional)
No description.
Renorm_Normalization_NormalizeFSL_set_transformation_in_source_volume: a
boolean ([‘Bool’] - optional)
No description.
Renorm_Normalization_NormalizeSPM_NormalizeSPM_init_translation_origin: a
legal value ([‘Enum’] - optional)
No description.
PrepareSubject_Normalization_Normalization_AimsMIRegister_anatomical_template: a
file name ([‘File’] - optional)
No description.
PrepareSubject_TalairachFromNormalization_normalized_referential: a
file name ([‘File’] - optional)
No description.
SulciRecognition_recognition2000_forbid_unknown_label: a boolean
([‘Bool’] - optional)
No description.
HeadMesh_first_slice: an integer ([‘Int’] - optional)
No description.
SplitBrain_use_ridges: a boolean ([‘Bool’] - optional)
No description.
PrepareSubject_Normalization_NormalizeBaladin_set_transformation_in_source_volume: a
boolean ([‘Bool’] - optional)
No description.
SulciRecognition_1_SPAM_recognition09_global_recognition_model: a file
name ([‘File’] - optional)
No description.
posterior_commissure: a legal value ([‘List_Float’] - optional)
No description.
BiasCorrection_sampling: a float ([‘Float’] - optional)
No description.
SPAM_recognition_labels_translation_map: a file name ([‘File’] -
optional)
No description.
SplitBrain_use_template: a boolean ([‘Bool’] - optional)
No description.
PrepareSubject_Normalization_NormalizeBaladin_template: a file name
([‘File’] - optional)
No description.
HistoAnalysis_use_hfiltered: a boolean ([‘Bool’] - optional)
No description.
PrepareSubject_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_removeSource: a
boolean ([‘Bool’] - optional)
No description.
PrepareSubject_TalairachFromNormalization_acpc_referential: a file
name ([‘File’] - optional)
No description.
anterior_commissure: a legal value ([‘List_Float’] - optional)
No description.
BiasCorrection_wridges_weight: a float ([‘Float’] - optional)
No description.

Outputs

SulciSkeleton_1_roots: a file name
No description.
BiasCorrection_white_ridges: a file name
No description.
Renorm_skull_stripped: a file name
No description.
left_graph: a file name
No description.
SulciRecognition_1_recognition2000_energy_plot_file: a file name
No description.
SulciSkeleton_skeleton: a file name
No description.
commissure_coordinates: any value
No description.
SulciRecognition_SPAM_recognition09_markovian_recognition_posterior_probabilities: a
file name
No description.
SulciRecognition_SPAM_recognition09_global_recognition_output_t1_to_global_transformation: a
file name
No description.
GreyWhiteClassification_1_grey_white: a file name
No description.
BiasCorrection_edges: a file name
No description.
BiasCorrection_meancurvature: a file name
No description.
CorticalFoldsGraph_sulci_voronoi: a file name
No description.
BiasCorrection_field: a file name
No description.
normalization_baladin_native_transformation_pass1: a file name
No description.
MNI_transform: any value
No description.
SulciRecognition_SPAM_recognition09_local_recognition_output_local_transformations: a
directory name
No description.
normalization_baladin_native_transformation: a file name
No description.
normalization_spm_native_transformation: a file name
No description.
GreyWhiteMesh_white_mesh: a file name
No description.
sulcal_morpho_measures: a file name
No description.
CorticalFoldsGraph_cortex_mid_interface: a file name
No description.
split_brain: a file name
No description.
BiasCorrection_hfiltered: a file name
No description.
normalization_fsl_native_transformation: a file name
No description.
CorticalFoldsGraph_1_cortex_mid_interface: a file name
No description.
SulciSkeleton_roots: a file name
No description.
normalization_spm_native_transformation_pass1: a file name
No description.
SulciRecognition_recognition2000_energy_plot_file: a file name
No description.
normalization_spm_native_job_file_pass1: a file name
No description.
HistoAnalysis_histo: a file name
No description.
GreyWhiteTopology_1_hemi_cortex: a file name
No description.
SulciRecognition_1_SPAM_recognition09_global_recognition_posterior_probabilities: a
file name
No description.
normalization_spm_native_job_file: a file name
No description.
SulciRecognition_1_SPAM_recognition09_local_recognition_posterior_probabilities: a
file name
No description.
SulciRecognition_SPAM_recognition09_global_recognition_output_transformation: a
file name
No description.
PialMesh_pial_mesh: a file name
No description.
GreyWhiteClassification_grey_white: a file name
No description.
GreyWhiteTopology_hemi_cortex: a file name
No description.
normalized_t1mri: any value
No description.
PialMesh_1_pial_mesh: a file name
No description.
SulciRecognition_1_SPAM_recognition09_global_recognition_output_t1_to_global_transformation: a
file name
No description.
right_graph: a file name
No description.
SulciRecognition_SPAM_recognition09_local_recognition_posterior_probabilities: a
file name
No description.
left_labelled_graph: any value
No description.
SulciRecognition_1_SPAM_recognition09_global_recognition_output_transformation: a
file name
No description.
right_labelled_graph: any value
No description.
BiasCorrection_variance: a file name
No description.
SulciRecognition_SPAM_recognition09_global_recognition_posterior_probabilities: a
file name
No description.
BrainSegmentation_brain_mask: a file name
No description.
SulciRecognition_1_SPAM_recognition09_local_recognition_output_local_transformations: a
directory name
No description.
t1mri_nobias: a file name
No description.
SulciRecognition_1_SPAM_recognition09_markovian_recognition_posterior_probabilities: a
file name
No description.
reoriented_t1mri: any value
No description.
SulciSkeleton_1_skeleton: a file name
No description.
CorticalFoldsGraph_1_sulci_voronoi: a file name
No description.
HeadMesh_head_mesh: a file name
No description.
Talairach_transform: any value
No description.
normalization_fsl_native_transformation_pass1: a file name
No description.
GreyWhiteMesh_1_white_mesh: a file name
No description.
histo_analysis: a file name
No description.
HeadMesh_head_mask: a file name
No description.

Pipeline schema

../../../_images/morpho.png