CAT12 - Segment

None

Parameters

t1mri: Raw T1 MRI ( input )

subject: String ( input )

template: TPM template ( input )

affine_regularisation: Choice ( input )

inhomogeneity_correction: Choice ( input )

processing_accuracy: Choice ( input )

optimal_resolution: Choice ( input )

optimal_resolution_value: ListOf( Float ) ( input )

COM_to_set_origin: Boolean ( input )

affine_preprocessing: Choice ( input )

noise_correction: Choice ( input )

local_adaptative_segmentation: Choice ( input )

skull_stripping: Choice ( input )

clean_up: Choice ( input )

wm_hyperintensities_correction: Choice ( input )

spatial_registration_method: Choice ( input )

spatial_registration_template: CAT shooting template ( input )

shooting_method: Choice ( input )

voxel_size: Float ( input )

surface_thickness_estimation: Boolean ( input )

voxel_size_thickness_est: Float ( input )

cortical_surf_creation: Float ( input )

parahipp_surf_creation: Float ( input )

closing_parahipp: Boolean ( input )

lazy_processing: Boolean ( input )

error_handling: Boolean ( input )

verbose: Choice ( input )

create_report: Boolean ( input )

grey_native_space: Boolean ( input )

grey_native: T1 MRI tissue probability map ( output )

grey_normalized: Boolean ( input )

grey_normalized_output: T1 MRI tissue probability map ( optional, output )

grey_modulated_normalized: Choice ( input )

grey_mod_norm_output: T1 MRI tissue probability map ( output )

grey_dartel_export: Choice ( input )

grey_dartel_rigid_output: T1 MRI tissue probability map ( optional, output )

grey_dartel_affine_output: T1 MRI tissue probability map ( optional, output )

white_native_space: Boolean ( input )

white_native: T1 MRI tissue probability map ( optional, output )

white_normalized: Boolean ( input )

white_normalized_output: T1 MRI tissue probability map ( optional, output )

white_modulated_normalized: Choice ( input )

white_mod_norm_output: T1 MRI tissue probability map ( output )

white_dartel_export: Choice ( input )

white_dartel_rigid_output: T1 MRI tissue probability map ( optional, output )

white_dartel_affine_output: T1 MRI tissue probability map ( optional, output )

csf_native_space: Boolean ( input )

csf_native: T1 MRI tissue probability map ( optional, output )

csf_normalized: Boolean ( input )

csf_normalized_output: T1 MRI tissue probability map ( optional, output )

csf_modulated_normalized: Choice ( input )

csf_mod_norm_output: T1 MRI tissue probability map ( optional, output )

csf_dartel_export: Choice ( input )

csf_dartel_rigid_output: T1 MRI tissue probability map ( optional, output )

csf_dartel_affine_output: T1 MRI tissue probability map ( optional, output )

wmh_native_space: Boolean ( input )

wmh_native: T1 MRI tissue probability map ( optional, output )

wmh_normalized: Boolean ( input )

wmh_normalized_output: T1 MRI tissue probability map ( optional, output )

wmh_modulated_normalized: Choice ( input )

wmh_mod_norm_output: T1 MRI tissue probability map ( optional, output )

wmh_dartel_export: Choice ( input )

wmh_dartel_rigid_output: T1 MRI tissue probability map ( optional, output )

wmh_dartel_affine_output: T1 MRI tissue probability map ( optional, output )

other_tissue_proba_map_native_space: Boolean ( input )

skull_native: T1 MRI tissue probability map ( optional, output )

scalp_native: T1 MRI tissue probability map ( optional, output )

background_native: T1 MRI tissue probability map ( optional, output )

other_tissue_proba_map_normalized: Boolean ( input )

skull_normalized_output: T1 MRI tissue probability map ( optional, output )

scalp_normalized_output: T1 MRI tissue probability map ( optional, output )

background_normalized_output: T1 MRI tissue probability map ( optional, output )

other_tissue_proba_map_modulated_normalized: Choice ( input )

skull_mod_norm_output: T1 MRI tissue probability map ( optional, output )

scalp_mod_norm_output: T1 MRI tissue probability map ( optional, output )

background_mod_norm_output: T1 MRI tissue probability map ( optional, output )

other_tissue_proba_map_dartel_export: Choice ( input )

skull_dartel_rigid_output: T1 MRI tissue probability map ( optional, output )

skull_dartel_affine_output: T1 MRI tissue probability map ( optional, output )

scalp_dartel_rigid_output: T1 MRI tissue probability map ( optional, output )

scalp_dartel_affine_output: T1 MRI tissue probability map ( optional, output )

background_dartel_rigid_output: T1 MRI tissue probability map ( optional, output )

background_dartel_affine_output: T1 MRI tissue probability map ( optional, output )

pve_labels_native_space: Boolean ( input )

pve_labels_normalized: Boolean ( input )

pve_labels_dartel_export: Choice ( input )

bias_native_space: Boolean ( input )

bias_native: T1 MRI Bias Corrected ( optional, output )

bias_normalized: Boolean ( input )

bias_dartel_export: Choice ( input )

local_bias_native_space: Boolean ( input )

local_bias_normalized: Boolean ( input )

local_bias_dartel_export: Choice ( input )

jacobian_determinant: Boolean ( input )

jacobian_determinant_output: Jacobian determinant ( optional, output )

deformation_field_type: Choice ( input )

forward_field: SPM deformation field ( optional, output )

inverse_field: SPM deformation field ( optional, output )

registration_matrix: Boolean ( input )

forward_registration_affine: SPM transformation ( optional, output )

inverse_registration_affine: SPM transformation ( optional, output )

forward_registration_rigid: SPM transformation ( optional, output )

inverse_registration_rigid: SPM transformation ( optional, output )

batch_location: Matlab SPM script ( output )

Technical information

Toolbox : SPM

User level : 0

Identifier : SPM12CAT12Segment

File name : brainvisa/toolboxes/spm/processes/spm12/tools/CAT12/SPM12CAT12Segment.py

Supported file formats :

t1mri :

NIFTI-1 image, MINC image, NIFTI-1 image, SPM image, gz compressed NIFTI-1 image

template :

NIFTI-1 image, MINC image, NIFTI-1 image, SPM image

spatial_registration_template :

NIFTI-1 image, MINC image, NIFTI-1 image, SPM image

grey_native :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

grey_normalized_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

grey_mod_norm_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

grey_dartel_rigid_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

grey_dartel_affine_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

white_native :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

white_normalized_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

white_mod_norm_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

white_dartel_rigid_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

white_dartel_affine_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

csf_native :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

csf_normalized_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

csf_mod_norm_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

csf_dartel_rigid_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

csf_dartel_affine_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

wmh_native :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

wmh_normalized_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

wmh_mod_norm_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

wmh_dartel_rigid_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

wmh_dartel_affine_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

skull_native :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

scalp_native :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

background_native :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

skull_normalized_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

scalp_normalized_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

background_normalized_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

skull_mod_norm_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

scalp_mod_norm_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

background_mod_norm_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

skull_dartel_rigid_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

skull_dartel_affine_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

scalp_dartel_rigid_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

scalp_dartel_affine_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

background_dartel_rigid_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

background_dartel_affine_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

bias_native :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

jacobian_determinant_output :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

forward_field :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

inverse_field :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

forward_registration_affine :

Matlab file, Matlab file

inverse_registration_affine :

Matlab file, Matlab file

forward_registration_rigid :

Matlab file, Matlab file

inverse_registration_rigid :

Matlab file, Matlab file

batch_location :

Matlab script, Matlab script