Simplified Morphologist 2025

None

Parameters

t1mri: Raw T1 MRI ( input )

perform_segmentation: Boolean ( input )

perform_bias_correction: Boolean ( input )

method_ACPC: Choice ( input )

commissure_coordinates: Commissure coordinates ( output )

anterior_commissure: Point3D ( optional, input )

posterior_commissure: Point3D ( optional, input )

interhemispheric_point: Point3D ( optional, input )

left_hemisphere_point: Point3D ( optional, input )

older_MNI_normalization: Transform Raw T1 MRI to Talairach-MNI template-SPM ( optional, input )

anatomical_template: anatomical Template ( optional, input )

transformations_information: SPM2 normalization matrix ( output )

normalized_t1mri: Raw T1 MRI ( optional, output )

talairach_MNI_transform: Transform Raw T1 MRI to Talairach-MNI template-SPM ( output )

source_referential: Referential of Raw T1 MRI ( optional, input )

normalized_referential: Referential ( input )

tal_to_normalized_transform: ListOf( Transformation ) ( input )

t1mri_nobias: T1 MRI Bias Corrected ( output )

hfiltered: T1 MRI Filtered For Histo ( output )

white_ridges: T1 MRI White Matter Ridges ( output )

variance: T1 MRI Variance ( output )

edges: T1 MRI Edges ( output )

field: T1 MRI Bias field ( output )

meancurvature: T1 MRI Mean Curvature ( output )

histo_analysis: Histo Analysis ( output )

histo: Histogram ( output )

brain_mask: T1 Brain Mask ( output )

skull_stripped: Raw T1 MRI Brain Masked ( output )

anatomical_template_skull_stripped: anatomical Template ( optional, input )

split_brain: Split Brain Mask ( output )

split_template: Hemispheres Template ( input )

talairach_ACPC_transform: Transform Raw T1 MRI to Talairach-AC/PC-Anatomist ( output )

left_grey_white: Left Grey White Mask ( output )

right_grey_white: Right Grey White Mask ( output )

perform_meshes_and_graphs: Boolean ( input )

left_hemi_cortex: Left CSF+GREY Mask ( output )

right_hemi_cortex: Right CSF+GREY Mask ( output )

left_white_mesh: Left Hemisphere White Mesh ( output )

right_white_mesh: Right Hemisphere White Mesh ( output )

left_skeleton: Left Cortex Skeleton ( output )

left_roots: Left Cortex Catchment Bassins ( output )

right_skeleton: Right Cortex Skeleton ( output )

right_roots: Right Cortex Catchment Bassins ( output )

left_pial_mesh: Left Hemisphere Mesh ( output )

right_pial_mesh: Right Hemisphere Mesh ( output )

left_graph: Cortical folds graph ( output )

left_sulci_voronoi: Sulci Voronoi ( output )

left_cortex_mid_interface: Grey White Mid-Interface Volume ( output )

right_graph: Cortical folds graph ( output )

right_sulci_voronoi: Sulci Voronoi ( output )

right_cortex_mid_interface: Grey White Mid-Interface Volume ( output )

perform_sulci_recognition: Choice ( input )

labels_translation_map: Label translation ( input )

left_labelled_graph: Labelled Cortical folds graph ( output )

left_posterior_probabilities: Sulci Labels Segmentwise Posterior Probabilities ( output )

left_labels_priors: Sulci Labels Priors ( input )

left_model_file: Any Type ( input )

left_param_file: Any Type ( input )

left_global_model: Sulci Segments Model ( input )

left_tal_to_global_transform: Sulci Talairach to Global SPAM transformation ( output )

left_t1_to_global_transform: Raw T1 to Global SPAM transformation ( output )

left_local_model: Sulci Segments Model ( input )

left_local_referentials: Sulci Local referentials ( input )

left_direction_priors: Sulci Direction Transformation Priors ( input )

left_angle_priors: Sulci Angle Transformation Priors ( input )

left_translation_priors: Sulci Translation Transformation Priors ( input )

left_global_to_local_transforms: Sulci Local SPAM transformations Directory ( output )

right_labelled_graph: Labelled Cortical folds graph ( output )

right_posterior_probabilities: Sulci Labels Segmentwise Posterior Probabilities ( output )

right_labels_priors: Sulci Labels Priors ( input )

right_model_file: Any Type ( input )

right_param_file: Any Type ( input )

right_global_model: Sulci Segments Model ( input )

right_tal_to_global_transform: Sulci Talairach to Global SPAM transformation ( output )

right_t1_to_global_transform: Raw T1 to Global SPAM transformation ( output )

right_local_model: Sulci Segments Model ( input )

right_local_referentials: Sulci Local referentials ( input )

right_direction_priors: Sulci Direction Transformation Priors ( input )

right_angle_priors: Sulci Angle Transformation Priors ( input )

right_translation_priors: Sulci Translation Transformation Priors ( input )

right_global_to_local_transforms: Sulci Local SPAM transformations Directory ( output )

sulci_file: Sulci groups list ( input )

sulcal_morpho_measures: Sulcal morphometry measurements ( output )

left_csf: Left CSF Mask ( output )

right_csf: Right CSF Mask ( output )

subject: String ( input )

bids: String ( input )

sulci_label_attribute: String ( input )

brain_volumes_file: Brain volumetry measurements ( output )

normative_brain_stats: Normative brain volumes stats ( optional, input )

report: Morphologist report ( output )

report_json: Morphologist JSON report ( optional, output )

inter_subject_qc_table: QC table ( optional, output )

Technical information

Toolbox : Morphologist

User level : 0

Identifier : morphologistProcess

File name : brainvisa/toolboxes/morphologist/processes/segmentationpipeline/morphologistProcess.py

Supported file formats :

t1mri :

gz compressed NIFTI-1 image, Aperio svs, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, Ventana bif, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

commissure_coordinates :

Commissure coordinates, Commissure coordinates

older_MNI_normalization :

Transformation matrix, Transformation matrix

anatomical_template :

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

transformations_information :

Matlab file, Matlab file

normalized_t1mri :

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

talairach_MNI_transform :

Transformation matrix, Transformation matrix

source_referential :

Referential, Referential

normalized_referential :

Referential, Referential

tal_to_normalized_transform :

Transformation matrix, Transformation matrix

t1mri_nobias :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

hfiltered :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

white_ridges :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

variance :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

edges :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

field :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

meancurvature :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

histo_analysis :

Histo Analysis, Histo Analysis

histo :

Histogram, Histogram

brain_mask :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

skull_stripped :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

anatomical_template_skull_stripped :

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

split_brain :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

split_template :

gz compressed NIFTI-1 image, Aperio svs, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, Ventana bif, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

talairach_ACPC_transform :

Transformation matrix, Transformation matrix

left_grey_white :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

right_grey_white :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

left_hemi_cortex :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

right_hemi_cortex :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

left_white_mesh :

GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh

right_white_mesh :

GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh

left_skeleton :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

left_roots :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

right_skeleton :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

right_roots :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

left_pial_mesh :

GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh

right_pial_mesh :

GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh

left_graph :

Graph and data, Graph and data

left_sulci_voronoi :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

left_cortex_mid_interface :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

right_graph :

Graph and data, Graph and data

right_sulci_voronoi :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

right_cortex_mid_interface :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

labels_translation_map :

Label Translation, DEF Label Translation, Label Translation

left_labelled_graph :

Graph and data, Graph and data

left_posterior_probabilities :

CSV file, CSV file

left_labels_priors :

Text Data Table, Text Data Table

left_model_file :

mdsm file, mdsm file

left_param_file :

JSON file, JSON file

left_global_model :

Text Data Table, Text Data Table

left_tal_to_global_transform :

Transformation matrix, Transformation matrix

left_t1_to_global_transform :

Transformation matrix, Transformation matrix

left_local_model :

Text Data Table, Text Data Table

left_local_referentials :

Text Data Table, Text Data Table

left_direction_priors :

Text Data Table, Text Data Table

left_angle_priors :

Text Data Table, Text Data Table

left_translation_priors :

Text Data Table, Text Data Table

left_global_to_local_transforms :

Directory, Directory

right_labelled_graph :

Graph and data, Graph and data

right_posterior_probabilities :

CSV file, CSV file

right_labels_priors :

Text Data Table, Text Data Table

right_model_file :

mdsm file, mdsm file

right_param_file :

JSON file, JSON file

right_global_model :

Text Data Table, Text Data Table

right_tal_to_global_transform :

Transformation matrix, Transformation matrix

right_t1_to_global_transform :

Transformation matrix, Transformation matrix

right_local_model :

Text Data Table, Text Data Table

right_local_referentials :

Text Data Table, Text Data Table

right_direction_priors :

Text Data Table, Text Data Table

right_angle_priors :

Text Data Table, Text Data Table

right_translation_priors :

Text Data Table, Text Data Table

right_global_to_local_transforms :

Directory, Directory

sulci_file :

JSON file, JSON file

sulcal_morpho_measures :

CSV file, CSV file

left_csf :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

right_csf :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

brain_volumes_file :

CSV file, CSV file

normative_brain_stats :

JSON file, JSON file

report :

PDF File, PDF File

report_json :

JSON file, JSON file

inter_subject_qc_table :

TSV file, TSV file