Simplified Morphologist 2015

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_SPAM_recognition: Boolean ( 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_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_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 )

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, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIF image, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, VIDA image, Ventana bif, XBM image, XPM image, 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, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

hfiltered :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

white_ridges :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

variance :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

edges :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

field :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

meancurvature :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM 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, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

skull_stripped :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM 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, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

split_template :

gz compressed NIFTI-1 image, Aperio svs, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIF image, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, VIDA image, Ventana bif, XBM image, XPM image, 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, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

right_grey_white :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

left_hemi_cortex :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

right_hemi_cortex :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM 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, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

left_roots :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

right_skeleton :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

right_roots :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM 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, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

left_cortex_mid_interface :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM 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, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

right_cortex_mid_interface :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM 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_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_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