Surfaces and Sulci Extraction

This pipeline applies some of the Morphologist steps (extraction of white matter and pial surfaces, sulci segmentation, extraction of sulci graphs) to a Primatologist segmentation. Briefly, Primatologist output volumes are converted to Morphologist-compatible input volumes (split brain mask, gray/white mask, inversion of T2-weighted to make them look like T1w), and processed with Morphologist.

Description

Pipeline steps

Convert Segmentation

  1. Compute Brain and Hemispheres Mask: includes some morphomathematical processing.
  2. Compute Cortex Mask: includes some morphomathematical processing.
  3. Histogram Analysis: performs a morphologist-compliant histogram analysis.
  4. (Invert T2 MRI): if the input MRI is T2-weighted, inverts it to make it T1-like (Morphologist only works with T1-weighted images).
  5. Talairach Transform Estimation: computes a transformation to Talairach space (mandatory for Morphologist processing).

Surfaces and Sulci Segmentation

  1. Topological Transform of the Cortex: fills the cortex mask towards the intracranial space boundaries.
  2. White Matter Surface Extraction.
  3. Skeletonization: skeletonizes the topologically transformed cortex to segment the sulci.
  4. Pial Surface Extraction.
  5. Cortical Folds Graph: extracts the sulci graph.

Paramètres

input_mri_nobias: P:MRI Bias Corrected ( entrée )

Bias-corrected MRI.

specie: OpenChoice ( optional, input )

Specie (Human, Macaque...).

contrast: OpenChoice ( optional, input )

Contrast (T1, T2).

is_mapping: Booléen ( optional, input )

Is the image a T1 or T2 map ?

commissure: Commissure coordinates ( optional, entrée )

File containings AC-PC landmarks.

parcellation: P:EM Parcellation ( optional, entrée )

Primatologist segmentation.

posterior: P:EM Parcellation Proba ( optional, entrée )

Primatologist posterior probabilities.

lateralization: P:Atlas Registered Lateralization ( optional, entrée )

Lateralization mask.

hierarchy: P:Atlas Labels Hierarchy ( optional, entrée )

Atlas hierarchy.

output_brain: Masque du cerveau ( optional, sortie )

Output brain mask.

output_brain_split: Séparation du masque du cerveau ( optional, sortie )

Output split brain mask (containing 3 regions: cerebral left, cerebral right and cerebellar)

output_greywhite_left: Grey White Mask ( optional, sortie )

Left hemisphere gray/white segmentation.

output_greywhite_right: Grey White Mask ( optional, sortie )

Right hemisphere gray/white segmentation.

output_greywhite_mesh_left: Maillage de la matière blanche d'un hémisphère ( optional, sortie )

Left hemisphere white matter mesh.

output_pial_mesh_left: Maillage d'un hémisphère ( optional, sortie )

Left hemisphere pial mesh.

output_sulci_left: Graphe de sillons corticaux ( optional, sortie )

Left hemisphere sulci graph.

output_greywhite_mesh_right: Maillage de la matière blanche d'un hémisphère ( optional, sortie )

Right hemisphere white matter mesh.

output_pial_mesh_right: Maillage d'un hémisphère ( optional, sortie )

Right hemisphere pial mesh.

output_sulci_right: Graphe de sillons corticaux ( optional, sortie )

Right hemisphere sulci graph.

Informations techniques

Toolbox : Primatologist

Niveau d'utilisateur : 0

Identifiant : primate_SurfacesAndSulciPipeline

Nom de fichier : brainvisa/toolboxes/primatologist/processes/pipelines/primate_SurfacesAndSulciPipeline.py

Supported file formats :

input_mri_nobias :
gz compressed NIFTI-1 image, Aperio svs, BMP image, DICOM image, Répertoire, 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 :
Commissure coordinates, Commissure coordinates
parcellation :
gz compressed NIFTI-1 image, Aperio svs, BMP image, DICOM image, Répertoire, 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
posterior :
gz compressed NIFTI-1 image, Aperio svs, BMP image, DICOM image, Répertoire, 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
lateralization :
gz compressed NIFTI-1 image, Aperio svs, BMP image, DICOM image, Répertoire, 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
hierarchy :
Hiérarchie, Hiérarchie
output_brain :
gz compressed NIFTI-1 image, BMP image, DICOM image, Répertoire, 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
output_brain_split :
gz compressed NIFTI-1 image, BMP image, DICOM image, Répertoire, 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
output_greywhite_left :
gz compressed NIFTI-1 image, BMP image, DICOM image, Répertoire, 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
output_greywhite_right :
gz compressed NIFTI-1 image, BMP image, DICOM image, Répertoire, 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
output_greywhite_mesh_left :
GIFTI file, GIFTI file, Maillage MESH, MNI OBJ mesh, PLY mesh, Maillage TRI
output_pial_mesh_left :
GIFTI file, GIFTI file, Maillage MESH, MNI OBJ mesh, PLY mesh, Maillage TRI
output_sulci_left :
Graph and data, Graph and data
output_greywhite_mesh_right :
GIFTI file, GIFTI file, Maillage MESH, MNI OBJ mesh, PLY mesh, Maillage TRI
output_pial_mesh_right :
GIFTI file, GIFTI file, Maillage MESH, MNI OBJ mesh, PLY mesh, Maillage TRI
output_sulci_right :
Graph and data, Graph and data