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.

Parameters

input_mri_nobias: P:MRI Bias Corrected ( input )

Bias-corrected MRI.

specie: OpenChoice ( optional, input )

Specie (Human, Macaque...).

contrast: OpenChoice ( optional, input )

Contrast (T1, T2).

is_mapping: Boolean ( optional, input )

Is the image a T1 or T2 map ?

commissure: Commissure coordinates ( optional, input )

File containings AC-PC landmarks.

parcellation: P:EM Parcellation ( optional, input )

Primatologist segmentation.

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

Primatologist posterior probabilities.

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

Lateralization mask.

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

Atlas hierarchy.

output_brain: Brain Mask ( optional, output )

Output brain mask.

output_brain_split: Split Brain Mask ( optional, output )

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

output_greywhite_left: Grey White Mask ( optional, output )

Left hemisphere gray/white segmentation.

output_greywhite_right: Grey White Mask ( optional, output )

Right hemisphere gray/white segmentation.

output_greywhite_mesh_left: Hemisphere White Mesh ( optional, output )

Left hemisphere white matter mesh.

output_pial_mesh_left: Hemisphere Mesh ( optional, output )

Left hemisphere pial mesh.

output_sulci_left: Cortical folds graph ( optional, output )

Left hemisphere sulci graph.

output_greywhite_mesh_right: Hemisphere White Mesh ( optional, output )

Right hemisphere white matter mesh.

output_pial_mesh_right: Hemisphere Mesh ( optional, output )

Right hemisphere pial mesh.

output_sulci_right: Cortical folds graph ( optional, output )

Right hemisphere sulci graph.

Technical information

Toolbox : Primatologist

User level : 0

Identifier : primate_SurfacesAndSulciPipeline

File name : brainvisa/toolboxes/primatologist/processes/pipelines/primate_SurfacesAndSulciPipeline.py

Supported file formats :

input_mri_nobias :
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 :
Commissure coordinates, Commissure coordinates
parcellation :
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
posterior :
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
lateralization :
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
hierarchy :
Hierarchy, Hierarchy
output_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
output_brain_split :
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
output_greywhite_left :
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
output_greywhite_right :
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
output_greywhite_mesh_left :
GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh
output_pial_mesh_left :
GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh
output_sulci_left :
Graph and data, Graph and data
output_greywhite_mesh_right :
GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh
output_pial_mesh_right :
GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh
output_sulci_right :
Graph and data, Graph and data