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, 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 :
Commissure coordinates, Commissure coordinates
parcellation :
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
posterior :
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
lateralization :
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
hierarchy :
Hierarchy, Hierarchy
output_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
output_brain_split :
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
output_greywhite_left :
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
output_greywhite_right :
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
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