Generate cortical traverses

Create cortical traverses

Description

The only mandatory input is classif, the output is cortical_traverses. The goal_diameter parameter controls the target diameter of merged regions (in millimetres). The advection_step_size parameter is also relevant for this process.

For a full description of this method, see this poster:

Yann Leprince, Clara Fischer, Jean-François Mangin, Benoît Larrat, Sébastien Mériaux, Cyril Poupon, Isabel Reillo, Victor Borrell, Ophélie Foubet, Roberto Toro, and Denis Rivière. Architectonics-informed partition of the cortex at sub-millimetre resolution. 20th Annual Meeting of the Organization for Human Brain Mapping (OHBM), Jun 2014, Hamburg, Germany. 5, pp.951, 2014, F1000Posters. https://hal-cea.archives-ouvertes.fr/cea-01074735

Parameters

classif: Any Type ( input )

classification image of the cortex (100 inside, 0 in CSF, 200 in white matter)

verbosity: Integer ( optional, input )

Verbosity level

laplace_precision: Number ( optional, input )

target maximum relative error in first-order finite differences

laplace_typical_cortical_thickness: Number ( optional, input )

typical thickness of the cortex (mm), used for accelerating convergence

advection_step_size: Number ( optional, input )

size of the advection step (millimetres)

goal_traverse_diameter: Number ( optional, input )

goal region diameter (millimetres)

cortical_traverses: Any Type ( output )

output label image

use_capsul_completion: Boolean ( input )

edit_pipeline: Boolean ( input )

capsul_gui: Boolean ( input )

edit_study_config: Boolean ( input )

Technical information

Toolbox : highres-cortex

User level : 0

Identifier : traverses

File name : brainvisa/toolboxes/highres_cortex/processes/traverses.py

Supported file formats :

classif :

Directory, BMP image, Directory, ECAT i image, ECAT v image, File, GIF image, GIS image, JPEG image, MINC image, MNG 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

cortical_traverses :

Directory, BMP image, Directory, ECAT i image, ECAT v image, File, GIF image, GIS image, JPEG image, MINC image, MNG 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