Compute equivolumetric depth

Compute Bok’s equivolumetric depth, which models the depth of cortical layers while compensating for local cortical curvature.

Description

The only mandatory input is classif, the output is equivolumetric_depth. You can fine-tune the process with optional parameters, most importantly advection_step_size can be adapted to the spatial resolution and required accuracy.

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

Yann Leprince, Fabrice Poupon, Thierry Delzescaux, Dominique Hasboun, Cyril Poupon, Denis Rivière. Combined Laplacian-equivolumic model for studying cortical lamination with ultra high field MRI (7 T). 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI), IEEE, Apr 2015, New York, United States. pp.580-583, DOI: 10.1109/ISBI.2015.7163940. https://hal-cea.archives-ouvertes.fr/cea-01119475

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

smoothing_sigma: Number ( optional, input )

X standard deviation of the gaussian filter [default=largest voxel size]

advection_step_size: Number ( optional, input )

size of the advection step (millimetres)

advection_max_dist: Number ( optional, input )

maximum advection distance (millimetres)

equivolumetric_depth: Any Type ( output )

output 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 : isovolume

File name : brainvisa/toolboxes/highres_cortex/processes/isovolume.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

equivolumetric_depth :

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