Creation of Kernels for fMRI data projection

Description

This process creates anatomically-informed convolution kernels out of a mesh of the cortical surface (ideally the grey white matter interface). These kernels are then used by a second process for projection of 3D data onto the cortical surface. These kernels embed local geometric and anatomical information that is taken account of by the projection.



These kernels are stored as a (4D) sequence of small volumes, each of which is related to a mesh node. Each kernel describes, for each node, the contribution given to each voxel of a small neighboring volume by the node. The final value assigned to each node is then a linear combination of these voxels intensities, weighted by these estimated kernel values.

This is the first step of the process for projection fMRI data onto the cortical surface. (see process Create Surface-Based Functional Data)

Parameters

intmesh: Hemisphere White Mesh ( input )

intmesh represents the mesh of the inner cortical surface, i.e. the grey / white matter interface

output: Projection convolution kernels ( output )

output represents the convolution kernels, stored in a 4D volume.

size: Integer ( input )

size sets the extent (in number of voxels) of a convolution kernel. This parameter must be high enough so as to cover all the voxels with nonnull weights.

resolution: ListOf ( input )

Warning : the resolution parameter (given as a vector of three floats) must equal the resolution of the images that will be consecutively projected on the cortical surface.

geod_decay: Float ( input )

geod_decay (in mm) is a geodesic distance beyond which the influence between two points on the surface is considered null

norm_decay: Float ( input )

norm_decay (in mm) is a euclidian distance beyond which the influence between two points in the volume, outside from the cortical ribbon, is considered null

Technical information

Toolbox : Cortical Surface

User level : 0

Identifier : CreateKernels

File name : brainvisa/toolboxes/cortical_surface/processes/functional/projection_to_cortical_surface/CreateKernels.py

Supported file formats :

intmesh :

TRI mesh, Z compressed TRI mesh, PLY mesh, gz compressed TRI mesh, MESH mesh, Z compressed MESH mesh, gz compressed MESH mesh, gz compressed PLY mesh, Z compressed PLY mesh, GIFTI file, Z compressed GIFTI file, MNI OBJ mesh, gz compressed GIFTI file, Z compressed MNI OBJ mesh, gz compressed MNI OBJ mesh

output :

GIS image, Z compressed GIS image, gz compressed GIS image, VIDA image, NIFTI-1 image, gz compressed ECAT i image, MINC image, gz compressed MINC image, TIFF image, XBM image, PBM image, PGM image, BMP image, XPM image, PPM image, gz compressed NIFTI-1 image, TIFF(.tif) image, gz compressed VIDA image, Z compressed VIDA image, Z compressed ECAT i image, gz compressed ECAT v image, ECAT i image, Z compressed ECAT v image, PNG image, JPEG image, MNG image, GIF image, Z compressed SPM image, SPM image, gz compressed SPM image, ECAT v image