4D neonatal head model

Introduction

Diffuse optical imaging methods require accurate knowledge of the anatomy of the brain and head in order to make optimal use of the spatial information contained in the data. Where the MRI of the individual subject or patient is unavailable, the best-practice approach is to use a suitable generic head atlas. Although diffuse optical methods have a long history of application to infants, there is no standard atlas model that provides the necessary, age-matched models of the brain and extra-cerebral tissues for pre-term and term age infants that are necessary for accurate use of diffuse optical imaging approaches.

In collaboration with researchers at King's College London, we have taken the MRI atlas described by Kuklisova-Murgasova et al. (2011) to produce a 4D neonatal head model for diffuse optical imaging. The model is based on spatially averaged and segmented MRI data from 324 infants (160 female) between the ages of 27 and 47 weeks (post-menstrual age).

The infant head models available below will soon be incorporated into the HOMER2 fNIRS processing package.

Murgasova_MRI

The 4D Neonatal Head Model Package

The package available below contains the following components (in .txt and .mat Matlab(R) formats) for every age from 29 to 44 weeks gestation age in 1-week intervals:

TissueMask_#weeks.mat
The voxel space tissue mask with voxel size 0.86 x 0.86 x 0.86 mm. Each voxel is assigned an index which defines tissue type.

TissueTypes_#weeks.txt
A text file which links each segmented tissue type to its index value (this is the same for all ages).

HeadVolumeMesh_#weeks.mat
The whole-head tetrahedral volume mesh in a matlab structure (.node, .elem, .face). The node coordinates are in mm. Each element is assigned an index which defines its tissue type (this is the 5th column of the associated matlab field HeadVolumeMesh_#weeks.elem). The 4th column of the face field also defines its tissue type. The 4th column of the node field defines the nodal tissue type.

ScalpSurfaceMesh_#weeks.mat
The surface mesh of the external surface of the extra-cerebral tissue layer in a matlab structure (.node, .face.). The node coordinates are in mm.

GMSurfaceMesh_#weeks.mat
The surface mesh of the external surface of the grey matter tissue layer in a matlab structure (.node, .face.). The node coordinates are in mm.

WMSurfaceMesh_#weeks.mat
The surface mesh of the external surface of the white matter tissue layer in a matlab structure (.node, .face.). The node coordinates are in mm.

LandmarkPoints_#weeks.txt
The 3D locations of the Inion, Nasion, Ar and Al cranial landmarks in mm. These points were defined on the tetrahedral volume mesh and correspond to particular nodes in that mesh.

10-5_Points_#weeks.txt
The 3D positions of 10-5 locations defined on the tetrahedral volume mesh in mm. Includes the vertex, Cz.

Head_Model_44_weeks

DOWNLOAD AND USE

This material is subject to copyright. It is freely available for use but may not be used as part of any commercial product. Please ensure that any use of this package is fully acknowledged (including the citation below) in any publication.

The 4D neonatal head model totals 1.0 Gb. To receive the download link please email robert.cooper@ucl.ac.uk.

For any questions relating to the construction, download or use of this package please contact Dr. Sabrina Brigadoi at s.brigadoi@ucl.ac.uk, or Dr. Rob Cooper at robert.cooper@ucl.ac.uk.

Publications

Brigadoi et al., 2014: A 4D neonatal head model for diffuse optical imaging of pre-term to term infants. NeuroImage 100: 385:394.