UCL Medical Physics and Biomedical Engineering
- General teaching pages
- Adam's homepage
- Jem's Homepage
- Prospective Students
- UCLH Department
- Careers in Medical Physics and Biomedical Engineering
- International Links
- Optical Topography
- How to Apply
- Open Day
- 4D neonatal head model
Search Medical Physics
4D neonatal head model
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.
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:
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.
A text file which links each segmented tissue type to its index value (this is the same for all ages).
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.
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.
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.
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.
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.
The 3D positions of 10-5 locations defined on the tetrahedral volume mesh in mm. Includes the vertex, Cz.
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 firstname.lastname@example.org.
For any questions relating to the construction, download or use of this package please contact Dr. Sabrina Brigadoi at email@example.com, or Dr. Rob Cooper at firstname.lastname@example.org.
Brigadoi et al., 2014: A 4D neonatal head model for diffuse optical imaging of pre-term to term infants. NeuroImage 100: 385:394.