Two MSc graduate projects: The baby brain pipeline: MRI analysis in craniosynostosis

Two MSc graduate projects: The baby brain pipeline: MRI analysis in craniosynostosis

Background

Syndromic craniosynostosis is a congenital disorder in which several skull sutures close prematurely,
causing skull and facial anomalies. For example in trigonocephaly, a specific type of craniosynostosis,
there is no growth between the two frontal bones, resulting in a keel-shaped, very narrow forehead,
oval-shaped orbits, and eyes that are closely set together (Fig. 1). The prevalence is rising and is
currently 0.9 in 10000 live births for The Netherlands. Given the complex care for these children and
the low prevalence, care is concentrated in centers of expertise. For the Netherlands, this is the
Dutch Craniofacial Center at the Erasmus MC, which is leading world-wide in scientific research.
Over the years, research made it clear that syndromic craniosynostosis is accompanied by an
increased risk on behavioural and neurocognitive problems. Currently, treatment is directed at
restoring the shape of the forehead by surgery within the first year of life.

Aim
The Dutch Craniofacial Center aims to get a better understanding of the disease process and its
consequences, particularly relating to visual, behavioural and neurocognitive functioning. It is yet
unclear whether surgery of these children is beneficial. We hypothesize that in some patients
refraining from surgery might result in similar outcome, but this cannot yet be proven.
In a current study, we aim to use advanced MRI techniques to study the impact of craniosynostosis
on the structure and function of the brain, i.e. high-resolution structural MRI, arterial spin labelling
(ASL) MRI to quantify the perfusion of the brain and diffusion tensor imaging (DTI) MRI to get insight
into the brain’s microstructure. For the analysis of these brain scans, in small children with brain
deformations, no automated approaches exist. The two proposed projects aim at development of
dedicated image analysis tools for children with craniosynostosis.

Project 1: Baby brain tissue – tissue segmentation in young infants.
Accurate segmentation of the brain white and gray matter is essential for the analysis of brain
volume, ASL and DTI data. For adult MRI data, many well-validated tools available, but for infants
specific pipelines need to be developed given the fact that white and gray matter is less distinctive at
very young ages. This project therefore aims to develop a dedicated infant brain tissue segmentation
tool using machine learning methods. The tool will be evaluated on brain MRI scans of healthy
children and children with craniosynostosis.

Project 2: Baby brain atlas – image registration in craniosynostosis.
Regional analysis of brain volume, ASL and DTI data requires atlas tools for identifying brain regions.
However, the brain and skull deformations in children with craniosynostosis hamper the use of
standard tools. Registration –the process of spatial alignment of two images –is much more difficult
in this case. This project therefore aims to develop a robust registration technique for atlas-based
analysis of brain regions in infants with craniosynostosis. Both conventional and learning-based
registration method will be considered.

Work environment
The MSc project will be conducted in collaboration between two departments: the Department of
Radiology & Nuclear Medicine and the Department of Plastic and Reconstructive Surgery and Hand
Surgery. You will be working in a multi-disciplinary team including image analysis experts,
neuroradiologists, clinicians and biomedical scientists.

Requirements
If you are an MSc student with an affinity for developing and validating advanced techniques for the
analysis of medical image data sets, machine learning, plus some experience in software
development and scripting languages (e.g. some understanding of Linux, Python), we are looking for
you! Furthermore, good communication and writing skills are a pre-requisite.

Information and application
Supervisors:
• Dr. Esther E. Bron, Radiology & Nuclear Medicine, Erasmus MC
• Dr. Henri Vrooman, Radiology & Nuclear Medicine, Erasmus MC
• Prof.dr. Irene Mathijssen, Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC
• Nine de Planque, Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC
• Prof.dr. Wiro Niessen, Radiology & Nuclear Medicine, Erasmus MC

To apply, please e-mail your CV along with a motivation letter to e.bron@erasmusmc.nl