The Cape Universities Brain Imaging Centre (CUBIC) is among the many research institutions that are reaping the benefits of high performance computing (HPC). CUBIC has partnered with the Centre for High Performance Computing (CHPC) to conduct a long-term project that seeks to analyse structural brain changes in patients suffering from brain diseases such as schizophrenia, obsessive compulsive disorder (OCD) and bipolar disorder.
In the first study of schizophrenia, CUBIC aims to assess structural brain changes that occur after the first episode of the disease. The relationship between these changes and the course and outcome of the illness is evaluated by means of a subcortical volume analysis using the Freesurfer Programme running on the CHPC’s Sun Nehalem system.
The second study of schizophrenia aims to compare structural and functional magnetic resonance imaging (MRI) changes during acute treatment with two kinds of treatment: an atypical and a conventional antipsychotic; and to evaluate the relationship between these changes and treatment response.
“We can make people with schizophrenia better, but we don’t fully understand the effects the medication has on the brain. That is why this study is vital,” said Dr Stéfan du Plessis, research scientist for CUBIC.
The next study involves scanning of patients with OCD and trichotillomania (TTM) (self-induced and recurrent loss of hair) following an antidepressant (escitalopram) /placebo challenge. This study investigates the serotonergic or soothing effects of escitalopram using cortical/subcortical volume analysis, functional MRI and diffusion tensor imaging. The OCD study consists of 1 000 patients affected by the disease, from countries around the globe.
Enabled by the CHPC, CUBIC is continuously measuring the growth and shrinkage of the brain’s grey matter and volumes of the subcortical areas, to determine whether there is a difference in the size of the brain. “The next phase of the study will be to understand why there is such a difference and what it means,” says Du Plessis.
All these studies require the simulation and monitoring of the brain of each patient. On a conventional machine, the reconstruction of one brain takes about 24 hours. Given the numbers of patients involved in the studies on schizophrenia (120) and OCD (1 000), this would be a mammoth undertaking. In the case of the studies on schizophrenia, the CHPC’s Sun Visualisation Nodes reconstructed 120 brains in 14 hours, ensuring that the time factor would not be a hindrance to progress.
Another research challenge for CUBIC was storage. The nature of its research has special, long-term and stable storage requirements. Such storage should be secure from abuse, but also easily accessible for international collaborations. The CHPC has been serving this storage requirement and plans to expand on this service through the procurement of the Very Large Database (VLDB) for data storage and sharing. VLDB has a storage capacity of up to 1 petabyte.
HPC continues to act as a cardinal catalyst in health sciences research and many other fields. Where studies took years to yield results in the past, research can now be achieved in a fraction of the time, making possible savings not only in time and financial resources, but even of lives. “It’s never easy using a high performance system. It has, however, proven essential in our current neuro-imaging research and will likely prove to be so in the future as well, as new algorithms are developed in exploring the brain's structure and its associated pathologies,” Du Plessis concludes.
- The CHPC is part of the national cyberinfrastructure initiative funded by the Department of Science and Technology, and implemented by the CSIR Meraka Institute.
An overview of the Freesurfer analysis pipeline: Grey matter and white matter are segmented. The cortical surface is reconstructed as vertices on top of the segmented white matter. Cortical measurements are calculated from the reconstructed surface.