Monash Biomedical ImagingAnnual Report 2012

www.mbi.monash.edu

Monash Biomedical Imaging

Member

Supporters

Collaborators

Partners

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Table of Contents

Pro-Vice Chancellor’s Report 4

Director’s Report 5

Overview 6 Facilities Research Highlights Strategic Plan Governance

Personnel 8-9

Research Teams 10-15 Cognitive Neuroimaging Clinical Imaging Animal Imaging Imaging Analysis and Informatics MRI Methods X-Ray and CT Imaging

Operations Team 16-19

Collaborations 20

Partnerships 22

Research Outputs 24-26 Publications Grants Collaborative Projects Selected Presentations

Professional Contributions 27

Abbreviations 27

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Pro-Vice Chancellor’s Report

In 2010, Monash University as part of a Victoria wide consortium, was awarded a grant from the Victorian State Government to support the establishment of a state-of-the-art multimodal, biomedical imaging facility at Clayton. In May 2012, this vision became reality when Monash Biomedical Imaging (MBI) was officially opened by the Honourable Louise Asher MP, Victorian Minister for Innovation, Professor Edward Byrne AO, Monash University Vice-Chancellor and President, and Mr Jeff Connolly, CEO, Siemens Australia Pty Ltd.

The vision for MBI is now being realised, largely reflecting the dedication and hard work of the inaugural Director, Professor Gary Egan. Over the past twelve months, Professor Egan has built an outstanding research and administrative team, which has set MBI on a path to achieving our vision of a world class, integrated, collaborative, multimodal imaging platform at Monash University.

MBI has already made a significant contribution to the research environment at Monash University through successful grant applications, high quality papers and the attraction of new research groups and students. In addition, strategic partnerships for the development of infrastructure have also been established, particularly with our two major industry partners, Siemens and Agilent in the area of Magnetic Resonance Imaging (MRI). The facility has supported and developed collaborative activities with research and government organisations including CSIRO, the Imaging and Medical Beam Line of the Australian Synchrotron, Monash Health (formerly Southern Health), Prince Henry’s Institute, Alfred Health, and Monash Institute for Medical Research. Other benefits of the MBI infrastructure are also already being realised, with a cohort of participants from the international ASPREE (ASPirin in Reducing Events in the Elderly) trial soon to undergo MRI scans to determine the impact of aspirin on the development and progression of osteoarthritis in the elderly. Involvement in this world-leading research would not have been possible without the combination of internationally renowned academic leadership and cutting-edge equipment available through MBI.

I very much look forward to the year ahead, as we continue to increase the capabilities and capacity of MBI, support its contribution to the network of integrated technology platforms and further build biomedical imaging research at Monash University.

Ian SmithProfessor and Pro-Vice Chancellor (Research and Research Infrastructure)

The official opening of MBI. (from left to right Professor Gary Egan, Mr Michael Gidley MP, Member for Mount Waverley, The Honourable Louise Asher MP, Victorian Minister for Innovation, Professor Edward Byrne AO, Monash University Vice-Chancellor and President)

Director’s Report

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This is the first MBI annual report following the opening of the facility in May 2012. Our vision is to position Monash University as an international leader in biomedical imaging research and development.

The mission of MBI is to help deliver the next generation of significant biomedical research discoveries and to enhance excellence in biomedical imaging to benefit translational research. MBI is enhancing Monash University’s competitiveness in meeting the challenges of improving Australia’s priority health areas through:

Q providing access to cutting-edge imaging equipment and world class experts;

Q encouraging multidisciplinary collaborations with the university’s clinical research partners to solve complex clinical or disease challenges;

Q increasing knowledge by organising workshops and opportunities for skill development and knowledge transfer;

Q developing coordinated capability by linking imaging resources across the university;

Q developing the next generation of outstanding researchers and clinicians to support the applications of biomedical imaging in diagnosis and preventative health; and

Q pursuing additional investment in Victoria’s biomedical imaging human and capital infrastructure.

Our values are commitment to enabling research that is relevant and with the potential to have real world impact. We encourage creativity and innovation to tackle the big questions and challenges in the application of biomedical imaging to improving health. We pursue excellence in everything we do, including research and operational leadership and we focus on people in order to attract and support the world’s best talent to MBI and Monash University.

The first presentations at international conferences based on research imaging data collected at MBI were presented in late 2012, and reported important new findings related to brain damage in the acute perinatal setting. During 2012 the first research papers based on imaging data collected at MBI were accepted in a number of leading international journals. This is enormously exciting as these outcomes have been achieved within six months of opening the facility. We have completed the first research project grants that were awarded to early and mid career researchers in the School of Psychology and Psychiatry (SPP) in 2012. The MBI-SPP grants have produced results that have led to a number of presentations at international conferences, and manuscripts describing the research findings have been submitted for publication in leading journals.

We successfully completed the Victorian Science Agenda grant that was awarded in 2010 for the establishment of the Victorian Biomedical Imaging Capability. The final report, presented to the Victorian State Government Department of Business and Innovation in October 2012, highlighted the operational infrastructure, the significant collaborative gain, the enhanced networking between the four VBIC nodes, and the research advances achieved during the past two years.

During 2012 the partnerships between MBI and our industry partners, Siemens, Agilent and Bioscan, have entered the operational phase. The Monash Siemens Collaborative Management Committee approved four collaborative research projects, with the results from the first project producing a new accelerated method for image reconstruction. Monash is also a key alliance partner for Agilent in life science, chemical analysis, and bioimaging technologies. MBI is the lead research platform in the Monash partnership with Agilent in the development of new biomedical imaging technologies. Through its international network of campuses Monash is a global research partner for these companies, with MBI providing a unique strategic partnership opportunity in the Australian biomedical imaging research sector.

I would like to thank Professor Ian Smith, Pro-Vice Chancellor for Research and Research Infrastructure, for his unswerving support personally and his leadership of the Monash research platforms. Dr Lisa Hutton, Senior Operations and Research Manager, has been untiring in her efforts throughout 2012 to bring MBI into full operational mode, and also to provide me with support and assistance in developing the MBI research program. The MBI team heads, Drs James Pearson, David Barnes, Karen Siu, and Associate Professor Nicholas Ferris have provided terrific leadership to their teams that has ensured the successful provision of research support across the multidisciplinary areas of research undertaken at MBI. I also thank Ms Sue Renkin for her contribution as Chairperson of the MBI Advisory Board during 2012, and to all of the Advisory Board members for their support and advice.

The research and operational outcomes achieved during 2012 at MBI highlight Monash University’s aim to undertake internationally competitive research by establishing and maintaining deep, long term relationships with stakeholders from across the innovation spectrum. Achieving this aim, together with implementing effective mechanisms for communication, feedback, decision making, and future planning has positioned MBI on the national stage and is building an exciting future for the staff and research collaborators at MBI.

Gary EganProfessor and DirectorMonash Biomedical Imaging

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MBI Overview

Facilities Monash University is one of Australia’s leading institutions for biomedical research and has recently established new biomedical imaging capabilities to further its research and development activities in neurosciences, oncology, cardiovascular health, musculoskeletal disorders and developmental biology. MBI is a multi-node facility across the university’s Clayton, Prahran and Parkville campuses, in conjunction with a consortium of hospitals and research organisations that includes the Australian Synchrotron, CSIRO and Monash Health (formerly Southern Health). MBI undertakes and supports interdisciplinary and multimodal biomedical imaging research. This includes preclinical and clinical collaborations among world class experts in medicine, science and engineering, in cooperation with industry and government, to create innovative solutions to clinical health challenges. The $15 million investment by Monash University and its partners has led to the establishment of a unique bioimaging facility that integrates synchrotron biomedical imaging with established biomedical imaging technologies, including MRI, positron emission tomography (PET), X-ray computed tomography (CT), and fluorescence imaging. MBI was initially developed through extensive refurbishment of a 5,000m2 facility that is now operational as the MBI Clayton node. This site has a comprehensive suite of biomedical imaging equipment including an MRI scanner for clinical research, and preclinical MRI and PET SPECT CT scanners.

Research HighlightsMR imaging of the kidney with new contrasts will significantly advance our understanding of renal disease. The assessment of total glomerular number in a kidney using current gold standard methods requires access to the entire kidney at autopsy and is extremely time consuming and costly. To overcome this problem, we have developed new noninvasive MR susceptibility imaging methods to study experimental models of the kidney. We are developing improved imaging techniques for the identification of neuroanatomical structures using diffusion guided Quantitative Susceptibility Mapping (dQSM) techniques. Traditional methods have included neural tracing, which requires ex vivo examination of the tissues. Understanding how the brain becomes ‘wired’ together and rearranges following a lesion is a problem that has puzzled scientists for decades, and the significance of in vivo brain imaging is the ability to map connections during development and follow injury in the same animal. The MR methods team has developed bespoke MR image reconstruction algorithms, and advanced image analysis and visualisation techniques. The techniques are enabling technological advances that have resulted in new and faster MR sequences. A new research project is being undertaken to understand unexpected losses of consciousness – one of the biggest problems in human life. Loss of consciousness can be induced by epileptic attacks, severe head trauma and coma (amongst others). The aim of the project is to understand the neural mechanisms that regulate the level of consciousness and its integration across the entire brain, by recording whole brain activity in human subjects, and neural activity from the entire surface of the brain in animal models during consciousness and under variable depths of anaesthesia.

Since MRI is crucial to healthcare and biomedical research, the advancement of MRI technologies at MBI is beginning to directly impact on the National Research Priority areas of Frontier Technologies for Building and Transforming Australian

Industries. Furthermore, MBI’s use of these technologies as part of understanding disease is making a substantial contribution towards the National Research Priority area of Promoting and Maintaining Good Health.

Strategic planThe MBI strategic plan has been developed in close alignment with the key objectives of the university’s 2025 vision: to be known internationally for a commitment to quality, and differentiated by a research intensive, international focus that will enable the university to address the important challenges of our times. The MBI strategy is also closely aligned with the Monash Research Strategy (2011-15), which sets out to achieve impact through research excellence and relevance. Underpinning this pursuit of research excellence and ability to deliver impact from our research, is a commitment by the university to six key enabling “pillars” including: talent enhancement, world class research infrastructure, encouraging interdisciplinary research, superior research training, professional research management, and a focus on research translation.

MBI is a core university Technology Research Platform under the World Class Research Infrastructure pillar. Through provision of world-class biomedical imaging capability and close integration with other core Technology Platforms, MBI is well positioned to support the university’s research aspirations. The MBI strategic plan is contributing to the Monash Research Strategy by:

Q providing and maintaining world-class instrumentation and expertise in biomedical imaging, that provides Monash researchers and collaborating partners with access to a capability that enables innovative research of the highest quality possible;

Q operating at world’s best practice to maximise the efficiencies and effectiveness of the MBI capability and capacity;

Q providing strong leadership and connections within key national and international bioimaging and research networks;

Q enabling academic and industry collaboration and partnership; and

Q working towards a sustainable funding model to maintain and expand the bioimaging capability to ensure continued relevance.

The MBI research platform also greatly contributes towards other key university strategies, including enhancing the attraction and retention of high performing researchers, enabling multidisciplinary research, providing opportunities for superior research training, and strengthening and contributing to the translation of research with potential to deliver impact. MBI is now providing the university’s interdisciplinary research teams with an advanced biomedical imaging research environment and partnerships to investigate, define and propagate imaging based solutions with impact. The research projects being undertaken at MBI are being led by some of the best researchers in the world, connected to their national and international peers, and supported by one of Australia’s leading biomedical imaging research platforms.

GovernanceMBI has an Advisory Board, with an independent chairperson and meets quarterly. The functions of the board are to assist the Director with strategic planning including advice in alignment with government policy on research infrastructure and industry trends; monitor the performance of MBI with help defining appropriate metrics (key performance indicators); provide representation for stakeholders; and make recommendations on strategies for the further development of MBI.

Chair

Ms Sue Renkin, Director, Intuitively Focused

Deputy Chair

Professor Ian Smith, Pro Vice Chancellor, Research and Research Infrastructure, Monash University

Members

Professor Paul Bonnington, Director, Monash e-Research Centre

Professor Gary Egan, Director, Monash Biomedical Imaging, Monash University

Dr Daniel Hausermann, Principal Scientist – Imaging and Medical Therapy Beamline, Australian Synchrotron

Dr Gareth Moorhead, Research Program Leader, Devices, Systems and Engineering, Materials Science and Engineering (CMSE), CSIRO

Professor Andrew Peele, Head of Science, Australian Synchrotron

Professor Stephen Stuckey, Director Diagnostic Imaging at Monash Health (formerly Southern Health)

Dr Nicholas Ferris, Clinical Head, Monash Biomedical Imaging, Monash University

Professor Ross Coppel, Deputy Dean (Research), Faculty of Medicine, Nursing and Health Sciences, Monash University

Professor Gillian Duchesne (until quarter 3, 2012), Director of Radiation Oncology, Peter MacCallum Cancer Centre

Dr George Borg (until quarter 3, 2012), Chief Operating Officer, Australian Synchrotron

Professor Nellie Georgiou-Karistianis, Head of the Experimental Neuropsychology Research Unit (ENRU), School of Psychology and Psychiatry, Monash University.

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MBI Governing Board

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Professor Gary EganDirector, MBI Distinguished Professorial Fellow, School of Psychology and Psychiatry,Computational Imaging Theme Leader, LSCC, VLSCI

Mr Richard McIntyreRadiographer, Monash Health and MBI

Ms Meg Lester(From 1 October, 2012)Executive Assistant to the Director, MBI

Mr Bryan Paton (from 1 July, 2012)Research assistant, School of Psychology and Psychiatry and Research Fellow, MBI

Dr Lisa HuttonSenior Research and Operations Manager, MBI

Associate Professor Nicholas Ferris (from 1 March, 2012)Head, Clinical MRI, MBI and Clinical Radiologist, Monash Health

Dr David BarnesSenior Research Fellow and Head, Image Analysis and Informatics, MBI and Monash e-Research Centre; LSCC, VLSC Senior Research Fellow (Adjunct) Faculty of IT

Dr James PearsonSenior Research Fellow and Head, Animal Imaging Research, MBIStaff Scientist, Imaging and Medical Beam Line, Australian Synchrotron

Dr Karen SiuSenior Research Fellow and Head, X-ray and CT Imaging Research, MBIStaff Scientist, Imaging and Medical Beam Line, Australian Synchrotron

Mr Dale TomlinsonBuilding and Resources Manager, MBI

Ms Fiona Rohan (until 31 July, 2012)Executive Assistant to the Director, MBI

Dr Govinda Poudel(from 1 February, 2012)Computational MR Imag-ing Scientist, School of Psychology and Psy-chiatry, MBI and Monash e-Research Centre; LSCC, VLSCI

Dr Parnesh Raniga(from 1 March, 2012)Medical Imaging Scientist, MBIResearch Scientist, ICT Centre, CSIRO

Mr Owen KaluzaSoftware programmer, MBI and Monash e-Research Centre

Mr Michael Eager(from 13 Feb 2103)Software programmer, MBI and Monash e-Research Centre

Dr Marcus Gray(until 30 September, 2012)Research Fellow, School of Psychology and Psychiatry and MBI

Dr Toan Dinh Nguyen(from 1 March, 2012)Imaging Informatics Officer, MBI and Monash e-Research Centre

Dr Sharna Jamadar(from 1 February, 2012)Research Fellow, School of Psychology and Psychiatry and MBI

Personnel

Staff

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Sulaiman Al HasaniDepartment of Electrical and Computer Systems Engineering and MBI

Ms Lina Juzokaite (May - August, 2012)Institute of Neuroscience, Newcastle University, UK and MBI

Mr Steffen Kreiger (from 1 May, 2012)MBI and Max Planck Institute, University of Leipzig, Germany

Mr Kamlesh PawarDepartment of Electrical and Computer Systems Engineering and MBI;Indian Institute of Technology Bombay Monash Research Academy, India

Mrs Louise Mitchell (from 1 July, 2012)MRI Administrator, MBI

Mr Saman KashukMBI and School of Engineering and Science, Victoria University

Mr Igor Grossman (from 1 December, 2012)Computational Biomedical Imaging student, MBI and Monash e-Research Centre; LSCC, VLSCI

Dr Qi-Zhu Wu(from 1 March, 2012)Research Fellow and MR Physicist, MBIResearch Scientist, CMSE, CSIRO

Dr Ruth VreysMR Imaging Scientist, MBI and Business Manager, Victorian Biomedical Imaging Capability

Ms Amanda Ng (from 1 April, 2012)Computational Biomedical Imaging Scientist, MBI and Monash e-Research Centre; LSCC, VLSCI

PhD and Research Students

Ms Ruchi Guptai(to March 2012)VLSCI Summer Intern student

Dr David Wang(to March 2012)VLSCI Summer Intern student

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Research Teams

Cognitive NeuroimagingDuring 2012 the team focused on laboratory set up, testing of equipment, data acquisition for first studies and optimisation of MBI’s MRI scanner for cognitive neuroscience experiments. Simultaneous ocular motor functional MRI equipment was installed and commissioned during the first half of 2012, together with stimulus presentation computers and projection equipment configured with multiple stimulus presentation software packages that are now available to researchers.

The simultaneous electroencephalography (EEG) functional MRI (fMRI) equipment was used extensively in the second half of 2012 and two full studies have now been completed. Movement coils for the recording of head movements and for the detection of gradient artefacts in the scanner are under development. Once complete they will enable a superior method for artefact correction. Data fusion of EEG and fMRI data is also an ongoing project with technical developments enabling improved accuracy for extraction of the EEG source when it is recorded simultaneously with the fMR images. Automatic EEG electrode localisation is a joint project between the Imaging Analysis and Cognitive Neuroimaging teams using imaging processing routines that automatically detect the location of the EEG electrodes on a subject’s scalp. The preliminary results are promising with high detection rates and fast processing times.

We currently have productive collaborations with Monash University’s School of Psychology and Psychiatry and also researchers outside the university. The Cognitive Neuroimaging team has been involved in successfully conducting ocular motor studies in a number of difficult patient groups, across both child and adult populations. During 2012, three studies completed data collection: a study of Williams Syndrome individuals conducted by Hanna Kirk and Darren Hocking, and Professor Kim Cornish; a study of Fragile X permutation carriers by Ms Annie Shelton and Dr Joanne Fielding, and Professor Kim Cornish; and a study of alcohol exposure and sleep deprivation conducted by Drs Joanne Fielding and Clare Anderson. There are two ocular motor studies: a study of autism individuals being conducted by Drs Esther Ginsberg and Joanne Fielding; and a study in individuals with attention deficit hyperactivity disorder (ADHD) (being conducted by Ms Amanda Connolly and Dr Joanne Fielding. A number of Honours projects using EEG were also successfully completed throughout the year.

Hypo-myelination of the superior cerebellar peduncle in individuals with Friedreich Ataxia: an MRI magnetisation transfer imaging study

Louise Corben, Saman Kashuk, Hamed Akhlaghi, Sharna Jamadar, Martin Delatycki, Joanne Fielding, Nellie Georgiou-Karistianis, Beth Johnson

The dentate nucleus is the major relay station for neural connection between the cerebellum and cortex, and is a significant component of the neuropathological profile of Friedreich ataxia (FRDA). We have previously shown that the size of the superior cerebellar peduncle, which links the dentate nucleus to cortical and subcortical structures, is significantly reduced in individuals

with FRDA compared to control participants. This study used magnetisation transfer imaging to examine the integrity of white matter in the superior cerebellar peduncle in FRDA. The white matter of the superior cerebellar peduncle and the corpus callosum (as a control region) was examined in ten individuals with FRDA and ten controls. Individuals with FRDA demonstrated a significant reduction in the magnetisation transfer ratio (MTR) in the superior cerebellar peduncle when compared to control participants. There was no significant difference between the groups in MTR in the corpus callosum. Moreover, there was a significant reduction in MTR in the superior cerebellar peduncle compared to the corpus callosum in participants with FRDA only. We suggest the reduction in MTR in the superior cerebellar peduncle may be indicative of hypomyelination in white matter tracts in individuals with FRDA.

A sample of a 3D mask created manually for the right superior cerebellar peduncle (Left).

Comparison of the mean magnetisation transfer ratio results between patients and control

groups in superior cerebellar peduncle (SCP) and the corpus callosum (CC) (Right).

Simultaneous ocular motor functional MRI of anti-saccade performance in healthy individuals

Sharna Jamadar, Meghan Clough, Beth Johnson, Joanne Fielding

The anti-saccade task is a classic task of ocular motor (OM) control that requires participants to inhibit a saccade to a target and instead make a voluntary saccade to the mirror opposite location – that is participants look at a point on a wall, they are then presented with a new point and asked not to track it (the saccade). Instead, they are asked to respond by moving their eyes to the same distance in the opposite direction of the new point (the anti-saccade). By comparison, the pro-saccade task requires participants to make a visually guided saccade to the target. These tasks have been studied extensively using behavioural ocular motor, electrophysiological and neuroimaging in both non-human primates and humans. In humans, the anti-saccade task is under active investigation as a potential biomarker for multiple psychiatric and neurological disorders. Here, we used simultaneous OM-fMRI to study the neural correlates of anti-saccade and pro-saccade performance in healthy individuals. Anti-saccade trials were performed slower but more accurately than pro-saccade trials. Anti-saccade versus pro-saccade trials activated a distributed ocular motor network including frontal eye fields, supplementary eye fields, dorsolateral prefrontal cortex, insula, anterior cingulate,

Clinical Imaging

The clinical team began sequence testing and protocol development work on the Siemens Skyra 3 Tesla (3T) human whole body MRI scanner in January 2012, with the first formal experiments commencing in June 2012. Since then, 20 different projects have made use of the scanner and there is ongoing development work for additional projects.

Several of these projects have taken advantage of special arrangements at MBI that allow for the recording of brain electrical activity using EEG and/or eye movements while the subject lies in the MRI scanner, even while MR images are being acquired. A wide range of research questions have been addressed by the MRI projects, with a particular focus on the neuropsychology of perception. These studies have addressed questions about how the activity of different brain regions correlates with key processes associated with learning and decision making.

High-resolution imaging of the cervical carotid artery

Atherosclerotic plaque at the bifurcation of the common carotid artery in the neck is known to be an important cause of stroke. Plaque can contribute to stroke both by narrowing the artery, reducing blood flow to the brain, and by acting as a source of blood clots which can travel along large blood vessels into the brain, where they can block smaller vessels. We are using special new receiver coils to obtain high-resolution images of the carotid artery wall and lumen, with a view to better assessing stroke risk in patients with known plaques.

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intraparietal sulcus, superior and inferior parietal lobule and cerebellum. By defining the anti-saccade network in healthy individuals, these results will be of use for developing biomarkers for illnesses that show robust anti-saccade deficits, including multiple sclerosis and schizophrenia.

Anti-saccade greater than pro-saccade ocular motor performance (top) and fMRI activity (bottom).

Cardiac MR images showing a three dimensional volume rendering of the chest (top-left), three orthogonal two dimensional sections through the heart (top-right), and an ECG trace acquired simultaneously during the scanning (bottom).

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Research Teams Continued

Improving the imaging of brain blood flow

Parnesh Raniga, Nicholas Ferris, Steffen Kreiger, Qi-Ziu Wu

Blood flow to the brain is thought to be an important indicator of brain health, particularly in the aged. Traditional methods of measuring brain blood flow have required injection of a tracer or contrast medium. More recently, an MRI technique called Arterial Spin Labelling (ASL) has been developed which uses magnetic tagging of the subject’s own blood with no injection of contrast agent required. However, earlier versions of the ASL technique produced images of low anatomical resolution; using the 3T MRI system and a new imaging approach, we have substantially improved the quality of brain blood flow images.

Research, MRI and magnetic resonance (MR) spectroscopy were used to investigate how injurious ventilation techniques contribute to brain injury. The findings suggest that in the absence of gross lesions in the neonate brain, chemical changes measured with MR spectroscopy may reveal abnormal accumulation of metabolites that correlate with cellular (and therefore brain) injury.

Investigating the time course and treatment of cardiorenal syndrome with cardiac and BOLD imaging

James Pearson, Roger Evans, Kate Denton, Rob Widdop, Ruth Vreys, Qi-zhu Wu

Cardiorenal syndrome occurs where disease in one of the cardiac or renal systems causes disease in the other system. This project aims to determine if activation of the hormones in the renin-angiotensin system after a heart attack drives cardiorenal syndrome. Using blood-oxygen level dependent (BOLD) MRI, we are determining whether hypoxia in the kidney occurs after a myocardial infarction, and how this impacts on already compromised heart function. Building on this, we are assessing if prophylactic treatment with a routinely used anti-hypertensive sartan drug is an effective preventative measure for patients at risk of a heart attack.

Cardiac MRI image of a rat heart after a myocardial infarction shown at stages of relaxation and peak contraction. The left side of the heart muscle wall (in dark grey) in both panels shows thinning and poor contraction due to myocardial infarction.

Improving images of brain blood flow with 3D arterial spin labelling. Image on left shows blood flow map (higher flow in brighter shades) derived from traditional 2D arterial spin labelling. An example of the new 3D arterial spin labelling technique is shown on the right. Note the improved distinction between high blood flow grey matter and low blood flow white matter.

A sagittal brain slice of a ventilated lamb showing the region of interest and MR spectroscopy measurements of brain injury.

Animal ImagingThe animal imaging research team is focussed on high resolution and functional in vivo imaging of animals for basic and preclinical research. Using complementary MRI and synchrotron radiation techniques, the team is investigating neural network development, the impact of brain injury in developing and adult animals, as well as changes in function associated with cardiovascular disease. Of particular focus during 2012, the team has worked on developing protocols for routine evaluation of cardiac function, anatomical and functional imaging of kidney inflammation in heart failure, hypertension and diabetes, as well as advanced imaging of neural tracts in rodents, lambs and non-human primates.

Early detection of ventilation induced brain injury with magnetic resonance spectroscopy

Beatrice Skiöld, Graeme Polglase, James Pearson, Stuart Hooper, Qi-zhu Wu, Ruth Vreys

In the clinic, assessment of the efficacy and impact of ventilatory strategies used for respiratory support for premature newborns is very difficult. Many widely used ventilation techniques deliver too much volume and thereby cause lung injury and have been shown to subsequently cause brain injury. In this study, with a team from the Ritchie Centre at the Monash Institute of Medical

Automated analysis of ultra-high resolution kidney images. GlomViewer being used to manually mark glomerular tissue (red circles) and Bowman’s space and capsule (green circles) on ultra-high-resolution optical microscopy data from the Monash Aperio Scanscope.

Automated analysis of ultra-high resolution kidney images. Volume rendered computer graphic showing the initial stages of automated processing of a human kidney imaged ex vivo using the MBI Agilent 9.4T MR. White (unprocessed) component shows the overall structure of the kidney and red shows the processed image beginning to reveal the many thousands of glomeruli throughout the sample. Images were acquired with 0.05mm resolution.

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Image Analysis and InformaticsThe Image Analysis and Informatics team supports all major imaging activities at MBI by developing and supporting high availability image and clinical data management systems, and researching and developing advanced image analysis and visualisation methods. The team brings together experts in biomedical imaging, computational science, e-research, visualisation and software engineering to provide broad expertise and to create bespoke data management solutions.

We apply contemporary computing technologies, including parallel programming and large scale batch processing using the high performance Multimodal Australian ScienceS Imaging and Visualisation Environment (MASSIVE) facility at Monash University. These technologies accelerate imaging and image analysis tasks involving high computation density and extremely large data collections.

In 2012, we enhanced the MBI data management system to support optical microscopy and EEG data, and to provide advanced query mechanisms for finding, fetching and processing images. We developed, tested and refined imaging protocols for a large cohort neuroimaging study, and we developed advanced processing and automated analysis for MR images of kidneys. In the computer graphics domain, we developed PDF and web-based 3D visualisation tools for displaying anatomy. Our work featured at the International Neuroinformatics Coordinating Facility 2012 Congress held in Munich, and at the OzViz and Accelerated Computing Workshop 2012 held in Perth. Members from the image analysis and informatics team were invited to attend the New Horizons in Human Brain Imaging 2013 workshop held in Hawaii in early 2013, and were also invited to contribute to the International Brain Research Organisation Advanced Imaging Course held at MBI in January, 2013.

Automated analysis of ultra-high-resolution kidney images

Michael Eager, Qi-zhu Wu, David Barnes, John Bertram, Luise Cullen-McEwen, Victor Puelles, James Armitage, Kevin Bennett (University of Hawaii), Norbert Gretz (University of Heidelberg)

Working with kidney researchers led by Professor John Bertram at Monash University, we have developed and delivered a multimodal kidney image integration and analysis pipeline. A new method for counting and sizing every glomerulus in the kidney has recently been described involving in vivo labelling of glomeruli with cationic ferritin, and then visualisation using MRI. The number of glomeruli (the filtration units of the kidney) in any individual kidney is believed to be a good measure of renal health and susceptibility to disease. We developed a software tool known as xGlom that uses MRI and high-end computing power to deliver 3D images of the kidney in unprecedented detail and in a fraction of the time possible using traditional methods. The tool fetches MR, X-ray Computed Tomography (CT) and optical microscopy images stored on the MBI image management infrastructure. The tool automatically segments and counts glomeruli in high-resolution MR and CT images, which is significantly faster than manual counting of glomeruli in ultra-high-resolution optical microscopy images.

The automated pipeline places Australian researchers at the absolute forefront of the nascent field of clinical diagnostic kidney imaging.

The convergence in the Monash Clayton precinct of world-class kidney research teams, multi-scale imaging modalities (including the immediately-adjacent Australian Synchrotron and MBI facilities), and computational expertise and capability including MASSIVE, enabled us to quickly establish a world class team with the necessary expertise to push the field forward. The Multimodal Kidney Image Analysis Project is a collaborative project between Monash University’s Department of Anatomy and Developmental Biology, MBI, the Monash eResearch Centre, and was supported by the Australian National Data Service.

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Research Teams Continued

3D visualisation of high-resolution anatomical MR scans. A deep structural scan with the MBI human MR instrument was conducted at 0.3mm resolution. FABLab team members painstakingly segmented the image into the constituent soft tissue components, and this visualisation was created combining bone data from the same subject. In the interactive 3D PDF version, the reader can rotate, zoom and re-light the model, as well as click on components to identify them.

Three dimensional visualisation of high resolution anatomical MR scans

David Barnes, M. Quayle, C. Law, N. Tharakan, S. Mouer, Colin McHenry (Monash FABLab)

Working with the Functional Anatomy and Bio-mechanics Research Laboratory (FABLab) at Monash University, we have applied our advanced, multi-media 3D visualisation techniques to high resolution anatomical scans take using MBI’s 3T MRI. Our work has enabled and simplified the publication of complete, 3D data sets (volumes and surfaces) in PDF documents and on web pages, as fully interactive figures that can be rotated, zoomed and re-rendered using ubiquitous software such as Adobe Reader and Mozilla Firefox. Components of a visualisation can be switched on and off, and can be identified by name simply by clicking on the part of interest. Our visualisation research group has pioneered the capability to embed interactive volume renderings in 3D images, and produced an innovative technique that is gaining traction with the major journals in fields as diverse as biomedical imaging, materials science and astrophysics.

MRI Methods

The MRI Methods research team has been highly productive throughout 2012, culminating in the acceptance of abstracts for presentation at the International Society for Magnetic Resonance in Medicine 2013 Annual Scientific Meeting to be held in Salt Lake City. Team members have developed improved imaging techniques for the identification of neuroanatomical structures using diffusion guided Quantitative Susceptibility Mapping techniques. The MR methods team has also developed a number of bespoke MR image reconstruction algorithms, and advanced image analysis and visualisation techniques. These techniques have provided significant technological advances that have resulted in faster MR sequences and higher sensitivity imaging methods.

Deformation of artery walls under increasing pressure. Isocontours of structural stress. (a) p=100, (b) p=102.6, (c) p=105.2 mmHg.

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Noiselet encoded compressive sensing parallel MRI

Kamlesh Pawar, Arjun Arunachalam (Indian Institute of Technology Bombay, Mumbai, India), Jingxin Zhang (Department of Electrical and Computer System Engineering, Monash University).

In compressed sensing MRI, the sensing matrix is the randomly under sampled discrete Fourier transform matrix while the wavelet is used as the sparsifying transform. Compressed sensing reconstruction relies on the sparsity of the signal in the transform domain and on the incoherence between sensing and sparsifying transform matrices. We compared the compressed sensing reconstruction error with uniform under sampling of the Fourier encoded and the noiselet encoded MR images and showed that noiselet encoded MRI performs better than Fourier encoded MRI. A tailored spin echo sequence was proposed to encode the primary phase encode direction with a noiselet basis for MR imaging.

Visuo-motor learning measured via high-resolution fMRI

Steffen Kreiger and Robert Turner (Max Planck Institute, University of Leipzig, Germany) and Leigh Johnston (University of Melbourne).

Blood oxygenation level dependent (BOLD) fMRI has been used to investigate brain dynamics related to learning physical skills (motor skills). We investigated visuo-motor learning by measuring BOLD signal together with cerebral blood flow using the pulsed arterial spin labelling technique at 7T magnetic field strength which enhances the spatial resolution of pulsed arterial spin labelling. Subjects were required to match the movement of a manually controlled joystick to a vertical bar displayed on a screen. Significant improvement in motor performance was observed during the scanning, with activation of the claustrum and the anterior intra-parietal sulcus (amongst others). These two regions were not previously known to be associated with motor skill acquisition.

X-Ray and CT Imaging

The X-ray and CT imaging research team exploits the advantages of synchrotron radiation to investigate biomedical processes in living systems. With particular interests in lung disease and cardiovascular disease, the team members are using specialised synchrotron imaging and diffraction techniques to study these systems in real time at high resolution. The team has particular expertise in X-ray imaging physics and in vivo synchrotron physiological imaging.

Characterisation of vulnerable plaque formation for prediction of plaque rupture

Karen Sui, P Assemat, K Hourigan (Mechanical Engineering), J Armitage (Anatomy and Developmental Biology)

Atherosclerosis occurs due to the build up and infiltration of lipid streaks in the wall of an artery. Although such plaques can intrude into the lumen (centre) of the blood vessel and compromise flow, the greatest risk to heath occurs if the plaque ruptures, as the resulting debris can lodge in small vessels of the brain or heart and subsequently cause a stroke or heart attack. This project is studying the influence of mechanical effects (blood shear stress, pressure, structural stress) on plaque formation and rupture

processes. We are using synchrotron micro-computed tomography (micro-CT) as the first step in building a physiologically realistic model by characterising plaques in a 3D mouse model. The morphological data has allowed us to construct a numerical model to study the link between the topography of the plaques and the rupture sites. Computational fluid dynamics software is now being used to simulate blood velocity and pressure fields within this numerical model and thus determine how plaques are impacted by and act on blood velocity and pressure.

Early targets for preventing diabetic heart disease

James Pearson, Amanda Edgley, Darren Kelly, Mikiyasu Shirai

Diabetics have greater incidence of cardiovascular complications and double the mortality of non-diabetics. Many of the complications in diabetic heart disease are attributable to chronic hyperglycaemia and activation of cytokines and the renin-angiotensin system and the generation of oxidative stress. We speculate based on our recent data that an increase in protein kinase C/Rho-kinase activity independently causes dysfunction in the coronary vasculature and the myocardium at the onset of diabetes and is therefore a suitable therapeutic target to prevent DCM. Using our established synchrotron radiation angiography and small-angle X-ray scattering approaches on live diabetic rats we are investigating microvessel dysfunction and cardiac cross-bridge dynamics in vivo.

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Operations Team

OverviewVictorian Minister for Innovation, Services and Small Business, the Hon Louise Asher MP, and Professor Ed Byrne officially opened the MBI facility on Wednesday, 30 May 2012. The official launch marked the completion of the building works, although the installation and commissioning of scanners and associated equipment continued beyond this date.

By the end of 2012, six scanners were installed, and the majority were also operational and available for use by researchers:

Q Siemens 3T MRI: first scan undertaken in January 2012, and the instrument was commissioned in March 2012;

Q Siemens PET SPECT CT: commissioned for use in April, 2012;

Q Agilent 9.4T preclinical MRI: commissioned in December 2012 and was made operational in early 2013;

Q Bioscan PET CT: relocated from the Australian Synchrotron site to the Alfred Medical Research Education Precinct, Prahran in September 2012 and the scanner was re-commissioned in October 2012;

Q Bioscan CT: installed at the Monash Institute for Pharmaceutical Sciences (MIPS), Parkville in July 2012 and became operational in August 2012; and

Q Bioscan FLECT: installed at MIPS in December, 2012 and was put into full operation in early 2013.

The necessary documentation, processes and procedures, safety and operational training required to provide researchers safe access to quality instrumentation facility was also established and implemented in 2012. The booking systems, terms and conditions of usage, project application forms, screening forms, website and a launch report were prepared and distributed.

During 2012 training offered by MBI included: Siemens hosted information sessions on the operation of the 3T MRI and PET SPECT CT; Agilent training of the 9.4T MRI operators; as well as Bioscan PET CT and FLECT training across multiple sites. MBI has also hosted a number of training sessions for researchers and users of the facility, including MRI safety and information sessions, EEG and Matlab workshops and outreach activities including the five-day “Advanced Neuroimaging” workshop for the International Brain Research Organisation and Australian Neuroscience Society organised for early 2013. Throughout 2012, MBI hosted numerous other events for the Victorian Platform Technology Network, the South Eastern Melbourne Innovation Precinct, the Australian Synchrotron, CSIRO, ANSTO, the National Imaging Facility, the Centre for Nanofabrication, Siemens, Agilent and Monash University.

This year we have been involved in over 45 different research projects, many of which have focused on human imaging. The focus shifted slighter throughout the year as more animal scanners were commissioned. We expect this trend (increase in the usage of animal scanners) to continue throughout 2013.

Vice-Chancellor of Monash University, Professor Edward Byrne AO speaking at the opening of MBI.

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Professor Euan Wallace gave the keynote at MBI’s opening Symposium

The utilisation of the human MRI scanner was further boosted in mid-2012 by the provision of funding to researchers in the School of Psychology and Psychiatry (SPP) under an MBI-SPP Imaging Grant scheme. This funding scheme not only provided researchers with access to the imaging equipment, but also enhanced interactions between MBI and SPP staff and students. Ten applications were received and competitively assessed, with nine applications receiving full or partial funding to undertake MRI pilot studies. The results of these projects have been promising and outputs including publications and major grant applications have ensued. We look forward to providing similar access to small grants in 2013.

The first outputs from studies undertaken at MBI were also achieved in 2012. Completed studies included investigation of ocular motor function in humans, and perinatal brain injury in an ovine model. The first publications and conference presentations from the use of MBI infrastructure also came to fruition in 2012, and we are looking forward to a continued increase in the number of research outputs in 2013.

Training, Events and VisitorsTo mark MBI’s official opening, a Symposium on imaging brain development and plasticity was held, with keynote speaker Professor Euan Wallace, Director, Ritchie Centre and Director of Obstetrics and Gynaecology, Monash Health presenting “Cell therapies for tomorrow’s medicine: seeing the road ahead”. The symposium also showcased other clinical and fundamental research in the area of degenerative and developmental brain injury, focusing on the current and potential application of imaging technologies to enhance our understanding of brain injury mechanisms.

During May 2012, MBI hosted, Simulate and Visualise, New World Technologies for Real World Outcomes, a workshop forming part of the Innovation Workshop Series presented by the South Eastern Melbourne Innovation Precinct. Many distinguished Monash academics presented, including Professor Gary Egan.

With the aim of developing high quality cognitive neuroimaging research and fostering collaboration between MBI and SPP, researchers involved in cognitive neuroimaging research were invited to join to MBI for regular meetings. Held at MBI, presentations given by junior and senior staff, followed by networking opportunities. As part of this series, in August 2012 MBI hosted Dr David Glahn, from the Department of Psychiatry at Yale University, who presented his work on Imaging Genetics.

Bryan Paton conducted a two day workshop in August 2012, entitled Matlab for Cognitive Neuroscience. Met with very positive feedback, day one consisted primarily of introductory material whilst the second day focused on programming and advanced analysis options. Due to its success, these workshops will be held annually by MBI.

MBI Seminar SeriesThroughout 2012 MBI hosted a fortnightly seminar series showcasing the research expertise at MBI and sharing the innovative research methodology developed and used at MBI. Primarily focused at an internal audience, the seminars were also attended by researchers from across the university, particularly the School of Psychiatry and Psychology.

The seminar series also played host to researchers outside MBI, including Dr Matthew Mundy, head of the Cognitive Neuroscience of Implicit Learning Laboratory in the School of Psychology and Psychiatry at Monash University; Dr Stefan Bode, from the School of Psychological Sciences at the University of Melbourne; Dr Kai-Hsiang Chuang from the MRI Group at the A*STAR Bioimaging Consortium in Singapore; and Associate Professor Nao Tsuchiya from the School of Psychology and Psychiatry at Monash University.

Operations Team Continued

A delegation from the South East University, China, including the University President, Vice President (International Coordination) and Vice President (Graduate Education) made a visit to Monash Biomedical Imaging in July 2012. They were welcomed to the facility by Professor Gary Egan, Director MBI, and Professor Ian Smith, Pro Vice-Chancellor (Research and Research Infrastructure). During their tour of the facility they were shown the operational biomedical imaging scanners as well as the Imaging and Medical Beam Line located at the Australian Synchrotron adjacent to MBI.

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MBI-SPP GrantsA new small grant program jointly sponsored by MBI and the School of Psychology and Psychiatry (SPP) at Monash University was established in 2012. Adjudged highly successful, the scheme was aimed at early and mid career researchers to foster and develop MRI research projects, stimulate engagement between MBI staff and research groups across SPP, and provide SPP research projects with pilot data to strengthen grant applications for external funding. Preference was given to early career researchers with collaborations with researchers from outside of the School encouraged (Table 1)

Table 1: Projects funded through MBI-SPP grants in 2012

Chief Investigator Study title

Dr Sharna Jamadar A pilot study for the investigation of the genetic determinants of age- related changes in brain structure, function and connectivity

Dr Matthew Mundy Perceptual learning and the aging brain: the role of the medial temporal lobe in cognitive decline

Dr Louise Corben Examination of functional and structural changes underlying ocular motor deficits in individuals with FRDA

Dr Catherine Willmott The association between neuroanatomical correlates of attention and working memory, and response to methylphenidate in TBI rehabilitation

Dr Izelle Labuschagne Intranasal oxytocin modulation of socio-emotional brain regions in Huntington’s disease: a fMRI and resting state investigation

Professor Mairead Dolan A pilot study looking at the neural correlates of attachment/romantic love; rejection and aggression in healthy controls

Professor Louise Newman The neurobiology of parenting disturbance: An fMRI study of early interactional disturbance in parental neglect and substance dependence

Dr Nao Tsuchiya Neuronal basis of the opposing effects of attention and consciousness in afterimage formation

Dr Nao Tsuchiya Neuronal basis of conscious object recognition using a novel visual stimulation paradigm (SWIFT

MBI hosted a number of well attended symposia, training days, lectures and seminars throughout 2012

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MBI is focused on collaborative research efforts for both the development of biomedical imaging research techniques as well as their use in research projects. Throughout 2012 we sought to develop relationships with key research organisations or collaboratives across the university and Australia.

Victorian Biomedical Imaging CapabilityDuring 2012 the Victorian Biomedical Imaging Capability (VBIC) was managed from MBI at Monash University, and brought together the key organisations in biomedical imaging research across Victoria. The vision of VBIC is to become a world leading capability dedicated to advancing the biomedical imaging research community in Victoria. The collaborating partners, including Monash University, the Florey Institute of Neuroscience and Mental Health, The University of Melbourne and Swinburne University, are jointly working towards the VBIC mission to deliver the next generation of discoveries and enhance excellence in biomedical imaging to benefit translational research and to increase Victoria’s global competitiveness in Australia’s priority health areas.

The partners are now providing access to cutting-edge imaging equipment and world-class experts, increasing knowledge by organising workshops and state-wide opportunities for skill development and knowledge transfer, promoting VBIC to the wider community via presence at national and international conferences, developing human capital to support the applications of biomedical imaging modalities, and pursuing additional investment in Victoria’s biomedical imaging human and capital infrastructure.

VBIC has enabled increased collaboration and sharing of expertise and infrastructure to benefit translational research and global competitiveness in the high priority health areas that depend on imaging. The Capability operates in a collaborative structure to establish the processes and forums necessary to optimise the use of imaging resources in Victoria. Established in 2010, VBIC has become a $25 million investment that has ensured Victoria has biomedical imaging research infrastructure commensurate with its standing as an international biomedical research hub. Throughout 2012 the achievements of VBIC were reported in four key areas:

Q Enhanced biomedical imaging equipment – an extensive range of equipment now used in human and preclinical research imaging including MRI, PET CT and X-ray equipment;

Q Relationship with biotechnology industries – have been enhanced through the imaging equipment acquisition process, with VBIC partners establishing or consolidating relationships with local and international biotechnology companies;

Q World renowned researchers – staff were recruited to many of the partner organisations, partially due to the significant imaging infrastructure available across Victoria, and world renowned researchers have been recruited into these leadership roles; and

Q United front – enhanced cooperation and collegiality between the partner organisations. with Victoria being the only Australian state to formally organise its biomedical imaging research activities.

VBIC Business Manager: Dr Ruth Vreys

MASSIVEThe Multi-modal Australian ScienceS Imaging and Visualisation Environment (MASSIVE) is a national imaging and visualisation facility established by Monash University, the Australian Synchrotron, the Australian Commonwealth Scientific Industrial Research Organisation (CSIRO), and the Victorian Partnership for Advanced Computing (VPAC). MASSIVE is now fully operational as a nationally distributed and integrated facility for imaging research. The facility provides hardware, software and expertise to support computational imaging analysis at MBI, particularly in advanced brain imaging research. MASSIVE has integrated multiple neuroimaging analysis software components, enabled cross-platform and cross-modality integration of neuroinformatics tools, and integrated neuroimaging databases and analysis workflows.

LSCC Computational Bioimaging HubThe Computational Bioimaging hub of the Life Sciences Computational Centre, which is part of the Victorian Life Sciences Computation Initiative (VLSCI), is based at MBI. The hub staff provide expertise, support and training in biomedical imaging, assisting researchers to take advantage of informatics and imaging solutions, and enhancing their science output through the use of high performance computing facilities.

The computational imaging scientists based in the hub also undertake research into advanced image analysis algorithms, informatics for data management, and visualisation tools. The outputs from these developments are accelerating analyses of large cohort studies, improving the characteristics of biomedical images, and providing tools for visualisation led scientific discovery.

National Imaging Facility MBI continued its contribution to the provision of national imaging infrastructure through participation in the National Imaging Facility (NIF). This included commissioning the PET SPECT CT at MBI (referred to as MBI’s NIF flagship instrument) in April 2012. MBI also received staff support from NIF through the funding of the Informatics Officer Dr Toan Dinh Nguyen, a software engineer and researcher with an interest in imaging processing, computer vision, video coding, and 3D graphics.

Collaborations

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CSIROThe collaboration formed with CSIRO in 2011 (as part of the Victorian Biomedical Imaging Capability), has further developed throughout 2012 with the funding of two research fellows. These research fellows played a significant role in extensive MRI protocol optimisation to enable image acquisition for ASPREE studies in 2013. ASPREE is a clinical trial investigating the benefits of low dose aspirin in the elderly, and MBI will be involved in two sub studies focused on the brain (ASPREE IMAGE) and the knee (ASPREE IMAGE OA).

Axial image of the brain of a common marmoset.

Beyond ASPREE, collaborative activities with CSIRO are also focused on the development of an in vivo and an ex vivo MRI atlas of the brain of the common marmoset. These atlases will enable researchers to map marmoset brain images to a common reference space, provide a normative template, and enable comparison of results across different research projects that use this animal model.

Sagittal image of a human knee showing cartilage as a bright rim at the interface between the femur and tibia

International Neuroinformatics Coordinating FacilityThe International Neuroinformatics Coordinating Facility (INCF) was established in 2006 by the Organisation for Economic Co-operation and Development. Seventeen countries have INCF nodes including the USA, UK, Germany, Sweden, and Japan. Officially launched and headquartered at MBI, the INCF Victorian Node was established in 2012 through a collaboration between Monash University and The University of Melbourne. The INCF develops and maintains databases and computational infrastructure for neuroscientists. Software tools and standards for the international neuroinformatics community are being developed through the INCF Programs, which address infrastructure issues of high importance to the neuroscience community. The INCF also collects and makes available neuroinformatics tools in the INCF Software Center, where researchers can upload documentation, executables and related files; track use of their software; create a wiki; and establish development teams.

Monash University and The University of Melbourne, through their computational facilities, MASSIVE and the Victorian Life Sciences Computation Initiative (VLSCI) respectively, established the Victorian node of the INCF in 2012 for an initial three year period. The aims of the Victorian node are to support the neuroscience research communities at Monash University and The University of Melbourne using MASSIVE and the VLSCI supercomputers; to develop neuroimaging data management and analytic tools; and to develop a program in clinical neuroinformatics research in cooperation with clinical neuroscientists and informaticians. A particular area of interest that has developed is the initiation of a new taskforce in the area of multi-scale imaging connectomics.

The MASSIVE and the VLSCI super-computing infrastructure are now contributing to the development of scalable, portable, and extensible applications that are being used by neuroscience research laboratories across Victoria for storing, analysing and simulating brain mechanisms and processes. This is furthering our knowledge of the human brain and aiding our understanding of the causes of brain diseases. In particular, MASSIVE and VLSCI are being used for management, analysis and visualisation of bioimaging datasets from VBIC nodes, and from the Imaging and Medical Beam Line at the Australian Synchrotron.

V-Node Manager: Dr Wojtek Goscinski

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MBI recognises the importance of forming strategic alliances with key partners for the development of imaging infrastructure and research capabilities.

Siemens AustraliaMBI and Siemens Australia collaborate on a number of research projects in the field of MRI, Computed Tomography and Molecular Imaging. The creation of the joint Monash Siemens Collaboration Management Committee has enabled the provision and coordination of an internal competitive grants scheme, as well as the identification of linkage and fellowship grant opportunities for additional research or commercial seed funding investments. During 2012 the first collaborative projects were undertaken between Siemens and researchers from the Department of Chemistry, and from the Department of Electrical and Computer Engineering, Monash University.

Agilent TechnologiesAgilent has identified Monash University as a key research partner to work with in the Australian biomedical imaging research sector. MBI provides the opportunity within Monash University for collaborative biomedical imaging projects with Agilent, and the relationship has developed into a vital source of innovation for the development of new biomedical imaging technologies. Agilent has recently outlined a number of research and development areas of high importance, and their interest to work with MBI in the Australian research sector. Monash University is also considered a key alliance partner for Agilent to work with across the life science and in chemical analyses, particularly in spectroscopic and imaging technologies. The Agilent and Monash University partnership is likely to generate new opportunities for future areas of collaboration, potentially including the Agilent ‘Thought Leader Program’.

BioscanBioscan and Monash have entered a research and development collaboration for projects based on the preclinical CT, PET and FLECT imaging modalitites. Bioscan has established MBI as a Center of Excellence in Bioscan’s primary business area of molecular imaging. The Center of Excellence acknowledges Monash University’s standing as a preeminent university in biological research, particularly in biomedical, preclinical and translational research, and has been a key factor for the decision by the partners to enter into a three year research and development collaboration agreement.

Partnerships

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PublicationsCognitive Neuroimaging

1. M.J. Farrell, L.J. Cole, D. Chiapoco, G.F. Egan, S.B. Mazzone, “Neural correlates coding stimulus intensity and perception of capsaicin urge-to-cough”, Neuroimage 61 (2012) 1324-35.

2. C. Murawski, P.G. Harris, S. Bode, J.F. Dominguez D, G.F. Egan, “Led into temptation? Subliminally presented reward cues bias incidental economic decisions”, PLoS One 7 (2012) e34155.

3. L. Chen, S. Lui, Q. Wu, W. Zhang, D. Zhou,H. Chen, X. Huang, W. Kuang, R.C. Chan, A. Mechelli, Q. Gong. Impact of acute stress on human brain microstructure: an MR diffusion study of earthquake survivors. Human Brain Mapping 2013; 34(2): 367-373.

4. Q. Yue, M. Liu, X. Nie, Q. Wu, J. Li, W. Zhang, X.Q. Huang, Q.Y. Gong. Quantitative 3.0T MR spectroscopy reveals decreased creatine concentration in the dorsolateral prefrontal cortex of patients with social anxiety disorder. PLoSONE 2012; 7(10): e48105. Epub 2012 Oct 23.

5. X. Yang, K.M. Kendrick, Q. Wu, T. Chen, S. Lama, B. Cheng, S. Li, X. Huang, Q. Gong. Structural and functional connectivity changes in the brain associated with shyness but not with social anxiety. PLoS ONE 2013; 8(5): e63151.

6. S. Chen, X. Wu, S. Lui, Q. Wu, Z. Yao, Q. Li, D. Liang, D. An, X. Zhang, J. Fang, X. Huang, D. Zhou, Q.Y. Gong. Resting-state fMRI study of treatment-naïve temporal lobe epilepsy patients with depressive symptoms. NeuroImage 2012; 60(1) Mar: 299-304.

Clinical Imaging

7. H. Akhalghi, L. Corben, N. Georgiou-Karistianis, J. Bradshaw, M.B. Delatycki, E. Storey, G.F. Egan, “A functional MRI study of motor dysfunction in Friedreich’s ataxia”, Brain Research 1471 (2012) 138-154 [IF 8.8]

8. N. Georgiou-Karistianis, H. Akhlaghi, L. Corben, M. Delatycki, E. Storey, J. L. Bradshaw, G.F. Egan, “Decreased functional brain activation in Friedreich’s ataxia using the Simon effect task”, Brain & Cognition 79 (2012) 200-8.

9. N. Georgiou-Karistianis, M.A. Gray, D.J. Dominguez, A.R. Dymowski, I. Bohanna, L.A. Johnston, A. Churchyard, P. Chua, J.C. Stout, G.F. Egan,

“Automated differentiation of pre-diagnosis Huntington’s disease from healthy control individuals based on quadratic discriminant analysis of the basal ganglia: The IMAGE-HD study”, Neurobiology of Diseases 2012 Oct 13.

10. N. Georgiou-Karistianis, J. Stout, S.P. Carron, A.R Dymowski, A. Ando, A. Churchyard, P. Chua, I. Bohanna, G.F. Egan, “An fMRI investigation of the neural correlates of spatial working memory in pre-diagnosis and early symptomatic Huntington’s disease: IMAGE-HD cross-sectional analysis”, accepted Human Brain Mapping (May, 2012).

11. S.K. Goergen, F.J. Pool, T.J. Turner, J.E. Grimm, M.N. Appleyard, C. Crock, M.C. Fahey, M.F. Fay, N.J. Ferris, S.M. Liew, R.D. Perry, A. Revell, G.M. Russell, S-C. Wang, C. Wriedt, “Evidence-based guideline for the written radiology report: Methods, recommendations, and implementation challenges”, J. Med Imaging Radiat Oncol, 57:1-7, 2013.

12. M.A. Gray, G.F. Egan, A. Ando, A. Churchyard, P. Chua, J.C. Stout, N. Georgiou-Karistianis, “Prefrontal activity in Huntington’s disease reflects cognitive and neuropsychiatric disturbances: The IMAGE-HD study”, Exp. Neurology 239 (2012) 218-228.

13. S.C. Kolbe, M. Marriott, A. van der Walt, J. Fielding, A. Klistorner, P.J. Mitchell, H. Butzkueven, T.J. Kilpatrick, G.F. Egan, “Diffusion tensor imaging correlates of visual impairment in multiple sclerosis and chronic optic neuritis”, Investigative Ophthalmology & Visual Science (IOVS) 53 (2012) 825-32.

14. S.C. Kolbe, L. Millist, P.J. Mitchell, T.J. Kilpatrick, O. White, G.F. Egan, J. Fielding, “Dysfunctional inhibitory eye movements are associated with cerebellar injury in multiple sclerosis”, accepted by Human Brain Mapping (November, 2012) subject to revisions

15. Y. Liu, P.J. Mitchell, T.J. Kilpatrick, M.S. Stein, L.C. Harrison, J. Baker, M. Ditchfield, K. Li, G.F. Egan, H. Butzkueven, S.C. Kolbe, “Diffusion tensor imaging of acute inflammatory lesion evolution in multiple sclerosis”, accepted in J. Clinical Neuroscience (2012) Dec;19(12):1689-94

16. D.K. Thompson, T.E. Inder, N. Faggian, S.K. Warfield, P.J. Anderson, L.W. Doyle, G.F. Egan, “Corpus callosum alterations in very preterm infants: perinatal correlates and 2 yearneurodevelopmental outcomes”, Neuroimage. 59 (2012) 3571-81.

17. D.K. Thompson, S.J. Wood, T.E. Inder, S.K. Warfield, L.W. Doyle, G.F. Egan, “Optimizing hippocampal volumetry in newborn infants utilizing MRI post-acquisition processing”, Neuroinformatics 10 (2012) 173-80

18. Y. Wang, A. van der Walt, M. Paine, A. Klistorner, H. Butzkueven, G.F. Egan, T.J. Kilpatrick, S.C. Kolbe, “Optic nerve magnetization transfer ratio after acute optic neuritis predicts axonal and visual outcomes”, accepted in PLoS One (Nov, 2012).

19. Q. Gong, L. Li, S. Tognin, Q. Wu, W. Pettersson-Yeo, S. Lui, X. Huang, A.F. Marquand, A. Mechelli. Using structural neuroanatomy to identify trauma survivors with and without post-traumatic stress disorder at the individual level. Psychological Medicine 2013; Epub. DOI: http://dx.doi.org/10.1017/S0033291713000561.

20. W.W. Chen, N. Wang, S. Cai, Z. Fang, M. Yu, Q. Wu, L. Tang, B. Guo, Y. Feng, J.B. Jonas, X. Chen, X. Liu, Q. Gong, Structural brain abnormalities in patients with primary open-angle glaucoma: a study with 3T MR imaging. Investigative Ophthalmology & Visual Science 2013; 54(1): 545-554.

21. Liao Y, Huang X, Wu Q, Yang C, Kuang W, Du M, Lui S, Yue Q, Chan RCK, Kemp GJ, Gong QY. Is depression a disconnection syndrome? Meta-analysis of diffusion tensor imaging studies in depression. Journal of Psychiatry and Neuroscience 2013; 38(1): 49-56.

22. D.D. Zhao, H.Y. Zhou, Q.Z. Wu, J. Liu, X.Y. Chen, D. He, X.F. He, W.J. Han, Q.Y. Gong. Diffusion tensor imaging characterization of occult brain damage in relapsing neuromyelitis optica using 3.0T magnetic resonance imaging techniques. NeuroImage 2012 Feb 15; 59(4): 3173-3177.

Animal Imaging

23. S. Dedeurwaerdere, K. Fang, M. Chow, Y. Shen, I. Noordman, L.Van Raay, N. Faggian, M. Porritt, G.F. Egan, T.J. O’Brien, “Manganese-Enhanced MRI reflects seizure outcome in a model for mesial temporal lobe epilepsy”, revision submitted to Neuroimage (Oct, 2012).

24. J.R. Duncan, A.L. Dick, G.F. Egan, S. Kolbe, M. Gavrilescu, D. Wright, A.J. Lawrence, “Adolescent toluene inhalation in rats affects white matter maturation with the potential for recovery following abstinence”, PLoS One accepted (August, 2012).

25. Y. Fujii, M. Shirai, S. Inamori, A. Shimouchi, T. Sonobe, H. Tsuchimochi, J.T. Pearson, Y. Takewa, E. Tatsumi, and Y. Taenaka. “Insufflation of hydrogen gas restrains the inflammatory response of cardiopulmonary bypass in a rat model”. Artificial Organs, accepted 13 July 2012.

26. M.M. Gresle, E.N. Alexandrou, Q. Wu, G.F. Egan, V. Jokubaitis, M.M Ayers, A. Jonas, W. Doherty, A.Friedhuber, G. Shaw, M. Sendtner, B.Emery, T.J Kilpatrick, H. Butzkueven, “Leukemia inhibitory factor protects axons in experimental autoimmune encephalomyelitis via an oligodendrocyte-independent mechanism”, PLoS ONE accepted (September, 2012).

27. M.J. Jenkins, A.J. Edgley, T. Sonobe, K. Umetani, D.O. Schwenke, Y. Fujii, R.D. Brown, D.J. Kelly, M. Shirai, J.T. Pearson. (2012). “Dynamic synchrotron imaging of diabetic rat coronary microcirculation in vivo.” Arteriosclerosis Thrombosis and Vascular Biology 32:370-377.

28. M.J. Jenkins, J.T. Pearson, D.O. Schwenke, A.J. Edgley, T. Sonobe, Y. Fujii, H. Ishibashi-Ueda, D.J. Kelly, N. Yagi, M. Shirai. “Myosin heads are displaced from actin filaments in the in situ beating rat heart in early diabetes.” Biophysical Journal 104 (2013) 1065-1072 (accepted 19 Nov 2012)

29. P. Lei, S. Ayton, D.I. Finkelstein, L. Spoerri, G.D. Ciccotosto, D.K. Wright, B.X.W. Wong, P.A. Adlard, R.A. Cherny, L.Q. Lam, B.R. Roberts, I. Volitakis, G.F. Egan, C. McLean, R. Cappai, J.A. Duce, A.I. Bush, “Tau deficiency induces a Parkinsonism with dementia phenotype by obtunding APP-mediated iron export and is prevented by clioquinol”, Nature Medicine 18 (2012) 291-5

30. M. Shirai, D.O. Schwenke, H. Tsuchimochi, N. Yagi, K. Umetani, and J.T. Pearson. (2012) “Synchrotron radiation imaging for advancing our understanding of cardiovascular function.” Circ Res 112:209-221 (accepted 12 Nov 2012)

31. J.P. Ullmann, M.D. Keller, C. Watson, A. Janke, N.D. Kurniawan, Z. Yang, K. Richards, G. Paxinos, G.F. Egan, S. Petrou, P.F. Bartlett, G.J. Galloway, D.C. Reutens, “Segmentation of the C57BL/6J mouse cerebellum in magnetic resonance images”, Neuroimage (2012).

32. K. Umetani, J.T. Pearson, D.O. Schwenke, M Shirai. (2011)

Research Outputs

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“Development of synchrotron radiation x-ray intravital microscopy for in vivo imaging of rat heart vascular function.” Conf Proc IEEE Eng Med Biol Soc. 2011:7791-94.

33. G. Vande Velde, J.R. Rangarajan, R. Vreys, C. Guglielmetti, T. Dresselaers, M. Verhoye, A. Van der Linden, Z. Debyser, V. Baeckelandt, F. Maes, U. Himmelreich, “Quantitative evaluation of MRI-based tracking of ferritin-labeled endogenous neural stem cell progeny in rodent brain.” NeuroImage, 2012, 1;62(1):367-380. doi: 10.1016/j.neuroimage.2012.04.040.

34. V. Zohdi, B.R. Wood, J.T. Pearson, K.R. Bambery, and M.J. Black, “Evidence of altered biochemical composition in the hearts of adult intrauterine growth-restricted rats”. European Journal of Nutrition, 52 (2013) 749-758 ( Accepted 29 May 2012)

Image Analysis and Informatics

35. O. Acosta, J. Fripp, V. Dore, P. Raniga, et al 2012. “Cortical surface mapping using topology correction, partial flattening and 3D shape context-based non-rigid registration for use in quantifying atrophy in Alzheimer’s disease.” Journal of Neuroscience Methods, 205, 96.

36. S. Chandra, J. Dowling, K. Shen, P. Raniga, et al 2012. “Patient specific prostate segmentation in 3-D magnetic resonance images.”, IEEE Transactions on Medical Imaging, 31, 1955.

37. J.-B. Fiot, L.D. Cohen, P. Raniga, J. Fripp, 2013. “Efficient brain lesion segmentation using multimodality tissue-based feature selection and Support Vector Machines.” International Journal for Numerical Methods in Biomedical Engineering, accepted.

38. G.R. Poudel, C.R.H. Innes, R. Watts, et al 2012. “Losing the struggle to stay awake: Divergent thalamic and cortical activity during behavioural microsleeps.” Human Brain Mapping, in press.

39. G.R. Poudel, C.R.H. Innes, R.D Jones, 2012. “Cerebral perfusion differences between drowsy and nondrowsy individuals after acute sleep restriction.” Sleep 35, 1085.

40. O.L. Kaluza, A.C.L. Ng, D.K. Wright, D.G. Barnes, et al “Fast diffusion-guided QSM using Graphical Processing Units.”, ISMRM 2013

41. N. Georgiou-Karistianis, J. Stout, G.R. Poudel, G.F. Egan, et al “Longitudinal functional and

connectivity changes during working memory performance in Huntington’s Disease: the ImageHD study.” JNNP.

42. A.C.L. Ng, D.K. Wright, P. Raniga, G.F. Egan, et al “Diffusion-guided Quantitative Susceptibility Mapping.”, ISMRM 2013

43. G.R. Poudel, G.F. Egan, A. Churchyard, et al “Resting-state functional connectivity in Huntington’s Disease.” CNS-2012

MRI Methods

44. D. Acharya, B.A. Moffat, A. Polyzos, L. Waddington, G. Coia, D. Wright, H. Wang, G.F. Egan, B.W. Muir, P. Hartley, “Cubic Mesophase Nanoparticles doped with Superparamagnetic Iron Oxide Nanoparticles; a new class of MRI contrast agent”, accepted in Royal Society Chemistry Advances (May, 2012).

45. C. Davey, D.B. Grayden, M. Gavrilescu, G.F. Egan, L.A. Johnston, “The equivalence of linear Gaussian connectivity techniques”, accepted Human Brain Mapping, (January, 2012) doi: 10.1002/hbm.22043

46. B.W. Muir, D. Acharya, D. Kennedy, X. Mulet, R. Evans, S. Pereira, K. Wark, T. Hinton, L. Waddington, N. Kirby, D. Wright, H. Wang, G.F Egan, B.A. Moffat, “Metal free T1 enhancing MRI contrast agents using lyotropic liquid crystal nanoparticles”, Biomaterials 33 (2012) 2723-33

47. Xing H, Fang L, Wu Q, Gong Q. Investigation of different boundary treatment methods in Monte-Carlo simulations of diffusion NMR. Magnetic Resonance in Medicine 2012 Nov 20; in press, doi: 10.1002/mrm.24551.

X-Ray and CT Imaging

48. M. Donnelley, K.S. Morgan, K.K.W. Siu and D.W. Parsons (2012). “Variability of in vivo fluid dose distribution in mouse airways is visualized by high-speed synchrotron x-ray imaging.” Submitted to Journal of Aerosol Medicine and Pulmonary Drug Delivery: Under revision.

49. M. Donnelley, K.K.W. Siu, R.A. Jamison and D.W. Parsons (2012). “Synchrotron phase-contrast X-ray imaging reveals fluid dosing dynamics for gene transfer into mouse airways.” Gene Ther 19(1): 8-14.

50. M. Donnelley, K.S. Morgan, K.K.W. Siu and D.P. Parsons (2012). “Dry deposition of pollutant and marker particles onto live mouse airway surfaces enhances monitoring of individual particle mucociliary

transit behaviour.” J. Synchrotron Rad. 19: 551-558.

51. S. Dubsky, S.B. Hooper, K.K.W. Siu and A. Fouras (2012). “Synchrotron-based dynamic computed tomography of tissue motion for regional lung function measurement.” Journal of the Royal Society Interface (published online 4 April 2012).

52. S. Dubsky, R.A. Jamison, S.P.A. Higgins, K.K.W. Siu, K. Hourigan and A. Fouras (2012). “Computed tomographic X-ray velocimetry for simultaneous 3D measurement of velocity and geometry in opaque vessels.” Experiments in Fluids 52: 543-54.

53. A. Fouras, B. Allison, M. Kitchen, S. Dubsky, J. Nguyen, K. Hourigan, K.K.W. Siu, R. Lewis, M. Wallace and S. Hooper (2012). “Altered Lung Motion is a Sensitive Indicator of Regional Lung Disease.” Annals of Biomedical Engineering: 40: 1160-69.

54. R.A. Jamison, K.K.W. Siu, S. Dubsky, J.A. Armitage and A. Fouras (2012). “X-ray velocimetry within the ex vivo carotid artery.” J. Synchrotron Rad. 19: 1050-1055.

55. D. Jones, A.R. Evans, E.J. Rayfield, K.K.W. Siu and P.C.J. Donoghue “Testing microstructural adaptation in the earliest dental tools.” Biology Letters. (published online 4 July 2012).

56. D. Jones, A.R. Evans, K.K.W. Siu, E.J. Rayfield and P.C.J. Donoghue (2012). “The sharpest tools in the box: Quantitative analysis of conodont element functional morphology.” Proc R Soc Lond B Biol Sci (published online 14 March 2012).

57. K.S. Morgan, M. Donnelley, D.M. Paganin, A. Fouras, N. Yagi, Y. Suzuki, A. Takeuchi, R.C. Boucher, D.W. Parsons and K.K.W. Siu (2012). “Measuring airway surface liquid depth in live airways by x-ray imaging for the assessment of cystic fibrosis airway therapies.” Submitted to PLoS ONE: Under revision.

58. K.S. Morgan, D.M. Paganin and K.K.W. Siu (2012). “X-ray phase imaging with a paper analyzer.” Appl. Phys. Lett.: 100, 124102.

Other Publications by MBI staff

59. A.P. Beardsley, B.J. Hazelton, M.F. Morales, D.G. Barnes, et al 2013. “The EoR sensitivity of the Murchison Widefield Array.” Monthly Notices of the Royal Astronomical Society Letters, 429, L5.

60. A.P. Beardsley, B.J. Hazelton, M.F. Morales, D.G. Barnes, et al

2012. “A new layout optimization technique for interferometric arrays, applied to the MWA.” Monthly Notices of the Royal Astronomical Society, 425, 1781.

61. A.H. Hassan, C.J. Fluke, D.G. Barnes, V.A. Kilborn, 2013. “Tera-scale Astronomical Data Analysis and Visualization.” Monthly Notices of the Royal Astronomical Society, accepted.

62. A.H. Hassan, C.J. Fluke, D.G. Barnes, 2012. “A Distributed GPU-Based Framework for Real-Time 3D Volume Rendering of Large Astronomical Data Cubes.” Publications of the Astronomical Society of Australia, 29, 340.

63. B. McKinley, F. Briggs, D.L. Kaplan, D.G. Barnes, et al 2013. “Low frequency observations of the Moon with the Murchison Widefield Array.” Astronomical Journal, 145, 23.

64. I. Sullivan, M. Morales, B. Hazelton, D.G. Barnes, et al 2012. “Fast holographic deconvolution: a new technique for precision radio interferometry.” Astrophysical Journal, 759, 17.

65. S.J. Tingay, R. Goeke, J.D. Bowman, D.G. Barnes, et al 2012. “The Murchison Widefield Array: the Square Kilometre Array Precursor at low radio frequencies.” Publications of the Astronomical Society of Australia, accepted.

66. C.L. Williams, J.N. Hewitt, A.M. Levine, D.G. Barnes, et al 2012.“Low-frequency imaging of fields at high Galactic latitude with the Murchison Widefield Array 32 Element Prototype.” Astrophysical Journal, 755, 47.

67. B.R. Barsdell, M. Bailes, D.G. Barnes, et al 2012. “Accelerating incoherent dedispersion.” Monthly Notices of the Royal Astronomical Society, 422, 379.

68. J. Kocz, M. Bailes, D.G. Barnes, et al 2012. “Enhanced pulsar and single pulse detection via automated radio frequency interference detection in multipixel feeds.” Monthly Notices of the Royal Astronomical Society, 420, 271.

Research Outputs Continued

25

GrantsCognitive Neuroimaging

1. 2013-2015 NHMRC Project Grant APP1042528, 2013-2015, “Activity in central cough networks in patients with cough hypersensitivity” Chief Investigators: S. Mazzone, M. Farrell, G.F. Egan

Clinical Imaging

2. Peter MacCallum Cancer Centre/Monash Health, N. Ferris. “A pilot Surveillance study in Multi-Organ Cancer prone syndromes (‘SMOC”)”. (CI G.J. Mitchell) Australian Sarcoma Study Group

3. NHMRC Project Grant APP1046037, 2013-2015, “A longitudinal neuroimaging study investigating reorganisation of cerebellar-cerebral networks in Friedreich ataxia” Chief Investigators: N. Georgiou-Karistianis, G.F. Egan, M. Delatycki, A. Churchyard, L. Corben

Animal Imaging

4. NHMRC Project Grant APP1050672: 2013-2015 The pathophysiology of septic acute kidney injury. C. May, R.G. Evans, J.T. Pearson.

5. Monash Strategic Collaborative Grant ECP006, 2013 “Can resuscitation at birth lead to brain damage?” M. Siew, G. Polglase, M. Kitchen, J.T. Pearson.

6. Monash Strategic Collaborative Grant ECD023, 2013: “AT2R agonist therapy: a new approach for treating diabetic nephropathy” L. Hilliard, K.M. Denton (mentor), J.T. Pearson (mentor).

7. Monash Strategic Collaborative Grant PAG007, 2012 “Assessment of the natural history and efficacy of treatment of cardiorenal syndrome with cardiac and renal BOLD MRI and x-ray imaging.” J.T. Pearson, R.G. Evans, K.M. Denton, R.E. Widdop.

8. International Synchrotron Access Program Grant IA123/5675, 2012 “Does rho-kinase activation contribute to actin-myosin dysregulation in the diabetic heart” J.T. Pearson, M. Waddingham, A. Astolfo.

9. International Synchrotron Access Program Grant IA123/5093, 2012 “Evaluation of coronary endothelial function in a diet-induced model of atherosclerosis in mice” J.T. Pearson, Y.C. Cheng, R. Sultani.

10. NHMRC Project Grant APP1042893, 2013-2015 “A role for the pulvinar nucleus in visual cortical development and plasticity” Chief Investigators: J. Bourne, D. Leopold, G.F. Egan

Image Analysis and Informatics

11. Faculty of Medicine, Nursing and Health Sciences Strategic Grant Scheme, 2013 - Early Career Development Grant ECD045: 2013, “Integrating computer modelling and regenerative medicine for better treatment of Pelvic Organ Prolapse.” C. McHenry et al. (including D.G. Barnes);

MRI Methods

12. ARC LE130100035, 2013 “Hyperpolarised gas functional lung and molecular imaging”, (2013) F.C. Thien, B.R. Thompson, G.F. Egan, S.B. Hooper, W-T. Lee, P.J. Robinson, G.J. Galloway, G.J. Cowin, I.M. Brereton

13. Collaborative Research Infrastructure Scheme (CRIS), 2013-2014- “Support for the National Imaging Facility”, Co-Principal Investigators – G. Galloway, D. Reutens, G.F. Egan, I. Brereton, C. Rae, M. Kyrios

X-Ray and CT Imaging

14. Major interdisciplinary research project support program, Monash University, 2012A. Fouras, S.B. Hooper, K.K.W. Siu, D. Paganin, 2012, “A Monash-led revolution in lung diagnostics”,

15. Women’s and Children’s Hospital (Adelaide) Foundation Research Project Grant, 2012. “Understanding the clearance of inhaled lead dust in the conducting airways using synchrotron imaging”, M. Donnelley, D. Parson, K.K.W. Siu, A. Fouras, K. Morgan, 2012,

Collaborative Projects1. Non-invasive kidney MRI John Bertram, School of Biomedical Sciences, Monash University and Dr Kevin Bennett, University of Hawaii (collaboration supported by International Institute for the Advancement of Medicine, the Musculoskeletal Tissue Foundation and the NIH Diabetic Complications Consortium).

2. Magnetic resonance imaging of renal glomeruli Bertram J.F. and N. Gretz, Group of Eight Australia-Germany Joint Research Co-operation Scheme. $19,200. 2012-2013

3. Diabetic heart disease origins Darren Kelly and Dr Amanda Edgley, St Vincent’s Hospital and Prof Mikiyasu Shirai, Department of Cardiac Physiology, National Cerebral and Cardiovascular Center (Japan)

4. Synchrotron microangiography of the mouse heart Mikiyasu Shirai, Department of Cardiac Physiology, National Cerebral and Cardiovascular Center (Japan)

5. Synchrotron imaging of cardiac repair with stem cells Yoshiki Sawa and Shigeru Miyagawa, Department of Cardiac Surgery, Osaka University Graduate School of Medicine and Prof Mikiyasu Shirai, Department of Cardiac Physiology, National Cerebral and Cardiovascular Center (Japan)

6. Measurement and prediction of vulnerable plaque formation and rupture K Hourigan, KKW Siu, P. Assemat, J. Armitage, Monash University; JP Chin-Dusting, AM Dart, Baker IDI; T Leweke, CNRS (supported by Australia Research Council)

7. Imaging lung motion for studying the dynamics of asthma and its treatments SB Hooper, A Fouras, RA Lewis, KKW Siu, Monash University (supported by American Asthma Foundation)

8. Counting glomeruli using synchrotron micro-CT J. Armitage, KKW. Siu (Monash University.

9. Using synchrotron X-ray tomography to reveal the early history of mammals T Rich, Museum of Victoria; A. Evans, KKW Siu, Monash University.

10. An integrative and distributed data management and workflow framework for e-research in biomedical imaging - Gary Egan, Slavisa Garic, David Abramson, Toan Nguyen (Monash University), Simon Milton, Neil Killeen, Andrew Lonie,

Wilson Lui (University of Melbourne), Jason Lohrey (arcitecta) (2011-13).

11. The cognitive control of saccades: Identifying neuroanatomical and neurophysiological substrates - Joanne Fielding (Monash University), Sharna Jamadar, Beth Johnson, Meaghan Clough, J Lee, Amanda Ng, Gary Egan (2011-13).

12. Early detection of resuscitation induced brain injury using Magnetic Resonance Spectroscopy - Beatrice Skiold, Stuart Hooper, Mary Tolcos, James Pearson, Qi-zhu Wu, Ruth Vreys, Gary Egan, S Barton, Peter Davis, Jeanie Cheong (Royal Women’s Hospital, Melbourne), Graeme Polglase (2012).

13. Mental rotation of hand as a task to evaluate motor imagery capability - Saman Kashuk, Graham Thorpe, Jacqueline Williams (Victoria University), Peter Wilson (RMIT University), Gary Egan (2012-13).

14. MASSIVE infrastructure and visualisation capabilities - Wojtek Goscinski, David Barnes, Toan Nyugen, Paul McIntosh, Gary Egan, Paul Bonnington.

15. Decoding of perceptual decisions from combined fMRI and EEG signals - Carsten Murawski, Stefan Bode(University of Melbourne), Bryan Paton, Gary Egan (2012-13).

16. Evaluation of lumbar biological intervertebral disc replacement in adult sheep – Graham Jenkin, David Oehme, Anne Gibbon, Courtney McDonald, Qizhu Wu, Gary Egan (2012-13).

17. Validating the use of nanoparticles to visualize brain inflammation following injury - Nicole Bye, Christina Morganti-Kossman, Ben Muir, James Pearson, Ruth Vreys, Qizhu Wu, Gary Egan

18. Early detection of early stage CF disease via quantitative imaging of lung motion - DW KKW Siu, KS Morgan, A Fouras, Monash University; DW Parsons, M Donnelley, Women’s and Children’s Hospital, Adelaide (collaboration supported by Australian Cystic Fibrosis Research Trust, National Health and Medical Research Council and Australian Research Council)

19. Accelerated computing and visualization of large data – David Barnes, Christopher Fluke (Swinburne University of Technology).

Research Outputs Continued

26

20. Model-driven engineering of Scientific Software for GPUs – David Barnes, .John Grundy, Prof. Richard Sadus, Dr Willem van Straten (Swinburne University of Technology); collaboration supported by ARC Discovery Project funding 2012-2014.

21. 3D figures for science communication – David Barnes, Owen Kaluza, Parnesh Raniga, A/Prof. Christopher Fluke (Swinburne University of Technology), Michail Vidiassov (Moscow State University), Dr. Bernhard Ruthensteiner (Zoologische Staatssammlung, Munchen), Dr. Colin McHenry, Michelle Quayle (Monash Functional Anatomy and Biomechanics Research Laboratory).

22. Visualisation of Dinosaur fossils – David Barnes, Matt White (Newcastle University).

Selected Presentations1. G.F. Egan, Monash Platforms (May, 2012) - “Partnerships and collaborations opportunities at Monash Biomedical Imaging”

2. G.F. Egan, BioMelbourne Network (March, 2012) - “Computational biomedical imaging using VLSCI & MASSIVE”

3. G.F. Egan, Graduate House, University of Melbourne (March 2012) - “Visualizing the brain”

4. G.F. Egan, Department of Physiology, Monash University (4 June, 2012) - “An update on imaging research opportunities at Monash Biomedical Imaging”

5. G.F. Egan, Monash University Business Seminar Series (May, 2012) - “The Imaging Continuum - Exploring Inner Space”

6. G.F. Egan, School of Medical Science (Physiology), University of Sydney (1 June, 2012) - “ Can structural and functional neuroconnectivity explain ocular motor behaviour?”

7. G.F. Egan, School of Psychology & Psychiatry, Monash University (April, 2012) - “Human imaging research opportunities at Monash Biomedical Imaging”

8. G.F. Egan, Australian Synchrotron Annual Scientific Meeting, Melbourne (November, 2012) - “Biomedical imaging research at Monash Biomedical Imaging: facility access and opportunities for collaboration”

9. G.F. Egan, Ausbiotech, Melbourne (November, 2012) - “Computational bioimaging at the Life Sciences Computational Centre”

10. G.F. Egan, IBRO-Asia Pacific Regional School and Symposium, Monash University, Malaysia (November 29-30, 2012) - “Functional Genomics, Molecular Morphology, Behavioural Neuroscience and Neuroimaging”.

11. N. Ferris, “MRI Approval, Diffusion, and Uptake in the Australian Healthcare System” Course in ‘Comparative Effectiveness Research : International Perspectives”, International Society for Magnetic Resonance in Medicine, Melbourne, May 2012

12. J.T. Pearson, Early diabetic diastolic dysfunction displaces myosin heads from actin in the beating heart. International Society of Hypertension 2012, Sept-Oct 2012, Sydney, Australia.

13. J.T. Pearson, Role for Rho-kinase in early diabetic coronary dysfunction in streptozotocin rats. International Society of Hypertension 2012, Sept-Oct 2012, Sydney, Australia.

14. G.R. Poudel, Multimodal neuroimaging: understanding the dynamics of the human brain, CSIRO Computational and Simulation Sciences and e-Research Conference, March 2012.

15. G.R. Poudel, G.F. Egan, A. Churchyard, P. Chua, J.C. Stout, N. Georgiou-Karistianis, “Resting State Functional Connectivity in Huntington’s Disease.”, Australian Cognitive Neuroscience Society Annual Conference 2012

16. D.G. Barnes, O.L. Kaluza, C. McHenry,P. Raniga, et al “Surfer: simple, interactive, cross-platform, multi-surface rendering.” OzViz 2012

17. O.L. Kaluza, A.C.L. Ng, D.G. Barnes, J. Grundy, “Accelerating diffusion-guided quantitative susceptibility mapping with OpenCL.” ACW 2012

18. G. Poudel, “Imaging Activities at Monash Biomedical Imaging.” CSIRO Computational and Simulation Sciences and eResearch Annual Conference and Workshops, March 2012.

Professional Contributions

David G Barnes

X Member International Astronomical Union

X Life Sciences Computation Centre (LSCC), Victorian Life Sciences Computational Initiative, Melbourne

Gary F Egan

X Governing Board Member, International Neuroinformatics Co- ordinating Facility (INCF) Stockholm

X Member, Board of Directors, Society for Brain Mapping and Therapeutics Australasia (SMBTA)

X Member, International Neuroinformatics Co-ordinating Facility (INCF) Training Committee

X Member, NHMRC Research Translation Faculty

X Member, NHMRC Assigners Academy

X Chairperson, Imaging and Visualisation Scientific Advisory Committee (IVSAC), Multimodal Australian Sciences Imaging and Visualisation Environment (MASSIVE) Computational Initiative, Melbourne

X Member & Ambassador, Club Melbourne, State Government of Victoria

X Theme Leader, Life Sciences Computation Centre (LSCC), Victorian Life Sciences Computational Initiative, Melbourne

X Associate Editor, Human Brain Mapping, Wiley Publishers, San Diego

X Member, Editorial Board, International Journal of Imaging Systems and Technology, Wiley, USA

X Member, Editorial Board, Frontiers in Neuroscience, Frontiers Research Foundation, Switzerland

Nicholas J Ferris

X Royal Australian and New Zealand College of Radiologists (RANZCR)

X Member, Standards of Practice and Accreditation Committee

X Chair, RANZCR MRI reference group

X Chair, RANZCR e-health reference group

X International Society for Magnetic Resonance in Medicine (ISMRM)

X Radiological Society of North America (RSNA ; corresponding)

X Society for Imaging Informatics in Medicine (SIIM)

X Australian Neuroscience Society (ANS)

X Australian and New Zealand Society for Neuroradiology (ANZSNR)

X Health Informatics Society of Australia (HISA)

James T Pearson

X High Blood Pressure Research Council of Australia

X American Physiological Society

27

Abbreviations

3T 3 Tesla

ADHD Attention Deficit Hyperactive Disorder

ANDS Australian National Data Service

ARC Australian Research Council

ASL Arterial Spin Labelling

ASPREE ASPirin in Reducing Events in the Elderly

CMSE Centre for Materials Science and Engineering

CSIRO Commonwealth Scientific and Industrial Research Organisation

CT Computed Tomography

EEG Electroencephalography

FLECT Fluorescence Emission Computed Tomography

FRDA Friedreich Ataxia

INCF International Neuroinformatics Coordinating Facility

MASSIVE Multi-Modal Australian Sciences Imaging and Visualisation Environment

MBI Monash Biomedical Imaging

MIPS Monash Institute for Pharmaceutical Sciences

MR Magnetic Resonance

MRI Magnetic Resonance Imaging

MTR Magnetism Transfer Ratio

NIF National Imaging Facility

OM Ocular Motor

PET Positron Emission Tomography

SPECT Single Photon Emission Computed Tomography

SPP School of Psychology and Psychiatry, Monash University

TBI Traumatic Brain Injury

VBIC Victorian Biomedical Imaging Capability

VLSCI Victorian Life Sciences Computation Initiative

www.mbi.monash.eduAll information contained in this document is current at time of publication. Monash University reserves the right to alter this information at any time – please check the Monash University website for updates (www.monash.edu.au).Published June 2013

Monash Biomedical Imaging Monash University 770 Blackburn Road Clayton 3800 Telephone - 99029752 email: enquiries.mbi@monash.edu