Investigating cortical pathways with diffusion-tensor imaging (DTI) manganese-enhanced MRI and modern histological techniques in monkeys and humans

Lead Research Organisation: University of Oxford
Department Name: Physiology Anatomy and Genetics


Studying brain anatomy used to mean opening up a skull and looking at post mortem brain slices. Not really a good option to study brain connections in living humans. Tracing connections in the human brain is particularly difficult because dead nerve cells do not transport dyes and tracers well. In experimental animals the neuronal tracers are transported in the living brain but to visualize at the results, the animal has to be sacrificed. Therefore, there has been tremendous excitement about recent developments in Magnetic Resonance Imaging (MRI) that allow us to trace connections non-invasively in the living brain. But these techniques measure anatomical structures indirectly by their effect on movement of water or ions. Therefore, their results need to be calibrated against more detailed and accurate measurement of connections with invasive neuroanatomical techniques in animals. We will carry out imaging experiments in monkeys and humans. These data will be compared with those obtained with more established and accurate anatomical techniques in the monkey in order to gain a better understanding about what these new methods exactly measure. The pathway we investigate with these methods connects neurons that contribute to making simple decisions. Imagine playing tennis: when a ball comes towards you, you have to look and decide on its approach before being able to hit it back. Our senses to gather such information about the world around us. Often, the next stage after getting this information is to decide what to do with it - we make a decision. In the tennis example, we decide which trajectory the ball is likely to take and how we would like to respond. Finally we may want to execute this movement based on what we have seen. Our brain accomplishes such transformations of sensory information into action fast and effectively all the time (maybe not for everybody with regards to tennis). Similar processes might underlie more deliberate, slower decision processes, like smelling apples in a fruit bowl and deciding which one to pick up to eat. Our brain is divided up into interconnected regions that deal separately with different types of sensory information, such as visual information from our eyes, touch information from our skin. In addition, various parts of the brain are responsible for controlling our muscles for movement or verbal responses. In between these sensory and motor regions, there are brain areas that we believe can transform the information into movements, including those that help us to make decisions. One area we are looking at is an area of the visual system, called area V5/MT, which is particularly sensitive to moving objects. We want to test whether this area is connected directly to another area, known as LIP that is believed to be central to decision-making. Alternatively other intermediate brain areas might be involved. We will take advantage of new non-invasive techniques in MRI that allow us to trace connections between different brain areas. Using MRI is particularly useful, as it can give us an insight into the connections of the human brain in healthy people as well as in patients, for instance after stroke. Better validation of what these new techniques measure could also mean that anatomy on animal brains could be done without the need to sacrifice the animal.

Technical Summary

Histological tracing remains the 'gold standard' for determining neuroanatomical connections. Recent advances in MRI have provided two new methods for studying neuronal connections in vivo: Manganese tracing and Diffusion Tensor Imaging (DTI). Transport of Manganese ions can be traced anterogradely at different time points post-injection. The connections across the whole brain can be measured with probabilistic tractography on DTI data (a non-invasive technique). By comparison with direct histological tracing of connections using both anterograde and retrograde tracers in the same animals, our project will assess the validity of the new MRI techniques. In particular, we will aim to develop methods that potentially allow quantitative comparisons of specificity, directionality and strength of brain connections. Human DTI data is already used extensively in both clinical and non-clinical environments. In order to gain a better understanding of the connection properties that are measured by human DTI, we will compare our animal data with results from fMRI and DTI in human subjects. These new methods have the potential ability to study connections across the whole brain, human and monkey, in vivo. In this project, we will evaluate how these methods reveal the connectivity of the dorsal visual and parietal cortex. Therefore, we will also gain more detailed picture of an important decision-making pathway in monkeys and humans.

Planned Impact

Who will benefit from this research and how? The purpose of this study is to improve MRI to make it as precise as possible for a wide variety of uses. The main beneficiaries of this research are clinical professionals in the NHS and academics in basic and applied research. Patients will benefit through the validation of diagnostic tools revealing the precise nature and state of nerve connections in brains. We already know that these nerve connections are disrupted or altered in a wide range of conditions, for instance stroke, multiple sclerosis (MS), Alzheimer, CJD, accidental brain damage, developmental disorders, like autism and possibly some psychological disorders, like schizophrenia. Research that impacts our understanding of the brain and on diagnostics in neurology, neurosurgery and psychiatry is also of great interest to the wider public. Academics will benefit from more precise, non-invasive MRI methods that can link neuronal function to underlying connectivity in the monkeys, without the need to sacrifice animals to study connectivity. This should provide new research avenues by enabling researchers to investigate brain connectivity in the same animals that are used to study behaviour and neuronal function. What will be done to ensure that they have the opportunity to benefit from this research? We will disseminate our results to researchers and health professionals through presentations that international conferences that draw neuroscientists and clinical staff as well as publications in first-rank neuroscience and medical journals. Once the first results are published, we also aim to write a more general review of the current state of imaging methods and their potential impact on clinical practice for a journal more directly geared at medical health professionals in the UK, e.g. The Lancet, BMJ or Brain. The applicants will also continue to be involved in teaching medical students and more general outreach, like for instance to schools.


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Description With our BBSRC funded project 'Investigating cortical pathways with diffusion-tensor imaging (DTI), manganese-enhanced MRI and modern histological techniques in monkeys and humans', we have made considerable progress in our understanding how accurately Magnetic Resonance (MR) Imaging signals and measurements acquired from the intact brain reflect the actual underlying anatomical structures and connections in primate brains.

Our findings include:
(i) MR signals from the living brain match actual anatomical brain structures defined by myelin in post mortem brain slices from the same individual monkey section-by-section.
(ii) These MR imaging techniques can be applied to humans, in whom measures correlate with functional structures identified by other imaging protocols.
(iii) The function of different parts of a single brain area in primates can be differentiated by which other regions a part is connected to. The results match functional maps in monkeys. Diffusion-weighted MR images of high enough resolution can be acquired post mortem as well as from the living brain.
(iv) Brain tracts measured with Diffusion-weighted imaging match qualitatively histological connections in the same brain. A quantitative comparison of connections in the decision-making networks of the brain is underway.
(v) Different intrinsic connectivity in area LIPv and LIPd.
To further aid translation of findings between monkeys and humans, we have established a collaboration with Prof David van Essen and Matt Glasser (WashU, Human Connectome Project, US) and Prof Catani (Kings College London) on comparing brain connections and brain area definitions across different primate species.

Five graduate students and two undergraduates have carried out associated research projects and were trained in the underlying techniques.
Exploitation Route Our validation that Magnetic Resonance techniques measure brain structures and connections accurately in the same individual furthers how such data can be interpreted and used in a wide range of research and clinical settings.

The methods we have developed allow the investigation of smaller scale structures and thus push the limits of resolution not just for research purposes but also for clinical imaging. Apart from publishing and presenting, we have trained several graduates and undergraduates in these methods as well as two postdocs.

The primate cross-species comparison of brain structure and function aids translation of research findings generally. Understanding homologies and differences between the brains of different primates is important in understanding how our brain gives rise to specific functions. Not just in research settings but also in outreach activities with school children and adults, this is a question that is often asked: how do brains differ and what does this tell us about thinking and experiences.
Sectors Education,Healthcare,Pharmaceuticals and Medical Biotechnology,Other

Description In conferences and through publication, we have started the conversation with researchers and clinicans about our findings into the validity of non-invasive imaging methods to measure structural differences in primate brains. We are sharing results and raw data, which is aiding method development, use and other research projects. We have also found interesting results indicating strong individual differences across human brains, which impact the way imaging data should be analysed and presented.
First Year Of Impact 2016
Sector Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Societal

Description Home Office, RSB and stakeholder discussion on Project Licenses for animal research
Geographic Reach National 
Policy Influence Type Participation in a national consultation
Description MRC Advisory Board Centre for Macaques
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact The CfM Board advices on the running and future planning of the national breeding facility of Rhesus macaques for research purposes. We have advised on staff and animal training, with a particular emphasis of embedding 3Rs research in the unit. this improves the wellbeing and quality of animals, and therefore leads to a high quality of animals being supplied across the UK. Best practice is also disseminated from CfM. We have also written to Government Regulators to advice on how to improve the regulatory environment and its efficiency to enhance research outcome and animal welfare.
Description MRC Advisory Board for Centre for Macaques (CfM
Geographic Reach National 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
Impact The availability of healthy Rhesus monkeys for Medical Research in the UK is central for cutting edge research into basic brain function and vaccine research. For instance deep brain stimulation for Parkinsons was developed in Rhesus monkeys. More recently, research with monkeys in the UK has been investigating the neural basis of deceision-making, 3D vision and the accuracy of non-invasive brain imaging.
Description Member of the Integrative Neuroscience Panel for the Agency Nationale de la Recherche (France's national science funding agency)
Geographic Reach Europe 
Policy Influence Type Participation in a advisory committee
Description BBSRC iCASE studentship
Amount £80,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 09/2021
Description MRC Studentship
Amount £60,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 10/2012 
End 09/2015
Description Wellcome Trust Strategic Award
Amount £4,900,000 (GBP)
Funding ID 101092/Z/13/Z 
Organisation Wellcome Trust 
Department Wellcome Trust Strategic Award
Sector Charity/Non Profit
Country United Kingdom
Start 01/2014 
End 04/2020
Description Comparative brain connectivity in primates 
Organisation King's College London
Department Institute of Psychiatry, Psychology & Neuroscience
Country United Kingdom 
Sector Academic/University 
PI Contribution Provided high resolution DTI scans of several Rhesus macaques for comparative connectivity studies across primates.
Collaborator Contribution High level analysis of connectivity in primate MRI scans carried out by experienced postgraduate and graduate researchers. Preparation of publications arising from this collaboration.
Impact Short parietal lobe connections of the human and monkey brain Marco Catani, Naianna Robertsson, Ahmad Beyh, Vincent Huynh, Francisco de Santiago Requejo, Henrietta Howells, Rachel LC Barrett, Marco Aiello, Carlo Cavaliere, Tim B Dyrby, Kristine Krug, Maurice Ptito, Helen D'Arceuil, Stephanie J Forkel, Flavio Dell'Acqua (2017). Cortex 97, 339-357
Start Year 2015
Description Comparing brain structures and connections across different primate species. 
Organisation Washington University in St Louis
Country United States 
Sector Academic/University 
PI Contribution Data on brain pathways and structures in the Rhesus Macaque
Collaborator Contribution Analysis expertise, human brain data and linking into a wider, international project of comparing brain pathways in the primate brain.
Impact We have received advice on imaging data analysis and Connectome-related software modified specifically for analysis of Rhesus macaque brains. 2016: Large I, Bridge H, Ahmed B, Clare S, Kolasinski J, Lam W, Miller K, Dyrby T, Parker AJ, Smith JET, Daubney G, Sallet J, Bell, Krug K. Individual differences in the alignment of structural and functional markers of the V5/MT complex in humans and macaques. Under Review (manuscript available on request)
Start Year 2013
Description Connections of the primate social brain 
Organisation University of Oxford
Department Department of Experimental Psychology
Country United Kingdom 
Sector Academic/University 
PI Contribution We shared imaging data obtained with this grant to investigate the neuronal connections between brain areas associated with visual and social behaviour.
Collaborator Contribution Dr Jerome Sallet and Prof Matthew Rushworth shared imaging data to investigate together the neuronal connections between brain areas associated with visual and social behaviour.
Impact MP Noonan, RB Mars, FX Neubert, B Ahmed, J Smith, K Krug & J Sallet. Organization of the social brain in macaques and humans. In Dreher/Tremblay: 'Decision Neuroscience: Handbook of Reward and Decision Making'. in press J Sallet, MP Noonan, A Thomas, JX O'Reilly, Jesper Anderson, G. Papageorgiou, FX Neubert, B Ahmed, J Smith, A Bell, M. Buckley, K Krug, RB Mars, MFS Rushworth Behavioral flexibility is associated with changes in structure and function distributed across frontal cortical networks in macaques. In preparation.
Start Year 2015
Description High resolution post mortem Magnetic Resonance Imaging 
Organisation Danish Research Centre for Magnetic Resonance (DRCMR)
Country Denmark 
Sector Academic/University 
PI Contribution Primate in vivo Diffusion Tensor Imaging (DTI) and structural imaging, brain processsing, histology.
Collaborator Contribution High Resolution Diffusion Tensor Imaging (DTI) of the post mortem primate brains for our project.
Impact Full paper is in preparation - based on two conference abstracts, which have already been published: Smith JET, Dyrby TD, Bridge H, Miller K, Ahmed B, Parker AJ, Krug K (2014) Predicting the topographic organisation of visual area V5/MT from probabilistic cortico-cortical connections to V1. Society for Neuroscience abstracts 820.06 Tang-Wright K, Bridge H, Kauer T, Dyrby TB, Sallet J, Miller K, Ahmed B, Krug K (2013) Delineating geniculo-cortical connectivity and topographical mapping in the ex vivo macaque brain using probabilistic tractography. Society for Neuroscience abstracts 737.18
Start Year 2011
Description Conversation on brain processes on BBC Worldservice programme 'The Strand' 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Interesting discussion with people from the arts about how the brain processes images.

Engaging other communities and the general public.
Year(s) Of Engagement Activity 2012
Description Interactive lecture: 'Close Encounter with the 3D mind' at Royal Society Summer Science Exhibition 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Talk included exhibits, 3D glasses and interactive polling/testing during the talk. Sparked some interesting questions and discussions afterwards about how the brain is wired, works and learns. Many people came up afterwards including any age from teenagers through to pensioners.

A girl, who was about to enter her last year at school, asked many interesting questions afterwards and subsequently came to spend a research day my lab. She has now secured a place to study Neuroscience as an undergraduate degree at UCL.
Year(s) Of Engagement Activity 2014
Description London Science Museum Late interactive exhibit 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact London Science Museum Late interactive exhibit: 'Your changing brain: from neurons to Nerf guns'. More than 100 members of the general public engaged in a set of interactive experiments explaining how our visual system's structure give rise to our sense of seeing.
Year(s) Of Engagement Activity 2015
Description Royal Society Summer Science Exhibition: live experiment 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Royal Society Summer Science Exhibition live experiment: 'Beat the vision expert'. A live perceptual decision experiment drew more than 100 interested participants at this national event in one evening. People engaged around the experimental set-up with scientists and students in discussions about how our visual system is wired, can change and supports function.
Year(s) Of Engagement Activity 2015
Description Understanding Animal Research Lab walk through (online) 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Participated in an online laboratory and monkey facility 'walk through'. I contributed an interview about my research project. This has a potentially wide reach - taking a broad audience into the lab from experiment to potential impact.
Year(s) Of Engagement Activity 2016
Description Workshop for Primary Schools on brains 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Showing different brains (plastic human, real monkey, real mouse brains) and discussing similarities and differences. Making brains and neurons out of play dough.

The children (4-7 year olds) were buzzing with excitement. There were many questions about how the brain works.
Year(s) Of Engagement Activity 2011,2012