Imaging the spatial organization of brain connections

Lead Research Organisation: University of Oxford
Department Name: FMRIB Centre

Abstract

Understanding how the human brain is able to solve complex problems remains a major challenge in neuroscience research. Humans are capable, even at an early age, of performing seemingly effortlessly many tasks that are still incredibly difficult for the most powerful computers.
Scientists believe that part of the brain's extraordinary abilities comes from its complex wiring. The brain is thought to be organised into specialised regions. The dense network of connections between these regions enables fast, efficient and massively parallel processing of information.
However, the concept of a brain region that is specialised in a given computation is not satisfactory for brain scientists. Indeed, if that were the case, the human brain's abilities would be rather limited. Only a few hundred "regions" can fit in the 2.5 square feet or so of cortex that our brain contains; the size of a large pizza. If every region was only able to perform one task, we wouldn't be able to do complicated things like speaking, playing tennis or thinking about the meaning of life.
An intermediate view would suggest that the brain could indeed be subdivided into a reasonable number of regions. These regions may have a certain degree of specialisation, but may also perform a variety of different tasks in different contexts. I call these different patterns of brain activity "functional modes".
Now the key feature of these functional modes is that they can interact. A region that can do many things can also do combinations of these things. For example, a brain region can calculate our position in space, while another region has a map of our face. A third region that integrates these two pieces of information can do something even more complex: it can allow us to intercept an object that is going to hit us in the face, by calculating a transformation between the outside space and the face coordinates. The two maps can interact because they overlap.
The number and organisation of these functional modes is still largely unknown. My research will provide tools to measure these complex maps by measuring connections between brain regions. By looking at how a brain region connects to different other regions, we can determine its overlapping functions. The more complex the connectivity of a region is, the more modes it can potentially have, and the more complex functions it can potentially perform.
Nowadays, we can measure brain connections "non-invasively", meaning using techniques, such as MRI, that are completely harmless, and can be used on any normal healthy human. We can therefore get a better sense of the complexity of brain function by measuring connections in a novel way.
The research I am planning to conduct aims at providing brain scientists with the tools that will enable them to investigate this intricate relationship between the connections in the brain and the complexity of brain function.

Technical Summary

This proposal aims to develop new approaches for defining and measuring functional organization in the human brain. The current paradigm in macro-connectomics is the idea that we can summarise brain connectivity using a network of "nodes" and "edges" - distinct brain units and the connections between them. However, the concept of "nodes" as segregated brain units remains elusive; and the simplistic view of the brain as a discrete set of units with edges representing their interactions overlooks complexities that have important functional consequences.

Brain connections often follow a spatial organisation. Tracer studies in non-human primates have shown that large-scale connections can be organised into local patterns such as topographies, gradients or sub-clusters. Crucially, different spatial patterns of connections can overlap within the same regions. These anatomical facts have important functional implications. The coexistence of spatial patterns of connections within a single cytoarchitectonic area suggests that neuronal activity may also follow spatial patterns dictated by superimposed connectivities. Overlapping connection patterns may interact in complex ways to enable more elaborate functions.

Spatial patterns of large-scale connectivity are currently ignored within the macro-connectomics research community. My proposal aims to fill a conceptual and methodological gap, and develop new approaches for defining and measuring the spatial organisation of human brain connections. These methodological developments will be carried out along two fronts: (i) development of novel methods for diffusion modelling and tractography; (ii) development of a mathematical framework for the characterisation of spatial connection patterns using in-vivo connectivity data. These novel methods will be useful to all researchers in the neuroimaging community, and will constitute a major advance in the way brain networks are currently modelled and interpreted.

Planned Impact

Understanding the human brain is one of the greatest challenges of the 21st century. Several active fields of research are studying the brain at all available scales, from microbiology to systems and behavioural neuroscience. My research is concerned with studying the human brain at a macroscopic, systems level. The current most important question that the field needs to address is how to map the human brain connectome, that is, the set of anatomical connections that support brain function.

A mechanistic understanding of the human connectome is not only important for understanding normal brain function, but will also help tackle the even more complex pathological brain. A number of large projects from both sides of the Atlantic have recently started, with FMRIB Centre being a major contributor in many (e.g. The NIH-funded Human Connectome Project [HCP], The EU-funded "Connect" and "Developing Human Connectome Project" [dHCP] and the UK "Biobank Imaging"). This research area is clearly of great importance for the UK, and worldwide. In December 2012, Science Magazine identified the Human Connectome Project as an area to watch for the coming year.

These large multi-centre projects are centred on acquiring large state-of-the-art data sets. However, without state-of-the-art methods, and new ways of analysing network data, such as those I am proposing, researchers will fail to get the most out of this vast wealth of upcoming data. This project will open new ways of analysing Connectome data. The tools developed, as part of this project, will be shared with the scientific community through our freely available and widely used software FSL. This software is currently used in over 500 universities worldwide, and is contributing to the UK's well-recognised prestige in the field.

The primary beneficiaries of this research are scientists that are interested in systems level neuroscience, and how structure relates to function in the brain. In addition, the methods that will be developed for this project are novel, and will also open a new avenue in methods research and development.

Publications

10 25 50
 
Title 21st Century Phrenology 
Description We created a play about the history of neuroscience, starting in the 19th Century and ending with a look to the future of neuroscience. I was part of the team that created the play and I also performed 3 different roles in the play. 
Type Of Art Performance (Music, Dance, Drama, etc) 
Year Produced 2017 
Impact We performed in museums and schools. The play generated a lot of interest. 
 
Description A cross-species, cross-modal approach to computational neuroanatomy
Amount £1,212,397 (GBP)
Funding ID 221933/Z/20/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 02/2021 
End 01/2025
 
Description EPSRC Research Grant
Amount £432,764 (GBP)
Funding ID EP/L023067/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 07/2014 
End 08/2017
 
Description Integrative imaging of brain structure and function in populations and individuals
Amount £4,106,203 (GBP)
Funding ID 215573/Z/19/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2019 
End 05/2024
 
Description MRC Proximity to discovery
Amount £3,436 (GBP)
Funding ID P2D/TT2015/06 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 07/2015 
End 09/2015
 
Description NIH Supplement to HCP Aging
Amount $563,000 (USD)
Organisation National Institutes of Health (NIH) 
Sector Public
Country United States
Start 09/2017 
End 12/2020
 
Title FSL 
Description FSL is a software library that is widely used throughout NeuroImaging labs. My team develops tools within FSL to analyse diffusion MRI data and assess brain connectivity in vivo in humans and animals. 
Type Of Material Improvements to research infrastructure 
Provided To Others? Yes  
Impact FSL is used by over 1000 universities worldwide. It is freely available for non-commercial use. We host a 5 day course every year with >150 attendees each year (has been running now for >15 years). We provide an email-based support list which has >2000 subscribers sending >7000 emails per year. 
URL http://www.fmrib.ox.ac.uk/fsl
 
Title Activation Prediction 
Description We invented a way to predict individual variability in brain activity under task from measurements at rest. 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact This method, which has just been accepted in the journal Science, will enable several applications, including: - Building task localisers: a software tool will be developed which will allow researchers to feed in a simple, quick acquisition of subjects' brains at rest, and then get individualised task maps of brain regions (such as primary visual areas, language areas, higher level visual areas, etc.). In general, each task localiser requires at least 10-20min of acquisition time. The tool that will be developed will offer the possibility of getting task localisers for free, which will be a major advance in the neuroimaging field. - Building models in healthy participants and applying them to patients undergoing surgery. Such models will be particularly useful when patients are unable to perform the task in the scanner prior to surgery. - More generally, one set of outcomes from this research will be to better understand the relationship between brain connectivity and brain function. 
 
Title Bayesian Analysis of Change 
Description This new technique allows inference on model parameters in microstructural models of the white matter. It works even when the model is degenerate, as it does the inference on change (e.g. between patients and controls). 
Type Of Material Data analysis technique 
Year Produced 2021 
Provided To Others? Yes  
Impact A comprehensive software tool has been released. The technique is being used in the UK Biobank Imaging project, which is the largest neuroimaging dataset worldwide. 
URL https://git.fmrib.ox.ac.uk/hossein/bench
 
Title Connectional comparative anatomy 
Description We created a general framework for comparative anatomy of the brain of different primate species. 
Type Of Material Data analysis technique 
Year Produced 2018 
Provided To Others? Yes  
Impact Since our first demonstration of the method in comparing macaques and humans, multiple publications extending the method (e.g. to more species) have since followed, bith from our groups and from other groups worldwide. 
URL https://pubmed.ncbi.nlm.nih.gov/29749930/
 
Title Diffusion SSFP 
Description SSFP is an MRI technique that uniquely enables, amongst other things, imaging of whole post-mortem brains at ultra-high spatial resolution. The analysis of such data (in terms of modelling) is however unusually complex. I developed a set of tools dedicated to analysing SSFP diffusion data. These unique tools are used by my collaborators in Oxford and elsewhere to analyse whole post-mortem brains. 
Type Of Material Data analysis technique 
Year Produced 2014 
Provided To Others? Yes  
Impact The tool has now allowed building a large database of post-mortem human brains with diseases such as ALS (motor neurone disease) or Alzheimer's disease, which will be used to relate imaging biomarker to tissue histology and further translated in the medium term to in vivo imaging of live patients. 
 
Title Dynamic MRS 
Description We created a new modelling framework for analysing many types of dynamic MRS data, including diffusion MRS, functional MRS, and edited MRS. The tool was incorporated into the FSL-MRS software toolbox generated in my lab. 
Type Of Material Data analysis technique 
Year Produced 2022 
Provided To Others? Yes  
Impact The will impact all analyses of dynamic MRS data. 
URL https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/
 
Title Hierarchical modelling of white matter 
Description We created a new analysis tool and accompanying software for the analysis of white matter in a cohort of subject. This tool solves a long-standing issue in the analysis of white matter tracts in a cohort of subjects where matching fibres across participants is non-trivial due to inter-subject variability. 
Type Of Material Data analysis technique 
Year Produced 2022 
Provided To Others? No  
Impact As this is a tool under development, it is not possible yet to talk about its impact. 
URL https://git.fmrib.ox.ac.uk/hossein/whim
 
Title Oxford Digital Brain Bank 
Description What is the Digital Brain Bank? Post-mortem MRI provides the opportunity to validate the origins of image contrast through comparisons with microscopy, and acquire high-resolution datasets to investigate structural & comparative anatomy. Amongst many research avenues at the WIN, post-mortem brain imaging has become a considerable component of our work with cross-scale and cross-species neuroimaging. This has led to the acquisition of: - High-resolution multi-modal (i.e. MRI and microscopy) post-mortem datasets obtained from the same brain, to facilitate the examination of neuroanatomy. - Multi-modal datasets from brains donated by people who have passed away after diagnosis of a neurological disease during their lifetime, to facilitate the examination of human neuropathology & MRI-pathology correlates. - Post-mortem imaging in multiple species (e.g. non-human primates and beyond). On this website, we have split this data under three themes, the Digital Anatomist, the Digital Pathologist, and the Digital Brain Zoo. These unique datasets provide multiple avenues of research. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact This database will impact research into brain structure and function in humans, primates, and in brain diseases. 
URL https://open.win.ox.ac.uk/DigitalBrainBank/#/about
 
Title SWAS detection 
Description We developed a technique for monitoring depth of anaesthesia based on scalp electrical recordings (EEG). I developed a model and analysis technique for tracking consciousness levels in the EEG signal and automatically detecting an event called SWAS (Slow-Wave Activity Saturation) which corresponds to loss of consciousness under Propofol-induced anaesthesia. 
Type Of Material Computer model/algorithm 
Year Produced 2013 
Provided To Others? Yes  
Impact This method has been patented (UK Patent (GB1209638.4)). We have also achieved a first major step in terms of clinical translation: the method was applied to a large database of patients undergoing surgery and replicated the findings from our research study in healthy controls. Potentially, a depth-of-consciousness monitoring device will be built to help tailor anaesthesia drug levels to individuals. 
 
Title Slide Registration 
Description Software tool for registering histology slices. 
Type Of Material Data analysis technique 
Year Produced 2022 
Provided To Others? Yes  
Impact The tool is being used by our collaborators in Boston to process one of the largest collections of macaque tracer data worldwide. This is a historical collection (40 years) and our effort to digitise it means that it can finally be utilised by the research community globally. 
URL https://git.fmrib.ox.ac.uk/seanf/slider
 
Description Connectivity based comparative anatomy 
Organisation University of Oxford
Department Nuffield Department of Clinical Neurosciences
Country United Kingdom 
Sector Academic/University 
PI Contribution My group develops models and software applications that have been essential to the success of this collaboration.
Collaborator Contribution My collaborator is an expert comparative neuroanatomist who brought invaluable primate data and expertise to the project.
Impact 4 Journal publications so far plus many more to come. Also software tools for doing comparative anatomy in primates.
Start Year 2015
 
Description Deep brain stimulation 
Organisation University College London
Department Institute of Neurology
Country United Kingdom 
Sector Academic/University 
PI Contribution Provided software tools and expertise to help set up method for targeting deep brain regions in surgery patients for deep brain stimulation.
Collaborator Contribution Added value to our software tools by enabling more precise surgical planning and improved surgery outcomes.
Impact A joint publication: https://www.ncbi.nlm.nih.gov/pubmed/28711737 And many other publications from the UCL group using our tools, including media covered work, see below: https://www.theguardian.com/society/2019/mar/08/patients-with-severe-ocd-undergo-deep-brain-stimulation-trial
Start Year 2016
 
Description Diffusion-prepared phase imaging (DIPPI) 
Organisation University of Oxford
Department Nuffield Department of Clinical Neurosciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Developed novel MRI sequence for probing tissue microstructure by combining two contrast mechanisms: diffusion sensitivity and phase/susceptibility imaging. My group developed the original idea and the software tools and analytic methods.
Collaborator Contribution The groups of Karla Miller and Wenchuan Wu were instrumental in coding up the new MRI sequence and providing expertise in phase imaging.
Impact Outputs so far: initial publication + new MRI sequence implemented on a Siemens scanner.
Start Year 2019
 
Description Human Connectome Project 
Organisation University of Minnesota
Country United States 
Sector Academic/University 
PI Contribution I bring expertise in analysis of MRI data, particularly diffusion MRI data, to this large big-data project. I have been involved since the project's grant application, and am still involved.
Collaborator Contribution Being part of the HCP team, I learnt a great deal about managing large-scale projects, and providing state-of-the-art data the scientific community. I also had privileged access to this data through being involved from the inset.
Impact Data: See the URL above (state-of-the art data and software freely available to the community). Publications: Jbabdi S, Sotiropoulos SN, Haber SN, Van Essen DC, Behrens TE (2015) Measuring macroscopic brain connections in vivo Nature Neuroscience 18(11):1546-55 Vu AT, Auerbach E, Lenglet C, Moeller S, Sotiropoulos SN, Jbabdi S, Anderson J, Yacoub E, Ugurbil K (2015) High resolution whole brain diffusion imaging at 7T for the Human Connectome Project NeuroImage 15;122:318-31 Ugurbil K, Xu J, Auerbach EJ, Moeller S, Vu A, Duarte-Carvajalino JM, Lenglet C, Wu X, Schmitter S, Van de Moortele P, Strupp J, Sapiro G, De Martino F, Wang D, Harel N, Garwood M, Chen L, Feinberg DA, Smith SM, Miller KL, Sotiropoulos SN, Jbabdi S, Andersson JL, Behrens TE, Glasser MF, Van Essen D, Yacoub E - for the WU-Minn HCP Consortium (2013) Pushing spatial and temporal resolution for functional and diffusion MRI in the Human Connectome Project NeuroImage S1053-8119(13)00506 Sotiropoulos SN, Jbabdi S, Xu J, Andersson JL, Moeller S, Auerbach EJ, Glasser MF, Sapiro G, Jenkinson M, Feinberg D, Yacoub E, Lenglet C, Van Essen D, Ugurbil K and Behrens TE - for the WU-Minn HCP Consortium (2013) Advances in diffusion MRI acquisition and processing in the Human Connectome Project NeuroImage S1053-8119(13)00551 Glasser MF, Sotiropoulos SN, Wilson JA, Coalson TS, Fischl B, Andersson JL, Xu J, Jbabdi S, Webster M, Polimeni JR, Van Essen DC, Jenkinson M - for the WU-Minn HCP Consortium (2013) The Minimal Preprocessing Pipelines for the Human Connectome Project NeuroImage S1053-8119(13)00505 Blumensath T, Jbabdi S, Glasser MF, Van Essen DC, Ugurbil K, Behrens TE, Smith SM (2013) Spatially constrained hierarchical parcellation of the brain with resting-state FMRI NeuroImage 76:313-24 Sotiropoulos SN, Moeller S, Jbabdi S, Xu J, Andersson JL, Auerbach EJ, Yacoub E, Feinberg D, Setsompop K, Wald LL, Behrens TE, Ugurbil K, Lenglet C (2013) Effects of Image Reconstruction on Fibre Orientation Mapping from Multi-channel Diffusion MRI: Reducing the Noise Floor Using SENSE Magnetic Resonance in Medicine [doi: 10.1002/mrm.24623] Sotiropoulos SN, Jbabdi S, Andersson JL, Woolrich MW, Ugurbil K, Behrens TE (2013) RubiX: Combining Spatial Resolutions for Bayesian Inference of Crossing Fibres in Diffusion MRI IEEE TMI 32(6):969-82 Jbabdi S, Sotiropoulos SN, Savio AM, Graña M, Behrens TE (2012) Model-based analysis of multi-shell diffusion MR data for tractography: How to get over fitting problems Magnetic Resonance in Medicine 68(6):1846-55
Start Year 2009
 
Description Human Connectome Project 
Organisation Washington University in St Louis
Country United States 
Sector Academic/University 
PI Contribution I bring expertise in analysis of MRI data, particularly diffusion MRI data, to this large big-data project. I have been involved since the project's grant application, and am still involved.
Collaborator Contribution Being part of the HCP team, I learnt a great deal about managing large-scale projects, and providing state-of-the-art data the scientific community. I also had privileged access to this data through being involved from the inset.
Impact Data: See the URL above (state-of-the art data and software freely available to the community). Publications: Jbabdi S, Sotiropoulos SN, Haber SN, Van Essen DC, Behrens TE (2015) Measuring macroscopic brain connections in vivo Nature Neuroscience 18(11):1546-55 Vu AT, Auerbach E, Lenglet C, Moeller S, Sotiropoulos SN, Jbabdi S, Anderson J, Yacoub E, Ugurbil K (2015) High resolution whole brain diffusion imaging at 7T for the Human Connectome Project NeuroImage 15;122:318-31 Ugurbil K, Xu J, Auerbach EJ, Moeller S, Vu A, Duarte-Carvajalino JM, Lenglet C, Wu X, Schmitter S, Van de Moortele P, Strupp J, Sapiro G, De Martino F, Wang D, Harel N, Garwood M, Chen L, Feinberg DA, Smith SM, Miller KL, Sotiropoulos SN, Jbabdi S, Andersson JL, Behrens TE, Glasser MF, Van Essen D, Yacoub E - for the WU-Minn HCP Consortium (2013) Pushing spatial and temporal resolution for functional and diffusion MRI in the Human Connectome Project NeuroImage S1053-8119(13)00506 Sotiropoulos SN, Jbabdi S, Xu J, Andersson JL, Moeller S, Auerbach EJ, Glasser MF, Sapiro G, Jenkinson M, Feinberg D, Yacoub E, Lenglet C, Van Essen D, Ugurbil K and Behrens TE - for the WU-Minn HCP Consortium (2013) Advances in diffusion MRI acquisition and processing in the Human Connectome Project NeuroImage S1053-8119(13)00551 Glasser MF, Sotiropoulos SN, Wilson JA, Coalson TS, Fischl B, Andersson JL, Xu J, Jbabdi S, Webster M, Polimeni JR, Van Essen DC, Jenkinson M - for the WU-Minn HCP Consortium (2013) The Minimal Preprocessing Pipelines for the Human Connectome Project NeuroImage S1053-8119(13)00505 Blumensath T, Jbabdi S, Glasser MF, Van Essen DC, Ugurbil K, Behrens TE, Smith SM (2013) Spatially constrained hierarchical parcellation of the brain with resting-state FMRI NeuroImage 76:313-24 Sotiropoulos SN, Moeller S, Jbabdi S, Xu J, Andersson JL, Auerbach EJ, Yacoub E, Feinberg D, Setsompop K, Wald LL, Behrens TE, Ugurbil K, Lenglet C (2013) Effects of Image Reconstruction on Fibre Orientation Mapping from Multi-channel Diffusion MRI: Reducing the Noise Floor Using SENSE Magnetic Resonance in Medicine [doi: 10.1002/mrm.24623] Sotiropoulos SN, Jbabdi S, Andersson JL, Woolrich MW, Ugurbil K, Behrens TE (2013) RubiX: Combining Spatial Resolutions for Bayesian Inference of Crossing Fibres in Diffusion MRI IEEE TMI 32(6):969-82 Jbabdi S, Sotiropoulos SN, Savio AM, Graña M, Behrens TE (2012) Model-based analysis of multi-shell diffusion MR data for tractography: How to get over fitting problems Magnetic Resonance in Medicine 68(6):1846-55
Start Year 2009
 
Description Imaging anaesthesia 
Organisation University of Oxford
Department Oxford Centre for Functional MRI of the Brain (FMRIB)
Country United Kingdom 
Sector Academic/University 
PI Contribution This collaboration aims at improving monitoring consciousness levels under anaesthesia and understanding brain mechanisms operating under anaesthesia. I provide expertise in data analysis, modelling and experimental design.
Collaborator Contribution My collaborators and partners (Prof Irene Tracey and Dr Catherine Warnaby) are world experts in pain and anaesthesia. Outcomes from this collaboration are currently being translated to the clinic.
Impact Intellectual Property (in which I am co-inventor): Perception Loss Detection. UK Patent (GB1209638.4) Grant (in which I am co-PI): 1 year MRC Confidence in concept grant (UK), ~£100K GBP 2014-2015 co-Publications: Warnaby CE, Seretny M, Ni Mhuircheartaigh R, Rogers R, Jbabdi S, Sleigh J, Tracey I (2015) Anaesthesia-induced suppression of human dorsal anterior insula responsivity at loss of volitional behavioral response Anesthesiology (in press) Wiech K, Jbabdi S, Lin CS, Andersson JL, Tracey I (2014) Differential structural and resting state connectivity between insular subbdivisions and other pain-related brain regions Pain 155(10):2047-55 Mhuircheartaigh RN*, Warnaby C*, Rogers R, Jbabdi S, Tracey I (2013) Slow Wave Activity Saturation And Thalamocortical Isolation During Propofol Anaesthesia In Humans Science Transl Med 208ra148 Mhuircheartaigh RN, Rosenorn-Lanng D, Wise R, Jbabdi S, Rogers R, Tracey I (2010) Cortical and subcortical connectivity changes during decreasing levels of consciousness in humans: an FMRI study using propofol Journal of Neuroscience 30(27):9095-102. Pattinson KT, Mitsis GD, Harvey AK, Jbabdi S, Dirckx S, Mayhew SD, Rogers R, Tracey I, Wise RG. (2009) Determination of the human brainstem respiratory control network and its cortical connections in vivo using functional and structural imaging NeuroImage 44:295-305
Start Year 2009
 
Description MRI-Histo registration 
Organisation Massachusetts General Hospital
Department Martinos Center for Biomedical Imaging Massachusetts
Country United States 
Sector Hospitals 
PI Contribution We have developed software tools for processing histological slices, include 2D registration, automated segmentation, etc. The code is open source and used by our collaborators to curate a large database of tracer data.
Collaborator Contribution Our partners have one of the largest data collections of tracers in the macaque monkey, collected over decades. Our partners also provide the expertise in neuroanatomy that is required to assess if the tools that we develop are accurate.
Impact Software tools: https://git.fmrib.ox.ac.uk/seanf/slider Curated database is work in progress.
Start Year 2019
 
Description MRS Tools 
Organisation University of Oxford
Department Department of Psychiatry
Country United Kingdom 
Sector Academic/University 
PI Contribution We created new tools for analysis of Magnetic Resonance Spectroscopy, including Single voxel, MRS Imaging, diffusion MRS, and functional MRS.
Collaborator Contribution The partner provided a wealth of MRS data to test the toolbox as well as expertise in MRI physics.
Impact Disciplines involved: MR Analysis methods, NMR physics, Cognitive neuroscience, Physiology Outcomes so far: Software toolbox + initial publication
Start Year 2019
 
Description Multiple diffusion encoding 
Organisation Lund University
Country Sweden 
Sector Academic/University 
PI Contribution We have imported to Oxford a new MRI sequence developed from our collaborators in Lund, and thereby added value to their sequence by showing how it can be used to address new questions in brain connectivity.
Collaborator Contribution Our collaborators developed a novel MRI sequence that can give new information on brain microstructure which was previously inaccessible with previous standard acquisitions. They shared the code with us, with agreement from the scanner vendors (Siemens).
Impact We published a paper together on the use of their sequence. The paper is under consideration in a journal but a preprint can be found here: https://arxiv.org/abs/1901.05820
Start Year 2017
 
Description Non-human primate connectivity 
Organisation University of Rochester
Country United States 
Sector Academic/University 
PI Contribution This collaboration is about bringing together standard anatomy tools in macaque monkeys and in vivo tools used in humans. My group provides expertise and guidance in applying in vivo tools to measuring connexions in the macaque brain.
Collaborator Contribution This collaboration is about bringing together standard anatomy tools in macaque monkeys and in vivo tools used in humans. Suzanne Haber's provides us with very unique data from macaque monkey tracers for comparisons with in vivo tools in macaques and translational studies in humans.
Impact Journal publications: Jbabdi S, Sotiropoulos SN, Haber SN, Van Essen DC, Behrens TE (2015) Measuring macroscopic brain connections in vivo Nature Neuroscience 18(11):1546-55 Jbabdi S, Lehman JF, Haber SN*, Behrens TE* (2013) Human and monkey ventral prefrontal fibers use the same organizational principles to reach their targets: tracing versus tractography Journal of Neuroscience 33(7):3190-201 Tziortzi AC, Haber SN, Searle G, Tsoumpas C, Long C, Shotbolt P, Douaud G, Jbabdi S, Behrens TE, Rabiner EA, Jenkinson M, Gunn RN (2013) Connectivity-based functional analysis of dopamine release in the striatum using DWI-MRI and Positron Emission Tomography Cereb Cortex 24(5):1165-77
Start Year 2012
 
Description Post-mortem human MRI 
Organisation University of Oxford
Department Oxford Centre for Functional MRI of the Brain (FMRIB)
Country United Kingdom 
Sector Academic/University 
PI Contribution I bring expertise in modelling diffusion MRI.
Collaborator Contribution My partner (Prof Karla Miller) brings expertise in MRI physics.
Impact Publications: Mars RB, Foxley S, Jbabdi S, Sallet J, Noonan MP, Neubert FX, Andersson JL, Verhagen L, Croxson PL, Dunbar RIM, Khrapitchev AA, Sibson N, Miller KL, & Rushworth MFS The extreme capsule fiber complex in humans and macaques: A comparative diffusion MRI tractography study Brain Structure and Function (in press) Mollink J, van Baarsen KM, Dederen PJWC, Foxley S, Miller KL, Jbabdi S, Slump CH, Grotenhuis JA, Kleinnijenhuis M, van Cappellen van Walsum AM (2015) Dentatorubrothalamic tract localization with post mortem MR Diffusion Tractography compared to histological 3D reconstruction Brain Structure and Function (in press) van Baarsen K, Kleinnijenhuis M, Jbabdi S, Sotiropoulos SN, Grotenhuis A, van Cappellen van Walsum A (2015) A probabilistic atlas of the cerebellar white matter NeuroImage (in press) Berns GS, Cook PF, Foxley S, Jbabdi S, Miller KL, Marino L (2015) Diffusion tensor imaging of dolphin brains reveals direct auditory pathway to temporal lobe. Proc Royal Society B (in press) Foxley S, Jbabdi S, Clare S, Lam WW, Ansorge O, Douaud G, Miller KL (2014) Improving diffusion-weighted imaging of post-mortem human brains: SSFP at 7T NeuroImage (in press) Lam WW, Jbabdi S*, Miller KL* (2014) A Model for Extra-axonal Diffusion Spectra with Frequency-Dependent Restriction Magnetic Resonance in Medicine (in press) Miller KL, McNab JA, Jbabdi S, Douaud G (2011) Diffusion tractography of post-mortem human brains: Optimization and comparison of spin echo and steady-state free precession techniques NeuroImage 59(3)2284:97 Miller KL, Stagg CJ, Douaud G, Jbabdi S, Smith SM, Behrens TE, Jenkinson M, Chance SA, Esiri MM, Voets NL, Jenkinson N, Aziz TZ, Turner M, Johansen-Berg H, McNab JA (2011) Diffusion imaging of whole, post-mortem human brains on a clinical MRI scanner NeuroImage 57(1):167-81. McNab JA, Jbabdi S, Deoni SC, Douaud G, Behrens TE, Miller KL. (2009) High Resolution Tractography in Fixed Human Brain Using Diffusion-Weighted Steady State Free Precession NeuroImage 46(3):775-85
Start Year 2007
 
Title PERCEPTION LOSS DETECTION 
Description The present invention relates to a device for detecting a state of true perception loss of a human, the device including processing means operable to detect from information on electrical signals sensed adjacent to the scalp of the human the activity of oscillations present in the electrical signals as a marker for the state of true perception loss of the human. 
IP Reference WO2013179048 
Protection Patent application published
Year Protection Granted 2013
Licensed No
Impact This perception loss monitoring technique is currently being tested on large databases of patients undergoing surgery for translation to the clinic.
 
Title BENCH : Bayesian EstimatioN of CHange 
Description BENCH (Bayesian EstimatioN of CHange) is a toolbox implemented in python for identifying and estimating changes in the parameters of a biophysical model between two groups of data (e.g. patients and controls). It is an alternative to model inversion, where one estimates the parameters for each group separately and compares the estimations between the groups (e.g. using a GLM). The advantage is that BENCH allows for using over-parameterised models where the model inversion approaches fail because of parameter degeneracies. Currently, BENCH only supports microstructural models of diffusion MRI, but it is extendable to other domains. For the latest version, follow this Gitlab link: https://git.fmrib.ox.ac.uk/hossein/bench 
Type Of Technology Software 
Year Produced 2021 
Open Source License? Yes  
Impact Bench is being applied to the UK Biobank imaging data, the world's largest neuroimaging data collection. 
URL https://zenodo.org/record/6362821
 
Title Comparative anatomy 
Description Set of tools associated with a publication on a general framework for comparative anatomy. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact This tool/approach provide a general framework for comparative anatomy in primate species. 
 
Title Cortical folding orientations 
Description Code for visualisation of white matter orientation near the cortex. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact This way of visualising the white matter greatly simplifies the complexity of the white matter in highly convoluted brains such as the human brains and may help in studying the development of white matter. See: https://www.ncbi.nlm.nih.gov/pubmed/29684644 
 
Title DIVE - Diffusion models Interactive ViEwer 
Description Overview DIVE is an interactive viewer for diffusion models. To get good interactivity with the app, it is recommended to install it locally on your computer. See the Git repo for instructions. If you don't want to install it locally, you can run the current working version online here, but note that the interactivity may be slower. The app allows you to visualise diffusion data predicted by user-defined microstructural models and interactively change the model parameters or data acquisition to visualise the effect that these have on the model predictions. Check out this demo for an overview of DIVE capabilities: 
Type Of Technology Software 
Year Produced 2021 
Open Source License? Yes  
Impact DIVE is very useful for teaching diffusion MRI modelling. 
URL https://zenodo.org/record/6362851
 
Title EDDY_QC 
Description This is a tool for automated quality control and reporting of diffusion MRI data. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact This will have global impact on all imaging projects (clinical and non-clinical) particularly when large datasets are collected and where manual QC is not a viable option. It will also facilitate integration between disparate datasets (harmonisation) and comparisons with massive datasets such as the UK biobank. 
 
Title FDT - SSFP 
Description This is the only tool (worldwide) that allows whole brain analysis of diffusion-weighted SSFP data. 
Type Of Technology Software 
Year Produced 2014 
Open Source License? Yes  
Impact This tool enabled researchers interested in big-brain post-mortem imaging to study structural connectivity at very high resolution with a high-SNR technique. 
 
Title FDT - probtrackx2 
Description Software tool for tracing brain connections using diffusion MRI. 
Type Of Technology Software 
Year Produced 2013 
Open Source License? Yes  
Impact This tool is used in over 1000 laboratories worldwide, and is the main structural connectivity tool used by major MRI data projects such as the human connectome project. It is also used in several clinical applications such as deep brain stimulation and pre-surgical planning. 
URL http://www.fmrib.ox.ac.uk/fsl/fdt
 
Title FSL-MRS 
Description A comprehensive toolbox for analysis of MRS data, including data conversion, density matrix simulations, pre-processing, visualisation, fitting, quantitation, and quality control. The toolbox is designed to handle multiple types of MRS, including SVS, multi-voxel MRS imaging, functional MRS, and diffusion MRS. 
Type Of Technology Software 
Year Produced 2020 
Open Source License? Yes  
Impact The MRS community has taken notice and is highly excited by this new product. So far the community was mostly tied to using a commercial and closed-source product. Our software is fully open source and much more flexible than existing tools. There is also a journal publication describing the software here: https://pubmed.ncbi.nlm.nih.gov/33280161 
URL https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/index.html
 
Title Modelling gyral white matter 
Description Python package for modelling white matter anatomy based on diffusion MRI. 
Type Of Technology Software 
Year Produced 2020 
Impact The software allows to solve a well known issue with diffusion MRI tractography near the cortex in order to recover anatomical connections much more faithfully that previously possible in human brains. 
URL https://git.fmrib.ox.ac.uk/ndcn0236/gyral_structure
 
Title XTRACT - Automated extraction of white matter connections 
Description Software tool for automated extraction of white matter tracts from diffusion MRI. 
Type Of Technology Software 
Year Produced 2020 
Open Source License? Yes  
Impact It is early days but this tool has already been used by others to discover differences in brain anatomy of different primate species. It is also designed to facilitate sharing protocols for tractography between labs and help with reproducible science. 
URL https://www.biorxiv.org/content/10.1101/804641v1
 
Description Banbury school visit 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact The purpose was to expand our primary school outreach activities beyond Oxford. The visit included an assembly followed by two workshops for years 4 and 5 pupils, where they learned about brains by playing games. Beyond learning about brains, another objective was to make the students relate to scientists and get a feel for what it is like and what it takes to be a scientist.
Year(s) Of Engagement Activity 2022
 
Description History of Neuroscience Play 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact We (a bunch of neuroscientists from the lab) created and performed a play on the history of neuroscience starting in the Victorian era and ending with a look into the future.
Year(s) Of Engagement Activity 2017
 
Description Oxford technology showcase 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Oxford Technology Showcase is an event organised by the Oxford University Innovation, who manages the University's technology transfer. I presented work done in my lab (advances in image analysis and dissemination via open source software) to companies and potential investors.
Year(s) Of Engagement Activity 2016
 
Description Primary school 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact 30 year 5 children from my local school and their teachers came to visit our lab facilities. They have seen how an MRI scanner works, including them coming up with their own experiments, and I talked to them about what I do, which is maths for understanding MRI and the brain. This event was preceded by me visiting the school and leading a 1h class where the same children did a worksheet/game on a neuroscience topic. The teacher who was present and the children will then do the same with the other classes. The idea behind these activities is to tell children about what real life science is like. I personally also like to tell them that maths is fun by showing them the type of applications in MRI/Neuroscience that one can do with maths and computers.
Year(s) Of Engagement Activity 2019
URL https://www.win.ox.ac.uk/for-the-public/engaging-with-the-public/primary-schools
 
Description Public lecture 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact This was part of an Oxford alumni day where I gave a talk about BIG data in brain imaging to an audience of people from a vast array of backgrounds who used to be at Oxford but are now scattered around the globe. The meeting resulted in lively debates after the talk.
Year(s) Of Engagement Activity 2013
URL https://www.alumni.ox.ac.uk/alumni_home
 
Description SET for Britain 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact SET for Britain is a Science workshop bringing together British members of parliament (MPs) and early career academics. My post-doctoral associate (Dr Oiwi Parker Jones) and I presented our work to MPs, including our local MP at the palace of Westminster in London. This was a great opportunity not only to learn about great science happening in the UK across the fields, but also a great way to communicate science to policy-makers.
Year(s) Of Engagement Activity 2016
URL http://www.setforbritain.org.uk
 
Description St Cross College public lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Other audiences
Results and Impact Public lecture at an Oxford college intended to stimulate discussion/debate with academics from a variety of fields outside of my own field. This is a great opportunity for creating new connections outside my circle and also thinking outside my box.
Year(s) Of Engagement Activity 2015
 
Description St Edmund Hall public lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Public lecture at an Oxford college intended to stimulate discussion/debate with academics from a variety of fields outside of my own field. This is a great opportunity for creating new connections outside my circle and also thinking outside my box.
Year(s) Of Engagement Activity 2015