Cardiff University-Equipment Account

Lead Research Organisation: Cardiff University
Department Name: Sch of Psychology

Abstract

MRI scanners are used widely to diagnose disease and to understand the workings of the healthy body. However, while useful for some diagnoses, they do not capture tissue properties at microscopic length scales (thousandths of a millimetre) where important processes occur, e.g. in the 'axons' connecting different brain areas, or in cells in vital organs, e.g. liver. Such detailed examination usually requires an invasive 'biopsy' which is studied under a microscope. However, biopsies only provide information about small regions of an organ, are destructive and so cannot be performed repeatedly for monitoring, and can be risky to collect, e.g. in the brain.

This project assembles engineers, physicists, mathematicians and computer scientists to develop new MRI methods for quantifying tissue structure at the microscopic scale. The principal approach looks at how fine tissue structure impedes the movement of water. Current MRI hardware restricts measurement to relatively large molecular displacements and from tissue components with a relatively strong and long-lived signal. This blurs our picture and prohibits us from quantifying important characteristics, such as individual cell dimensions, or packing of nerve fibres.

The sensitivity of MRI to smaller molecular movements and weaker signals is mainly limited by the available magnetic field gradients (controlled alterations in the field strength within the scanner). We have persuaded MRI manufacturers to build a bespoke MRI system with ultra-strong gradients (7 times stronger than available on standard MRI scanners) to be situated in the new Cardiff University Brain Research Imaging Centre. One similar system currently exists (in Boston, USA) but is used predominantly to make qualitative pictures of the brain's wiring pattern. Our team has the unique combination of expertise to develop and exploit this hardware in completely new directions. By designing new physics methods to 'tune' the scanner to important (otherwise invisible) signals, developing new biophysical models to explain these signals, and suppressing unwanted signals, we will be able to quantify important tissue properties for the first time.

Making such a system usable poses several key engineering challenges, such as modelling of electromagnetic fields, to deal with confounds that become significant with stronger gradients, and modelling of the effects on nerves/cardiac tissue, to impose safety constraints. However, the current work of the consortium of applicants provides strong starting points for overcoming these challenges. Established methods for accelerating MR data acquisition will be compromised with stronger gradients, requiring development of new physics methods for fast data collection. Once achieved, faster acquisition and access to newly-visible signal components will enable us to develop new mathematical models of microstructure incorporating finer length-scales to increase understanding of tissue structure in health and disease, and to make testable predictions on important biophysical parameters such as nerve conduction velocities in the brain. This will result in earlier and more accurate diagnoses, more specific and better-targeted therapy, improved treatment monitoring, and overall improved patient outcome. The ultimate goal is to develop the imaging software that brings this hardware to mass availability, in turn enabling a new generation of mainstream microstructure imaging and macrostructural connectivity mapping techniques to translate to frontline practice.

Planned Impact

A National Microstructure Imaging Facility will impact positively on a wide range of stakeholders that can put to important uses new, more sensitive medical imaging tools. This is directly in line with the EPSRC's Healthcare Technologies theme, particularly with respect to enhancing prediction and diagnosis and the technology to develop new biomarkers.

MR scanner manufacturers will benefit by extending MRI into new territory and clinical applications, setting new standards for a future generation of clinical hardware. Moreover, manufacturers and users will benefit through future exploitation on standard MR scanners of the new techniques and engineering solutions developed in order to bring the NMIF into operation.

Once the core technology is developed, diseases with a particularly high societal burden, including dementia and cancer, will be early targets for clinical translation and therefore rapid impact.

We have identified key industrial partnerships that will accelerate benefits to industry, particularly in the UK, focusing on the medical device and pharmaceutical industries.
These partnerships will precipitate bringing putative treatments to market, with subsequent major impact on the UK economy as well as the well-being of patients and carers.

The new methods will provide sensitive biomarkers of dementia promoting early diagnosis and the improved stratification of patient groups. This impact is exemplified by our partnership with Acuitas Medical which aims to use the high-gradient system to identify dementia-related changes in microstructural columns within the brain. The techniques we develop will aim to detect subtle microstructural changes in tumour cells, helping to diagnose cancer and monitor treatment response, allowing better therapeutic decision making and replacing the biopsy. The ultimate goal is earlier and more accurate diagnoses, more specific and better-targeted therapy, improved treatment monitoring, and overall improved patient outcome.

There is a pressing need for more sensitive and specific biomarkers in the pharmaceutical industry to reduce development costs by providing early signals of drug efficacy and allowing the most promising compounds to be taken forward in development as rapidly as possible. This will lead to more treatments to more patients more quickly. We will partner with GlaxoSmithKline, the UK's largest pharmaceutical company, to develop imaging markers useful in drug development. We will partner with Renishaw to improve models and software for neurosurgery and drug and stem cell delivery into the brain, accounting for the impact of tissue microstructure on the transport of the drug/cells.

Magstim, a world leading manufacturer of electromagnetic (EM) brain stimulation equipment, will partner with the NMIF. Modelling of the EM properties of tissue, using the microstructural measurements, will allow the company to improve both their coil designs and paradigms for brain stimulation.

The benefits to medical device and pharmaceutical research are likely to be realized in the next 3-5 years with the initiation of early clinical trials. The wider benefits to routine measurements would naturally take longer to realise, typically 5+ years. In addition, the NMIF and the associated research and industrial network will produce a professional training opportunity unparalleled in Europe producing highly skilled imaging methodologists to work in research and industry.

Finally, we will partner with the UK arts community to engage the public in our science, benefitting the scientists themselves (gaining new insights through two-way interaction), the artists (gaining new inspiration for their work), the museums and art galleries that will host the travelling exhibitions and members of the public that attend the exhibitions.

Publications

10 25 50
 
Title "In Vitro" and "The Left Hemisphere" videos and printed artworks 
Description Two video files entitlted "In Vitro" and "The Left Hemisphere" were created by our commissioned artist Shardcore (funded by the EPSRC engagement grant) and projected onto the large screen in the CUBRIC Reception area during the Brain Night event held on 6th Dec 2018. The artist was inspired by the unseeable structures revealed through science and their beautiful artworks were created from a 100,000 fibre connectom dataset. Six printed pieces of artwork around the two themes were also delivered to CUBRIC before Christmas 2018. 
Type Of Art Film/Video/Animation 
Year Produced 2018 
Impact The audience attending this public engagement event were very much impressed with the artistic way that the microstructural MRI brain imaging data was presented through the art-science collaboration. 
URL https://www.youtube.com/watch?v=KUG8pC5W5_Y
 
Title Lightbox with transparent digital Artsci work and oil/acrylic on canvas 
Description Our commissioned artist Penelope Rose Cowley on the EPSRC engagement grant has completed and delivered to us 6 pieces of artwork in August 2018, one of which is via a lightbox with transparent digital artsci work entitled "Illumunated Tractography", two are in the form of acrylic on canvas, entitled "Mindscape" and "Braintree", three are oil on canvas, entitled "The Magnet", "Behind My Face Coronal", and "Head Down Axial". 
Type Of Art Artwork 
Year Produced 2018 
Impact To create the artwork, the artist visited CUBRIC several times, sitting in the Connectom scanner lab, watching the researchers operating the scanner / monitoring the data acquisition based on the established protocols, and discussing with the researchers about the unique advantage of microstructural MRI imaging enabled by the Connectom scanner. The interaction with the scientists brought the artist inspiration for their artwork. The successful delivery of the artwork funded by EPSRC is itself a productive art-science collaboration which will maximise the research impact and better engage the public in the forthcoming exhibition. 
 
Title Oil paintings 
Description Four pieces of oil paintings were delivered before Christmas 2017 by one of our commissioned artists Lee Wright (funded by the EPSRC engagement award). 'Healthy and diseased human brains' were highlighted in the artworks. A fifth oil painting was further delivered by Lee in March 2019 which features diffusion MRI works. 
Type Of Art Artwork 
Year Produced 2017 
Impact The artworks were initially developed by the artist. The investigators on the EPSRC equipment award for the Connectom scanner were then consulted for feedback/input to the artwork, following which the artist refined and completed the artwork before Christmas 2017, and again in March 2019 for the final piece of artwork. Therefore, the delivered artwork itself was the result of art-science collaboration, the aim of which is to engage the public more with the advanced research and to maximise the impact of the scientific research. 
 
Description In relation to our objectives to establish a globally-unique hardware platform to enable the development of a new measurement science, redefining the MRI scanner as a quantitative microstructural measurement tool, we have purchased 2 of the 3 major pieces of the hardware platform: 3T Connectom MRI scanner and Skope Field Camera. We have yet to purchase the optical tracking system (pending decisions on the best available system). We are in discussion with a spin out company from Danish Technical University, TracInnovations - to collaborate on the development of a new technology for motion detection, using structured light. However, the challenge is that the system was developed for another MRI scanner - and interfacing it into the Connectom scanner (funded by this grant) is challenging due to reduced field-of-view afforded by the RF hardware, and due to the smaller bore of the scanner. We have therefore committed to explore ways in which we can develop solutions (with the company) to get the system to work in the Connectom. This includes some preliminary work on an alternative system in CUBRIC (a 3T Prisma system). The company has agreed to provide materials and spare parts to help develop solutions to this problem, with joint team meetings to review progress and results.
Each of the 3 major pieces will integrate into an optimised form which is unavailable anywhere else in the world. We have received a 64 channel head coil from Siemens for the Connectom scanner. Collaborations with the University of Manchester (UoM) has been developed. UoM will supply us with the manufacture, provision and installation of a suite of phantoms for diffusion MRI, which will benefit and maximise the use of the Connectom scanner. The suite will include 5 phantoms of different characteristics, (e.g. for anisotropy per se, 'axon diameter' mapping with different orientational dispersions, some phantoms for microscopic anisotropy measurements and some phantoms with variable membrane permeability.). The first of the phantoms has been delivered, and the first experiment planned to take place on 15th March 2019 when the Co-PI Prof Geoff Parker visits CUBRIC.
In terms of our strategic objective to establish a National Microstructural Imaging Facility (NMIF), we held our first NMIF conference on 31st January - 1st February 2017, show casing the facility - with 150+ international attendees, so we have started to promote and support the use of the NMIF for the UK EPS community and beyond to develop new methods for quantifying microstructure.
With CUBRIC researchers' efforts to get the Connectom scanner fully up and running in 2017-2018, this EPSRC funded equipment has acted as a catalyst for generation of grant applications, papers and abstracts submitted to conferences, such as the 25th, 26th and 27th Annual Scientific Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), a premier meeting for the MRI research, drawing attendees from all over the world.
Two applicants whose applications are based on the Connectom microstructural brain imaging study have successfully got through to the interview stage in November 2018 for the competitive Sir Henry Wellcome Fellowship scheme, with one successfully awarded: Matteo Mancini from Universities of Brighton and Sussex.
Two Marie Curie Individual Fellowship applications (with Cardiff University as the host institution) from Viljami Sairanen (University of Helsinki, Finland) and Simona Schiavi (University of Verona, Italy) are also based on the Connectom study.
CUBRIC scientists have been invited to be co-applicants/collaborators on the following four grants:
Collaborator on the grant to British Heart Foundation with PI from Imperial College London, focusing on cardiac microstructural imaging;
Co-applicant on the grant to Wellcome Trust with PI from University of Leeds, focusing on cardiac microstructural imaging;
Co-applicant on the grant to EPSRC with PI from University of Manchester, focusing on water exchange study;
Co-applicant on the grant with PI from Australian Catholic University - cognitive deficits associated with chemotherapy.
The Connectom was already the centrepiece to 3 international Fellowships (featured in the University newsletter) by Erika Raven (Marshall Sherfield Fellowship, USA), Maxime Chamberland (Canada), and Chantal Tax (Netherlands) who has recently been awarded the Sir Henry Wellcome Fellowship, project entitled "Making advanced characterisation of tissue microstructure clinically practical: a data-driven approach to efficient microstructural MRI".
We have developed collaborations on the EPSRC-funded Connectom study. Our UK collaborations include: Oxford, Manchester, Brighton and Sussex, Nottingham, UCL, KCL; Our international collaborations include: EPFL, Switzerland; Lund University, Sweden; Max Planck Institute, Leipzig Germany; CINR, Paris, France; Leiden University, Netherlands; Leuven University, Belgium; Champalimaud Centre for the Unknown, Portugal; New York University, USA; Australian Catholic University, Australia.
An audition slot on 9th March 2018 has been secured for the Automating Science Discovery Feasibility Studies EPSRC call. Relevant data from the new high-resolution scans by Connectom has been used for the Pitch. We took on the CD-MRI challenge data sharing initiative, where data collected on the EPSRC-funded scanner in Cardiff, formed the centrepiece to an international competition to harmonise data from different scanners.
On 14th March 2018, we hosted a " Connecting the Connectoms" meeting in CUBRIC with attendees from the Boston MGH Connectom team (U.S.) and Leipzig Connectom team (Germany) to discuss collaborative opportunities between the 3 sites.
Prof Derek Jones, Director of CUBRIC, has given a talk on Connectom entitled "New Windows on Brain Structure and Function" at the Siemens Lunch Symposium on 19th June 2018 during the 26th Annual Scientific Meeting of the ISMRM in Paris, reaching an audience of 4,000 to 4,500 people worldwide, https://www.healthcare.siemens.com/magnetic-resonance-imaging/magnetom-world/clinical-corner/clinical-talks/new-windows-on-brain-structure-and-function.html . The majority of the innovations were on the Connectom scanner, having been hugely supported by Dr Umesh Rudrapatna, the senior post-doctoral Research Associate (pledged as matched funding by Cardiff University in support of the EPSRC equipment grant) and resulting from both internal work and the collaborations listed above. As a direct result, Siemens Healthineers committed to putting a Siemens scientist permanently on site to work with the CUBRIC Connectom physicist. This includes a new venture, i.e. imaging 'below the neck' where Cardiff University will be the world's first site to explore these new applications.
Dr Umesh Rudrapatna, Dr Lars Mueller and CUBRIC research group, using spiral-EPI on the Connectom, have achieved unprecedentedly short echo times for human diffusion MRI, potentially providing sensitivity to myelin water diffusion. This required collaboration with Siemens, pulse-sequence development, and a new image reconstruction pipeline that corrects for B0 and gradient imperfection temporally (measured with the field camera) and spatially (gradient nonlinearities). This new sequence also allows us to probe contrast mechanisms in diffusion-weighted fMRI.
Substantial progress with development study on utilising Connectom scanner has been achieved by CUBRIC scientists with expertise in engineering and physics. Connectom scanner enables the most ambitious microstructural brain imaging study to be conducted as part of the WAND study http://www.cardiff.ac.uk/news/view/1286914-most-advanced-brain-imaging-study-in-wales . The Science Café programme featuring the WAND study was broadcast on 25th September 2018 on BBC Radio Wales - Prof Derek Jones, Dr Hannah Chandler and Dr John Evans were interviewed in the programme, https://www.bbc.co.uk/programmes/m0000hq7.
In terms of engagement with industrial users, we have been working very closely with Siemens Healthineers to explore physical limitations of imaging under the neck, which has never been done on this type of scanner before. Siemens Healthineers has agreed to sponsor a PhD student doing research on microstructure in the prostate.
Exploitation Route We will keep promoting and supporting the use of the NMIF for the UK EPS community and beyond to develop new methods for quantifying microstructure.
Sectors Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description We engaged with the BBC news to have a detailed 3 minute feature on the system on the main 6 pm and 10 pm bulletins (see https://vimeo.com/224202631), the BBC news website, and the feature was broadcast and taken up by news agencies around the world. This publicity clearly engaged the general public (based on number of enquiries received), raised their awareness of the Connectom scanner, following which they might volunteer to be the participants of the MRI physics development work. It has also provided additional inspiration for artists to produce the artwork and helped us with the delivery of the art-science collaboration project for better public engagement (all commissioned artworks delivered to us by March 2019). On 25th January 2018 BBC news, Dr Chantal Tax from CUBRIC talked with singer Charlotte Church about the Connectom scanner on the BBC http://www.bbc.co.uk/news/uk-wales-42805693. An actual picture of living brain connections taken by the Connetom scanner was included in the BBC news. In addition, the YouTube video about the Connectom scanner made by Tom Scott (and filmed by Paul Allen, School of Psychology) has just passed 228,350 views! Prof Derek Jones, Director of CUBRIC gave the lay talk in the video to raise the general public's awareness of the stunning images enabled by the Connectom scanner https://www.youtube.com/watch?v=diPiSHxfGyE&feature=youtu.be. The impressive number of YouTube hits showed the scale of engagement from the general public which maximised the impact of the methodological advances facilitated by the advanced facility. The EPSRC-funded Connectom scanner enables the most ambitious microstructural brain imaging study to be conducted in CUBRIC as part of the WAND (Welsh Advanced Neuroimaging Database) study http://www.cardiff.ac.uk/news/view/1286914-most-advanced-brain-imaging-study-in-wales . The Science Café programme featuring the WAND study was broadcast on 25th September 2018 on BBC Radio Wales - Prof Derek Jones, Dr Hannah Chandler and Dr John Evans were interviewed in the programme, https://www.bbc.co.uk/programmes/m0000hq7. It reaches the general public audience who will know more about the microstructural MRI imaging enabled by the Connectom scanner and how to volunteer to participate in the WAND study including MRI scan session in the Connectom. As of 28th Feb 2020, 79 participants have participated in the Connectom scan as part of their WAND study visit. COVID lock down and restrictions since March 2020 significantly delayed the human participants research conduction. As of 4th March 2021, a total of 94 participants (only 15 more participants in the reporting period) have participated in the Connectom scan as part of their WAND study visit.
Sector Communities and Social Services/Policy,Digital/Communication/Information Technologies (including Software),Education
Impact Types Cultural,Societal

 
Description BaMBoo: Building a Meaningful Biomarker of Myelin
Amount £300,000 (GBP)
Funding ID 213722/Z/18/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2019 
End 03/2023
 
Description Characterising brain network differences during scene perception and memory in young adult APOE-e4 carriers: multi-modal imaging in ALSPAC
Amount £1,420,574 (GBP)
Funding ID MR/N01233X/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 01/2017 
End 06/2021
 
Description Countering the curse of dimensionality in microstructural MRI
Amount € 250,000 (EUR)
Organisation NWO Rubicon Fellowship 
Sector Private
Country Netherlands
Start 02/2020 
End 02/2024
 
Description Diffusion-relaxometry in prostate using ultra-strong gradients
Amount £55,000 (GBP)
Organisation Siemens AG 
Department Siemens plc
Sector Private
Country United Kingdom
Start 10/2019 
End 09/2022
 
Description Enabling clinical decisions from low-power MRI in developing nations through image quality transfer
Amount £1,020,000 (GBP)
Funding ID EP/R014019/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 02/2018 
End 01/2021
 
Description Exploiting ultra-strong gradients in multi-modal MRI for comprehensive assessment of white matter microstructure in the living human brain
Amount £139,200 (GBP)
Organisation Netherlands Organisation for Scientific Research (NWO) 
Sector Public
Country Netherlands
Start 06/2017 
End 08/2020
 
Description Influence of Sleep on Human Brain Structure
Amount £250,000 (GBP)
Funding ID 209192/Z/17/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2018 
End 08/2022
 
Description Making advanced characterisation of tissue microstructure clinically practical: a data-driven approach to efficient microstructural MRI
Amount £300,000 (GBP)
Funding ID 215944/Z/19/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2019 
End 08/2023
 
Description Mapping Neurodevelopmental Trajectories for Adult Psychiatric Disorder: ALSPAC-MRI-II
Amount £1,791,731 (GBP)
Funding ID MR/S003436/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 03/2019 
End 02/2023
 
Description Microstructural Imaging Data Centre (MIDaC)
Amount £73,918 (GBP)
Funding ID ST/S00209X/1 
Organisation Science and Technologies Facilities Council (STFC) 
Sector Public
Country United Kingdom
Start 11/2018 
End 08/2019
 
Description Multi-scale and multi-modal assessment of coupling in the healthy and diseased brain.
Amount £4,923,467 (GBP)
Funding ID 104943 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 07/2016 
End 06/2021
 
Description National Facility for In Vivo MR Imaging of Human Tissue Microstructure
Amount £148,521 (GBP)
Funding ID EP/M029778/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 06/2015 
End 05/2022
 
Description New Horizons in Clinical Cardiac Diffusion Magnetic Resonance Imaging
Amount £1,766,596 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2020 
End 03/2024
 
Description OCEAN: One-stop-shop microstructure-sensitive perfusion/diffusion MRI: Application to vascular cognitive impairment
Amount £1,302,402 (GBP)
Funding ID EP/M006328/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 03/2015 
End 09/2018
 
Description Principal Investigator
Amount £1,000,000 (GBP)
Organisation The Wolfson Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 07/2014 
End 06/2019
 
Description Statistical reconstruction of histology data based on magnetic resonance imaging (HistoStat)
Amount £186,938 (GBP)
Funding ID BB/T011564/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 05/2020 
End 10/2020
 
Description Water Exchange in the Vasculature of the Brain (WEX-BRAIN)
Amount £86,059 (GBP)
Funding ID EP/S031375/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 11/2019 
End 10/2022
 
Description Wellcome Trust Strategic Award
Amount £4,953,467 (GBP)
Funding ID 104943/Z/14/Z 
Organisation Wellcome Trust 
Department Wellcome Trust Strategic Award
Sector Charity/Non Profit
Country United Kingdom
Start 07/2016 
End 06/2021
 
Title MICRA: Microstructural image compilation with repeated acquisitions 
Description This is a publically accessible data set collected on the scanner funded by this grant. The full details can be found in this paper: MICRA: Microstructural image compilation with repeated acquisitions Kristin Koller, Umesh Rudrapatna, Maxime Chamberland, Erika P Raven, Greg D Parker, Chantal M W Tax, Mark Drakesmith, Fabrizio Fasano, David Owen, Garin Hughes, Cyril Charron , C John Evans, Derek K Jones Neuroimage 2021 Jan 15;225:117406. PMID: 33045335 PMCID: PMC7779421 DOI: 10.1016/j.neuroimage.2020.117406 We have put this data set onto the Open Science Framework for the community to use it. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact The data set has been downloaded by multiple investigators around the globe given its unique features, to establish reproducibility of pipelines. It was used recently in the international BrainHack 
URL https://osf.io/z3mkn/
 
Title Noninvasive quantification of axon radii using diffusion MRI 
Description Axon size plays a crucial role in determining conductance velocity and, consequently, in the the timing and synchronization of neural activation. Noninvasive measurement of axon radii could have significant impact on the understanding of healthy and diseased neural processes. However, until now, accurate axon radius mapping has eluded in vivo neuroimaging, mainly due to a lack of sensitivity of the MRI signal to micron-sized axons. Here, we show how -- when confounding factors such as extra-axonal water and axonal orientation dispersion are eliminated -- heavily diffusion-weighted MRI signals becomes sensitive to axon radii. However, diffusion MRI is only capable of estimating a single metric representing the entire axon radius distribution within a voxel that emphasizes the largest axons. Our findings, both in rodents and humans, enable noninvasive mapping of critical information on axon radii, as well as resolve the long-standing debate on whether axon radii can be quantified. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL http://datadryad.org/stash/dataset/doi:10.5061/dryad.4qrfj6q66
 
Description Estimating axial diffusivity in the NODDI model 
Organisation University of Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution We provided the data acquisition, data sets, and pre-processing and had extended discussions with the team at Oxford about the complexities of estimating axial diffusivity from the NODDI model
Collaborator Contribution This was a real team effort (see above) but Dr Amy Howard really led the writing of the paper.
Impact Estimating axial diffusivity in the NODDI model. Howard AF, Cottaar M, Drakesmith M, Fan Q, Huang SY, Jones DK, Lange FJ, Mollink J, Rudrapatna SU, Tian Q, Miller KL, Jbabdi S. Neuroimage. 2022 Nov 15;262:119535.
Start Year 2021
 
Description GSK 
Organisation GlaxoSmithKline (GSK)
Country Global 
Sector Private 
PI Contribution We made the 3TM Connectom MRI scanner available for research. We will recruit a PhD student to do the research funded by GSK studentship.
Collaborator Contribution GSK agreed to fund a 3 year PhD studentship to carry out research on microstructural imaging technology.
Impact GSK agreed to fund a 3 year PhD studentship to carry out research on microstructural imaging technology.
Start Year 2016
 
Description Laboratorio de Procesado de Imagen - CUBRIC 
Organisation University of Valladolid
Country Spain 
Sector Academic/University 
PI Contribution We collaborated on a number of projects, including strategies to denoise diffusion MRI data, identify reduced acquisition strategies for faster encoding of diffusion anisotropy, and to establish conditions under which a power law can describe the signal decay for different microstructural substrates and diffusion encoding wave-forms.
Collaborator Contribution Santiago made an extended visit to CUBRIC for face-to-face discussions on the above topics, and we have continued Zoom calls ever since. He has now sent a postdoc to spend 2 years with us, as a result of the ongoing collaboration
Impact Direction-averaged diffusion-weighted MRI signal using different axisymmetric B-tensor encoding schemes. Afzali M, Aja-Fernández S, Jones DK. Magn Reson Med. 2020 Sep;84(3):1579-1591. Apparent propagator anisotropy from single-shell diffusion MRI acquisitions. Aja-Fernández S, Tristán-Vega A, Jones DK. Magn Reson Med. 2021 May;85(5):2869-2881 On the generalizability of diffusion MRI signal representations across acquisition parameters, sequences and tissue types: Chronicles of the MEMENTO challenge. De Luca A, Ianus A, Leemans A, Palombo M, Shemesh N, Zhang H, Alexander DC, Nilsson M, Froeling M, Biessels GJ, Zucchelli M, Frigo M, Albay E, Sedlar S, Alimi A, Deslauriers-Gauthier S, Deriche R, Fick R, Afzali M, Pieciak T, Bogusz F, Aja-Fernández S, Özarslan E, Jones DK, Chen H, Jin M, Zhang Z, Wang F, Nath V, Parvathaneni P, Morez J, Sijbers J, Jeurissen B, Fadnavis S, Endres S, Rokem A, Garyfallidis E, Sanchez I, Prchkovska V, Rodrigues P, Landman BA, Schilling KG. Neuroimage. 2021 Oct 15;240:118367 Anisotropy measure from three diffusion-encoding gradient directions. Aja-Fernández S, París G, Martín-Martín C, Jones DK, Tristán-Vega A. Magn Reson Imaging. 2022 May;88:38-43.
Start Year 2019
 
Description Maastricht-Cardiff Collaboration for Implementation of MDT into CUBRIC Pipeline 
Organisation Maastricht University (UM)
Department Psychology Maastricht
Country Netherlands 
Sector Academic/University 
PI Contribution This was a collaboration with Robbert Harms at Maastricht University to implement his MDT toolbox into the CUBRIC pipeline for fitting of complex tissue microstructural models to diffusion MRI data. We established the acquisition protocols, sequences etc. and the theory to estimate conduction velocity from microstructural measurements. We worked together to get in vivo estimates of conduction velocity, that are now being used in subsequent papers and grant applications. This approach is now central to our current work in linking measures of functional connectivity (e.g. from MEG) to structural connectivity
Collaborator Contribution Robbert Harms worked with us, including extended visits to CUBRIC, to implement the Maastricht Diffusion Toolbox (MDT) into the CUBRIC pipeline to provide more robust fitting of advanced models so that we could extract reliable estimates of axon density, diameter and g-ratio. (Ref for prior work: Robust and fast nonlinear optimization of diffusion MRI microstructure models. Harms RL, Fritz FJ, Tobisch A, Goebel R, Roebroeck A. Neuroimage. 2017 Jul 15;155:82-96)
Impact Estimating axon conduction velocity in vivo from microstructural MRI. Drakesmith M, Harms R, Rudrapatna SU, Parker GD, Evans CJ, Jones DK. Neuroimage. 2019 Dec;203:116186.
Start Year 2018
 
Description Magstim Co Ltd 
Organisation The Magstim Company Limited
Country United Kingdom 
Sector Private 
PI Contribution We made the 3TM Connectom MRI scanner available for research. We will recruit a PhD student to do the research funded by Magstim studentship.
Collaborator Contribution Magstim agreed to fund a 3 year PhD studentship to carry out research on microstructural imaging technology.
Impact Magstim agreed to fund a 3 year PhD studentship to carry out research on microstructural imaging technology. We will recruit a PhD student to do the research funded by Magstim studentship.
Start Year 2016
 
Description Microscopic susceptibility anisotropy imaging 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution This was a collaboration based on orientational effects, spherical averaging and diffusion MRI - following visits from Enrico Karen to CUBRIC to discuss with members of the WSA group about microstructure.
Collaborator Contribution The paper was predominantly written by the team at UCL, with Enrico Kaden and Naomi Gyori, with additional team conversations held with Mark Does at Vanderbilt University
Impact " - Microscopic susceptibility anisotropy imaging" https://pubmed.ncbi.nlm.nih.gov/32378746/
Start Year 2019
 
Description Multi-Dimensional Diffusion Prepped MR Fingerprinting 
Organisation Case Western Reserve University
Country United States 
Sector Academic/University 
PI Contribution This is a joint collaboration with the team at Case Western Reserve University (Dan Ma and Mark Griswold). They are the inventors of MR Fingerprinting (MRF), and had not incorporated multi-dimensional (b-tensor) encoding into the MRF pipeline. Our team in Cardiff contributed the diffusion MR expertise to implement, analyse, interpret and debug the multi-dimensional diffusion-prepped MRF approach. The Cardiff team identified the source of artefact (cardiac pulsation) and this has led to further collaborations (papers under review) to get dMRF working without external pulse gating. Moreover, the Case Western team are co-PIs on an MRC-funded grant (led by Derek Jones)
Collaborator Contribution As noted above, this was a team effort with face-to-face visits and many regular Zoom calls to implement a multi-dimensional diffusion encoding. We had input from Filip Szczepankiewicz at Lund University (on spherical tensor encoding). Dan Ma implemented the sequence first at Case Western and it was ported, via PulseSeq, to CUBRIC.
Impact MR Fingerprinting with b-Tensor Encoding for Simultaneous Quantification of Relaxation and Diffusion in a Single Scan. Afzali M, Mueller L, Sakaie K, Hu S, Chen Y, Szczepankiewicz F, Griswold MA, Jones DK, Ma D. Magn Reson Med. 2022 Nov;88(5):2043-2057.
Start Year 2020
 
Description Multi-Dimensional Diffusion Prepped MR Fingerprinting 
Organisation Lund University
Country Sweden 
Sector Academic/University 
PI Contribution This is a joint collaboration with the team at Case Western Reserve University (Dan Ma and Mark Griswold). They are the inventors of MR Fingerprinting (MRF), and had not incorporated multi-dimensional (b-tensor) encoding into the MRF pipeline. Our team in Cardiff contributed the diffusion MR expertise to implement, analyse, interpret and debug the multi-dimensional diffusion-prepped MRF approach. The Cardiff team identified the source of artefact (cardiac pulsation) and this has led to further collaborations (papers under review) to get dMRF working without external pulse gating. Moreover, the Case Western team are co-PIs on an MRC-funded grant (led by Derek Jones)
Collaborator Contribution As noted above, this was a team effort with face-to-face visits and many regular Zoom calls to implement a multi-dimensional diffusion encoding. We had input from Filip Szczepankiewicz at Lund University (on spherical tensor encoding). Dan Ma implemented the sequence first at Case Western and it was ported, via PulseSeq, to CUBRIC.
Impact MR Fingerprinting with b-Tensor Encoding for Simultaneous Quantification of Relaxation and Diffusion in a Single Scan. Afzali M, Mueller L, Sakaie K, Hu S, Chen Y, Szczepankiewicz F, Griswold MA, Jones DK, Ma D. Magn Reson Med. 2022 Nov;88(5):2043-2057.
Start Year 2020
 
Description Nonivasive quantification of axon radii using diffusion MRI 
Organisation Champalimaud Foundation
Department Champalimaud Centre for the Unknown
Country Portugal 
Sector Academic/University 
PI Contribution This has been a large group effort to gain better estimates of axon diameter than the method we originally proposed in the Wellcome Strategic Award proposal (based on AxCaliber / AxCaliber3D). The initial project/collaboration was just with New York University (Centre for Biomedical Imaging) to provide a demonstration of utilising ultra-strong gradients (on the CUBRIC Connectom scanner) to estimate axon diameter in the living human brain, exploiting deviations from a power-law relationship between signal and diffusion-weighting. Once this proof-of-principle was established (with histological validation with our partners in the Champalimaud Centre for the Unknown in Lisbon), we extended this work to include another Connectom scanner at the Max Planck Institute in Leipzig to establish inter- and intra-site reproducibility/ repeatability. We continue to collaborate with Jelle Veraart on a number of projects exploiting this way to estimate axon diameter.
Collaborator Contribution Team effort - as described above. The original theoretical approach to estimating the axon diameter from the deviation from the power law was led by the team (Jelle Veraart at NYU), and the histological validation by the team at Champalimaud (Noam Shemesh). The Leipzig team, in the second paper, implemented the protocols we developed in Cardiff - and data were shared to enable the cross-site comparisons.
Impact Nonivasive quantification of axon radii using diffusion MRI. Veraart J, Nunes D, Rudrapatna U, Fieremans E, Jones DK, Novikov DS, Shemesh N. Elife. 2020 Feb 12;9:e49855. The variability of MR axon radii estimates in the human white matter. Veraart J, Raven EP, Edwards LJ, Weiskopf N, Jones DK. Hum Brain Mapp. 2021 May;42(7):2201-2213
Start Year 2019
 
Description Nonivasive quantification of axon radii using diffusion MRI 
Organisation Max Planck Society
Department Max Plank Institute for Human Cognitive and Brain Sciences
Country Germany 
Sector Academic/University 
PI Contribution This has been a large group effort to gain better estimates of axon diameter than the method we originally proposed in the Wellcome Strategic Award proposal (based on AxCaliber / AxCaliber3D). The initial project/collaboration was just with New York University (Centre for Biomedical Imaging) to provide a demonstration of utilising ultra-strong gradients (on the CUBRIC Connectom scanner) to estimate axon diameter in the living human brain, exploiting deviations from a power-law relationship between signal and diffusion-weighting. Once this proof-of-principle was established (with histological validation with our partners in the Champalimaud Centre for the Unknown in Lisbon), we extended this work to include another Connectom scanner at the Max Planck Institute in Leipzig to establish inter- and intra-site reproducibility/ repeatability. We continue to collaborate with Jelle Veraart on a number of projects exploiting this way to estimate axon diameter.
Collaborator Contribution Team effort - as described above. The original theoretical approach to estimating the axon diameter from the deviation from the power law was led by the team (Jelle Veraart at NYU), and the histological validation by the team at Champalimaud (Noam Shemesh). The Leipzig team, in the second paper, implemented the protocols we developed in Cardiff - and data were shared to enable the cross-site comparisons.
Impact Nonivasive quantification of axon radii using diffusion MRI. Veraart J, Nunes D, Rudrapatna U, Fieremans E, Jones DK, Novikov DS, Shemesh N. Elife. 2020 Feb 12;9:e49855. The variability of MR axon radii estimates in the human white matter. Veraart J, Raven EP, Edwards LJ, Weiskopf N, Jones DK. Hum Brain Mapp. 2021 May;42(7):2201-2213
Start Year 2019
 
Description Nonivasive quantification of axon radii using diffusion MRI 
Organisation New York University
Country United States 
Sector Academic/University 
PI Contribution This has been a large group effort to gain better estimates of axon diameter than the method we originally proposed in the Wellcome Strategic Award proposal (based on AxCaliber / AxCaliber3D). The initial project/collaboration was just with New York University (Centre for Biomedical Imaging) to provide a demonstration of utilising ultra-strong gradients (on the CUBRIC Connectom scanner) to estimate axon diameter in the living human brain, exploiting deviations from a power-law relationship between signal and diffusion-weighting. Once this proof-of-principle was established (with histological validation with our partners in the Champalimaud Centre for the Unknown in Lisbon), we extended this work to include another Connectom scanner at the Max Planck Institute in Leipzig to establish inter- and intra-site reproducibility/ repeatability. We continue to collaborate with Jelle Veraart on a number of projects exploiting this way to estimate axon diameter.
Collaborator Contribution Team effort - as described above. The original theoretical approach to estimating the axon diameter from the deviation from the power law was led by the team (Jelle Veraart at NYU), and the histological validation by the team at Champalimaud (Noam Shemesh). The Leipzig team, in the second paper, implemented the protocols we developed in Cardiff - and data were shared to enable the cross-site comparisons.
Impact Nonivasive quantification of axon radii using diffusion MRI. Veraart J, Nunes D, Rudrapatna U, Fieremans E, Jones DK, Novikov DS, Shemesh N. Elife. 2020 Feb 12;9:e49855. The variability of MR axon radii estimates in the human white matter. Veraart J, Raven EP, Edwards LJ, Weiskopf N, Jones DK. Hum Brain Mapp. 2021 May;42(7):2201-2213
Start Year 2019
 
Description Renishaw Plc 
Organisation Renishaw PLC
Country United Kingdom 
Sector Private 
PI Contribution We have recruited one student Iain Majer to the PhD studentship. Iain, however, left the programme due to ill health. We are currently recruiting a replacement student.
Collaborator Contribution Renishaw provided the PhD CASE Studentship to fund the PhD research study to be carried out.
Impact Renishaw provided the PhD CASE Studentship to fund the PhD research study to be carried out.
Start Year 2016
 
Description Robust Diffusion Kurtosis Imaging 
Organisation Aarhus University
Country Denmark 
Sector Academic/University 
PI Contribution This was a team effort to robustify the estimate of diffusion kurtosis. The first author (Rafael Henriques) came to Cardiff to collect data on our Connectom scanner and this lead to conversations about characterisation of non-Gaussian diffusion. We have collectively implemented double diffusion encoding on the Connectom with a view to characterising micro-kurtosis using correlation tensor imaging.
Collaborator Contribution As noted - this is a joint collaboration. Rafael Henriques (Champalimaud Centre for the Unknown) was the main 'hands on' driver of this work, and our collaborators in Aarhus University (Sune Jespersen) and New York University (Jelle Veraart) provided additional theoretical input. We will continue to work on the implementation of correlation tensor imaging together (with a recently made plan to extend to characterisation of the tumour microenvironment in prostate cancer).
Impact Toward more robust and reproducible diffusion kurtosis imaging. Henriques RN, Jespersen SN, Jones DK, Veraart J. Magn Reson Med. 2021 Sep;86(3):1600-1613.
Start Year 2020
 
Description Robust Diffusion Kurtosis Imaging 
Organisation Champalimaud Foundation
Department Champalimaud Centre for the Unknown
Country Portugal 
Sector Academic/University 
PI Contribution This was a team effort to robustify the estimate of diffusion kurtosis. The first author (Rafael Henriques) came to Cardiff to collect data on our Connectom scanner and this lead to conversations about characterisation of non-Gaussian diffusion. We have collectively implemented double diffusion encoding on the Connectom with a view to characterising micro-kurtosis using correlation tensor imaging.
Collaborator Contribution As noted - this is a joint collaboration. Rafael Henriques (Champalimaud Centre for the Unknown) was the main 'hands on' driver of this work, and our collaborators in Aarhus University (Sune Jespersen) and New York University (Jelle Veraart) provided additional theoretical input. We will continue to work on the implementation of correlation tensor imaging together (with a recently made plan to extend to characterisation of the tumour microenvironment in prostate cancer).
Impact Toward more robust and reproducible diffusion kurtosis imaging. Henriques RN, Jespersen SN, Jones DK, Veraart J. Magn Reson Med. 2021 Sep;86(3):1600-1613.
Start Year 2020
 
Description Robust Diffusion Kurtosis Imaging 
Organisation NYU Langone Medical Center
Country United States 
Sector Academic/University 
PI Contribution This was a team effort to robustify the estimate of diffusion kurtosis. The first author (Rafael Henriques) came to Cardiff to collect data on our Connectom scanner and this lead to conversations about characterisation of non-Gaussian diffusion. We have collectively implemented double diffusion encoding on the Connectom with a view to characterising micro-kurtosis using correlation tensor imaging.
Collaborator Contribution As noted - this is a joint collaboration. Rafael Henriques (Champalimaud Centre for the Unknown) was the main 'hands on' driver of this work, and our collaborators in Aarhus University (Sune Jespersen) and New York University (Jelle Veraart) provided additional theoretical input. We will continue to work on the implementation of correlation tensor imaging together (with a recently made plan to extend to characterisation of the tumour microenvironment in prostate cancer).
Impact Toward more robust and reproducible diffusion kurtosis imaging. Henriques RN, Jespersen SN, Jones DK, Veraart J. Magn Reson Med. 2021 Sep;86(3):1600-1613.
Start Year 2020
 
Description Scanner manufacturer Siemens 
Organisation Siemens Healthcare
Country Germany 
Sector Private 
PI Contribution We've been collaborating with Siemens on multiple aspects.
Collaborator Contribution Siemens are closely involved from the start to ensure correct installation and working of the 3TM scanner Connectom. They are keen to remain involved in its development.
Impact The 3TM Connectom MRI scanner has been delivered and installed in CUBRIC Centre. We have received a 64 channel head coil from Siemens for the Connectom scanner.
Start Year 2016
 
Description Spherical averaging of diffusion MRI signals with imperfect coverage of the unit sphere 
Organisation Linkoping University
Department Department of Biomedical Engineering (IMT)
Country Sweden 
Sector Academic/University 
PI Contribution This was a collaboration to identify the best and most robust way to estimate the spherical average of the diffusion-weighted MRI signal and coping with imperfect coverage of a unit-sphere. This was really an extended discussion with iterations between data collection in Cardiff, in silico simulations and visualisation of results. the paper on this topic was written by Maryam Afzali in Cardiff.
Collaborator Contribution The Linkoping team (Ozarslan and Knuttson) predominantly contributed on the theoretical side of the different analyses of encoding schemes. All parties were involved in analysis and interpretation of the data and reviewing the paper.
Impact Computing the orientational-average of diffusion-weighted MRI signals: a comparison of different techniques. Afzali M, Knutsson H, Özarslan E, Jones DK. Sci Rep. 2021 Jul 12;11(1):14345.
Start Year 2020
 
Description TracInnovations 
Organisation TracInnovations ApS
Country Denmark 
Sector Private 
PI Contribution TracInnovations makes an markerless optical tracking system for prospective/retrospective motion correction in the MRI scanner (see: https://tracinnovations.com/) The EPSRC equipment grant includes provision for an optical tracking system. While we originally intended to purchase another system (from Kineticor), the TracInnovations solution appears optimal. However, the challenge is that the system was developed for another MRI scanner - and interfacing it into the Connectom scanner (funded by this grant) is challenging due to reduced field-of-view afforded by the RF hardware, and due to the smaller bore of the scanner. We have therefore committed to explore ways in which we can develop solutions (with the company) to get the system to work in the Connectom. This includes some preliminary work on an alternative system in CUBRIC (a 3T Prisma system)
Collaborator Contribution The company has agreed to hold regular (monthly) teleconferences with D. Jones, and to provide materials and spare parts to help develop solutions to this problem, with joint team meetings to review progress and results.
Impact None yet
Start Year 2020
 
Description Tract Specific Measurements 
Organisation Swiss Federal Institute of Technology in Lausanne (EPFL)
Country Switzerland 
Sector Public 
PI Contribution This has been an extended collaboration with the group at EPFL and team members that have moved on, where we exploit the power of the Connectom gradients in CUBRIC to obtain suppression of the extra-axonal signal (for intra-axonal T2 measurements), for robust estimates of axon diameter (for tract-specific axon diameter measurements). We have hosted Muhamed Barakovic, Simona Schiavi etc. - and have had extensive face-to-face and Zoom calls with various members of the team (some of which have moved on to University of Verona (Schiavi) and Basel (Barakovic), but we continue to collaborate
Collaborator Contribution Extended discussions - as noted above. Incoming lab visits and provided foreground 'know how' on the COMMIT framework which sits at the base of much of the collaboration.
Impact Resolving bundle-specific intra-axonal T2 values within a voxel using diffusion-relaxation tract-based estimation. Barakovic M, Tax CMW, Rudrapatna U, Chamberland M, Rafael-Patino J, Granziera C, Thiran JP, Daducci A, Canales-Rodríguez EJ, Jones DK. Neuroimage. 2021 Feb 15;227:117617. Measuring compartmental T2-orientational dependence in human brain white matter using a tiltable RF coil and diffusion-T2 correlation MRI. Tax CMW, Kleban E, Chamberland M, Barakovic M, Rudrapatna U, Jones DK. Neuroimage. 2021 Aug 1;236:117967. Bundle-Specific Axon Diameter Index as a New Contrast to Differentiate White Matter Tracts. Barakovic M, Girard G, Schiavi S, Romascano D, Descoteaux M, Granziera C, Jones DK, Innocenti GM, Thiran JP, Daducci A. Front Neurosci. 2021 Jun 15;15:646034. Bundle myelin fraction (BMF) mapping of different white matter connections using microstructure informed tractography. Schiavi S, Lu PJ, Weigel M, Lutti A, Jones DK, Kappos L, Granziera C, Daducci A. Neuroimage. 2022 Apr 1;249:118922.
Start Year 2020
 
Description Tract Specific Measurements 
Organisation University of Verona
Country Italy 
Sector Academic/University 
PI Contribution This has been an extended collaboration with the group at EPFL and team members that have moved on, where we exploit the power of the Connectom gradients in CUBRIC to obtain suppression of the extra-axonal signal (for intra-axonal T2 measurements), for robust estimates of axon diameter (for tract-specific axon diameter measurements). We have hosted Muhamed Barakovic, Simona Schiavi etc. - and have had extensive face-to-face and Zoom calls with various members of the team (some of which have moved on to University of Verona (Schiavi) and Basel (Barakovic), but we continue to collaborate
Collaborator Contribution Extended discussions - as noted above. Incoming lab visits and provided foreground 'know how' on the COMMIT framework which sits at the base of much of the collaboration.
Impact Resolving bundle-specific intra-axonal T2 values within a voxel using diffusion-relaxation tract-based estimation. Barakovic M, Tax CMW, Rudrapatna U, Chamberland M, Rafael-Patino J, Granziera C, Thiran JP, Daducci A, Canales-Rodríguez EJ, Jones DK. Neuroimage. 2021 Feb 15;227:117617. Measuring compartmental T2-orientational dependence in human brain white matter using a tiltable RF coil and diffusion-T2 correlation MRI. Tax CMW, Kleban E, Chamberland M, Barakovic M, Rudrapatna U, Jones DK. Neuroimage. 2021 Aug 1;236:117967. Bundle-Specific Axon Diameter Index as a New Contrast to Differentiate White Matter Tracts. Barakovic M, Girard G, Schiavi S, Romascano D, Descoteaux M, Granziera C, Jones DK, Innocenti GM, Thiran JP, Daducci A. Front Neurosci. 2021 Jun 15;15:646034. Bundle myelin fraction (BMF) mapping of different white matter connections using microstructure informed tractography. Schiavi S, Lu PJ, Weigel M, Lutti A, Jones DK, Kappos L, Granziera C, Daducci A. Neuroimage. 2022 Apr 1;249:118922.
Start Year 2020
 
Description Validating pore size estimates in a complex microfiber environment on a human MRI system 
Organisation East China Normal University (ECNU)
Country China 
Sector Academic/University 
PI Contribution We obtained the biomimetic phantoms, and oversaw the data collection and analysis - but this was really a team effort with colleagues from East China Normal University, National Yang Ming Chiao Tung University, Taipei, and University College London. The entire data collection / experiments were conducted in CUBRIC - hosting Chu-Chung Huang and Chin-Chin Hsu in CUBRIC for an extended visit to perform the validation
Collaborator Contribution Chu-Chung Huang and Chin-Chin Hsu were a key part of the MRI data acquisition and analysis for this collaboration, with Chu-Chung Huang leading the writing of the paper. Fenglei Zhou at UCL performed the electron-microscopy on the samples and did the analysis.
Impact Validating pore size estimates in a complex microfiber environment on a human MRI system. Huang CC, Hsu CH, Zhou FL, Kusmia S, Drakesmith M, Parker GJM, Lin CP, Jones DK. Magn Reson Med. 2021 Sep;86(3):1514-1530.
Start Year 2019
 
Description Validating pore size estimates in a complex microfiber environment on a human MRI system 
Organisation National Yang Ming University
Country Taiwan, Province of China 
Sector Academic/University 
PI Contribution We obtained the biomimetic phantoms, and oversaw the data collection and analysis - but this was really a team effort with colleagues from East China Normal University, National Yang Ming Chiao Tung University, Taipei, and University College London. The entire data collection / experiments were conducted in CUBRIC - hosting Chu-Chung Huang and Chin-Chin Hsu in CUBRIC for an extended visit to perform the validation
Collaborator Contribution Chu-Chung Huang and Chin-Chin Hsu were a key part of the MRI data acquisition and analysis for this collaboration, with Chu-Chung Huang leading the writing of the paper. Fenglei Zhou at UCL performed the electron-microscopy on the samples and did the analysis.
Impact Validating pore size estimates in a complex microfiber environment on a human MRI system. Huang CC, Hsu CH, Zhou FL, Kusmia S, Drakesmith M, Parker GJM, Lin CP, Jones DK. Magn Reson Med. 2021 Sep;86(3):1514-1530.
Start Year 2019
 
Description Validating pore size estimates in a complex microfiber environment on a human MRI system 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution We obtained the biomimetic phantoms, and oversaw the data collection and analysis - but this was really a team effort with colleagues from East China Normal University, National Yang Ming Chiao Tung University, Taipei, and University College London. The entire data collection / experiments were conducted in CUBRIC - hosting Chu-Chung Huang and Chin-Chin Hsu in CUBRIC for an extended visit to perform the validation
Collaborator Contribution Chu-Chung Huang and Chin-Chin Hsu were a key part of the MRI data acquisition and analysis for this collaboration, with Chu-Chung Huang leading the writing of the paper. Fenglei Zhou at UCL performed the electron-microscopy on the samples and did the analysis.
Impact Validating pore size estimates in a complex microfiber environment on a human MRI system. Huang CC, Hsu CH, Zhou FL, Kusmia S, Drakesmith M, Parker GJM, Lin CP, Jones DK. Magn Reson Med. 2021 Sep;86(3):1514-1530.
Start Year 2019
 
Title SYSTEM AND METHOD FOR MAGNETIC RESONANCE FINGERPRINTING WITH RELAXATION AND DIFFUSION DATA ACQUISITION 
Description A method for multi-dimensional, relaxation-diffusion magnetic resonance fingerprinting (MRF) includes performing, using a magnetic resonance imaging (MRI) system, a pulse sequence that integrates free-waveform b-tensor diffusion encoding into a magnet resonance fingerprinting pulse sequence to perform a multi-dimensional, relaxation-diffusion encoding while acquiring MRF signal evolutions, processing, using a processor, the acquired MRF signal evolutions to determine at least one relaxation parameter and at least one diffusivity parameter, and generating, using the processor, a report including at least one of the at least one relaxation parameter and the at least diffusivity parameter. 
IP Reference 17661736 
Protection Patent / Patent application
Year Protection Granted 2022
Licensed No
Impact None as yet. Follow-up papers that mean cardiac triggering is not needed are in the pipeline.
 
Description "Inside your Brain" - the Science Café programme featuring the WAND study 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact The Science Café programme "Inside your Brain" featuring the WAND (Welsh Advanced Neuroimaging Database) study was broadcast on 25th September 2018 on BBC Radio Wales - Prof Derek Jones, Dr Hannah Chandler and Dr John Evans from CUBRIC were interviewed in the programme, https://www.bbc.co.uk/programmes/m0000hq7. This promoted the WAND study to the general public, introduced the design of the study which included a session of the MRI scan in the EPSRC-funded Connectom scanner, and presented to the public the opportunity to participate in the study and how to contact the CUBRIC study team if they want to volunteer for it.
Year(s) Of Engagement Activity 2018
URL https://www.bbc.co.uk/programmes/m0000hq7
 
Description A presentation at the ISMRM 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We submitted the abstract entitled "Disentangling in two dimensions in the living human brain: Feasibilty of relaxometry diffusometry using ultra-strong gradients" by
Chantal MW Tax , Umesh S Rudrapatna , Thomas Witzel , and Derek K Jones and it was accepted for an oral presentation at the Annual Scientific Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM) on 22-28 April 2017. We intend to show our first results generated from 3TM scanner, and engage the MR physics community and beyond through the biomedical MR conferences like the ISMRM.
Year(s) Of Engagement Activity 2017
 
Description A talk on Connectom entitled "New Windows on Brain Structure and Function" at the Siemens Lunch Symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Prof Derek Jones, Director of CUBRIC, has given a talk on Connectom entitled "New Windows on Brain Structure and Function" at the Siemens Lunch Symposium on 19th June 2018 during the 26th Annual Scientific Meeting of the ISMRM in Paris, reaching an audience of 4,000 to 4,500 people worldwide, https://www.healthcare.siemens.com/magnetic-resonance-imaging/magnetom-world/clinical-corner/clinical-talks/new-windows-on-brain-structure-and-function.html . As a direct result, Siemens Healthineers committed to putting a Siemens scientist permanently on site to work with the CUBRIC Connectom physicist. This includes a new venture, i.e. imaging 'below the neck' where Cardiff University will be the world's first site to explore these new applications.
Year(s) Of Engagement Activity 2018
URL https://www.healthcare.siemens.com/magnetic-resonance-imaging/magnetom-world/clinical-corner/clinica...
 
Description Academic collaborations arisen from the 'outreach' activities 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We have initiated projects (with data collection) with: New York University (investigator = Jelle Veraart), Alicante (investigator = Silvia de Santis), University of Lund (investigator = Filip Szczepankiewiecz), University of Pavia (investigator = Giovanni Savini), University of Antwerp (investigator = Ben Jeurissen), University of Melbourne (investigator = Sila Genc), and with several UK Universities (Manchester University; Nottingham University; Swansea University; University College London). These academic collaborations have arisen from 'outreach' activities, including actively communicating with researchers who we believe could benefit from the enhanced capability of the system.
Year(s) Of Engagement Activity 2017,2018
 
Description BBC news release 
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 We engaged with the BBC news to have a detailed 3 minute feature on the system on the main 6 pm and 10 pm bulletins (see https://vimeo.com/224202631), the BBC news website, and the feature was broadcast and taken up by news agencies around the world. This publicity clearly engaged the general public (based on number of enquiries received), raised their awareness of the Connectom scanner, following which they might volunteer to be the participants of the MRI physics development work. It will also provide additional inspiration for artists to produce the artwork and help us with the delivery of the art-science collaboration project for better public engagement.
Year(s) Of Engagement Activity 2017
URL https://vimeo.com/224202631
 
Description BBC visit 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact The BBC is coming to visit CUBRIC Centre at the end of this month March 2017 - specifically to feature the National Microstructure Imaging Facility on the main news bulletin.
Year(s) Of Engagement Activity 2017
 
Description Brain Night 
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 During the Brain Night event held on 6th December 2018 in CUBRIC, to better engage the members of the public, we uploaded the two video files containing the artworks created by our commissioned artist Shardcore (funded by the EPSRC engagement grant) onto the large screen in the Reception area. While talking with the audience about our neuroimaging research conducted in CUBRIC, we referred them to the large screen show to see how fascinating the imaging data collected from the Connectom scanner are - the beautiful artworks were created from a 100,000 fibre connectom dataset. The audience were very much impressed with the artistic way that the brain imaging data was presented through the art-science collaboration.
Conducting MRI scans in the EPSRC-funded Connectom scanner is part of the WAND (Welsh Advanced Neuroimaging Database) study. We set up a WAND stand, promoting the study to the members of public and it was well received at this fun social occasion. More than 70 printouts of the Volunteer Information Sheets, Debriefing Form and Study Consent Form were all taken away by the audience after their chatting with the CUBRIC researchers. They showed genuine interest in the study and asked questions about the different scan sessions.
Year(s) Of Engagement Activity 2018
URL http://www.youtube.com/watch?v=tGRrAbkFViI
 
Description Connectom scanner included in the BBC news 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact On 25th January 2018 BBC news, Dr Chantal Tax from CUBRIC talked with singer Charlotte Church about the Connectom scanner on the BBC http://www.bbc.co.uk/news/uk-wales-42805693. An actual picture of living brain connections taken by the Connetom scanner was included in the BBC news. It helped maximise the impact of the methodological advances facilitated by the advanced facility.
Year(s) Of Engagement Activity 2018
URL http://www.bbc.co.uk/news/uk-wales-42805693
 
Description First NMIF Conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact On 31st January - 1st February 2017, we held our first National Microstructural Imaging Facility (NMIF) conference, show casing the facility - with 150+ international attendees, and supported by the EPSRC grant.
Year(s) Of Engagement Activity 2017
 
Description Oral Presentations, e-poster and power pitch at the 26th ISMRM 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We submitted abstracts to the Annual Scientific Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM). This is the premier international meeting for MRI research, drawing 6500-8000 attendees from all over the world. At the 26th Annual Scientific Meeting of the ISMRM (on 16-21 June 2018 in Paris, France) CUBRIC researchers will be giving three oral presentations based on the accepted abstracts entitled " The Dot - Wherefore Art Thou? Search for the isotropic restricted diffusion compartment in the brain with spherical tensor encoding and strong gradients ", "Strategies for correcting gradient-nonlinearity effects in ultra-high gradient Diffusion MRI experiments", "Cross-vendor and Cross-protocol harmonisation of diffusion MRI data: a comparative study", one Power pitch entitled "What is the feasibility of estimating axonal conduction velocity from in vivo microstructural MRI?", and one e-poster entitled "the neurosurgical implication of scanner, gradient performance and acquisition protocol on Meyer's loop reconstruction". They will show our early results generated from 3TM Connectom scanner. Also, based on their accepted abstracts, Collaborators from New York University will be presenting one oral presentation entitled "Breaking the power law scaling of the dMRI signal on the Connectom scanner reveals its sensitivity to axon diameter" and one e-poster entitled "In vivo feasibility and reproducibility study on bundle-specific axon diameter mapping at 300mT/m" to maximize the impact of research enabled by Connectom scanner. We will keep engaging the MR physics community and beyond through the biomedical MR conferences like the ISMRM.
Year(s) Of Engagement Activity 2018
 
Description Oral Presentations, power pitches, and e-posters at the 27th ISMRM 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We submitted abstracts to the Annual Scientific Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM). This is the premier international meeting for MRI research, drawing 6500-8000 attendees from all over the world. At the 27th Annual Scientific Meeting of the ISMRM (on 11-16 May 2019 in Montreal, Canada) CUBRIC researchers will give 6 oral presentations based on the accepted abstracts entitled "Comparison of different tensor encoding combinations in microstructural parameter estimation", "Metrics that Matter: Improved statistical power to detect differences in tissue microstructure through dimensionality reduction", "New insights into the development of white matter microstructure across childhood and adolescence from ultra-strong gradients", "Separating intra- and extra-axonal susceptibility effects using a Diffusion-Filtered Asymmetric Spin Echo (D-FASE) sequence", "Diffusion MRI with b=1000 s/mm2 at TE < 22 ms using single-shot spiral readout and ultra-strong gradients: Implications for microstructure imaging", "Characterizing diffusion of myelin water in the living human brain using ultra-strong gradients and spiral readout", and 2 power pitches entitled "Mapping axonal conduction velocities from in vivo MRI data", "A GRANDIOSE sequence to time-lock BOLD and diffusion-weighted fMRI contrasts in humans using ultra-strong gradients and spirals", as well as 6 digital posters, entitled "Characterising tissue heterogeneity in cerebral metastases using multi-shell multi-tissue constrained spherical deconvolution", "Powering Up Microstructural Imaging: assessing cross-metric and cross-tract statistical power on an ultra-strong gradient MRI system", "What are the consequences of ignoring non-Gaussian diffusion in models of convection-enhanced drug delivery to the human brain?", "Gradient profiles of myelin and microstructure metrics across the developing brain", "Can unprecedented echo times in human diffusion weighted fMRI help reveal its biological underpinnings?", "Tractography of complex white matter bundles: limitations of diffusion MRI data upsampling". Besides, based on the accepted abstracts on our collaborative work with others, 3 oral presentations will be given, entitled "Mapping of fibre-specific relaxation and diffusivities in heterogeneous brain tissue" (collaborating with Lund University), "Temporal Diffusion Ratio (TDR): A Diffusion MRI technique to map the fraction and spatial distribution of large axons in the living human brain" (collaborating with King's College London), "A Joint Recommendation for Optimized Preprocessing of Connectom Diffusion MRI Data" (collaborating with Max Planck Institute, Leipeig & Harvard Medical School). One digital poster will also be presented, entitled "Double diffusion encoding enables unique parameter estimation of the Standard Model in diffusion MRI" (collaborating with University of Leeds). The results generated from the EPSRC funded 3TM Connectom scanner will be presented at the ISMRM to maximize the impact of research enabled by Connectom scanner. We will keep engaging the MR physics community and beyond through the biomedical MR conferences like the ISMRM.
Year(s) Of Engagement Activity 2019
URL https://www.ismrm.org
 
Description Part of the Open Day tour presented to potential undergraduate candidates and their parents 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact We took the undergraduate candidates and their parents to the Connectom scanner lab as part of their Open Day tour. Images generated by the Connectom scanner were presented to them in comparison with those taken from 3T Prisma scanners and 7T scanner. The benefits for neuroimaging research and clinical applications enabled by the Connectom scanner were well received by the visitors. They were impressed by the advanced facilities and the impact of research in improving understanding of the human brain. We will hold more Open Day tours in the coming months.
Year(s) Of Engagement Activity 2018,2019
 
Description Public Understanding of Science in Health (PUSH) lecture series presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact On 8th Feb 2018, as part of the Public Understanding of Science in Health (PUSH) lecture series, Prof Derek Jones from CUBRIC gave a presentation entitled 'Advances in Imaging the Human Brain: The CUBRIC Story'. The presentation was supported by a team from CUBRIC and included live presentations of fMRI and MEG (via video link back to CUBRIC), and EEG and TMS (in the lecture theatre). This public lecture was open to all, but was to encourage A-level students to consider STEM subjects for their careers.
Year(s) Of Engagement Activity 2018
 
Description Seminar on phantoms 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact On Monday 5th Feb 2018, Prof Geoff Parker, from University of Manchester gave us a seminar entitled "Biomimetic phantoms for microstructural imaging". The talk focused on the latest developments in microstructural imaging phantoms, and covered the methods of production of phantoms derived from a range of novel materials for diffusion MRI, designed to mimic white matter, grey matter and pathology including tumours and examples of their use for validation diffusion MRI methods and in multicentre studies. The talk was of interest and beneficial to researchers on microstructural imaging brain research.
Year(s) Of Engagement Activity 2018
 
Description YouTube video about the Connectom scanner 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact The YouTube video about the Connectom scanner made by Tom Scott (and filmed by Paul Allen, School of Psychology) has just passed 201,110 views! Prof Derek Jones, Director of CUBRIC gave the lay talk in the video to raise the general public's awareness of the stunning images enabled by the Connectom scanner. The impressive number of YouTube hits so far showed the scale of engagement from the general public which maximised the impact of the methodological advances facilitated by the advanced facility.
Year(s) Of Engagement Activity 2017,2018
URL https://www.youtube.com/watch?v=diPiSHxfGyE&feature=youtu.be