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May 2014




Andrada Ianus and Ivana Dronjak launched the MISST software on 12.05.2014:

Microstructure Imaging Sequence Simulation Toolbox (MISST) is a practical diffusion MRI simulator for development, testing, and optimisation of novel MR pulse sequences for microstructure imaging. 



Gemma Morgan, Maria Tariq, Danny Alexander had paper accepted at MICCAI.

Tom Vercauteren joined as Senior Lecturer



March 2014



Joseph Jacobs has been awarded a Research Excellence Studentship by the Department of Computer Science for the duration of his PhD.

Alexandra Young's paper 'A data-driven model of biomarker changes in sporadic Alzheimer's disease' was accepted for publication in Brain.

Alexandra Young was accepted for an oral presentation at AAIC 2014.



January 2014




24th January 2014 -- A workshop on Computational Diffusion MRI is organised by Gemma Nedjati-Gilani and Torben Schneider, together with colleagues from Brigham and Women's Hospital Boston and University Hospital Freiburg. The workshop will take place at the MICCAI conference in Boston later this year and the proceedings will be published by Springer as a volume in the Mathematics and Visualization series. It is the 7th consecutive year in which this workshop is organised by members of CMIC's Microstructure Imaging Group.


Laura Panagiotaki's VERDICT paper got accepted to Cancer Research.

Uran Ferizi and Simon Richardson both had journal papers accepted to MRM.

Papers accepted to IPCAI: Max Allan, Geoffrey Jones, Martin Kochan, Ping-lin Chang, Gergely Zombori


September 2013



A US patent has been granted on a model-based registration method developed by Yipeng Hu and Dean Barratt.


Yipeng Hu's 2012 Medical Image Analysis paper on MR-US prostate registration has been nominated by the publishers as among the ScienceDirect "Hottest 25" papers of 2012 published in the journal, based on downloads and citations. It has been entered for a presentation competition connected with this.


Ivor Simpson has won one (of the 5) MICCAI Young Scientist Award at MICCAI 2013.


Uran Ferizi oral presentation at MICCAI 2013.


Papers accepted:


SCoRS - A method based on stability for feature selection and mapping in neuroimaging. Rondina JM, Hahn T, Oliveira L, Marquand A, Dresler T, Leitner T, Fallgatter AJ, Shawe-Taylor J, Mourao-Miranda J. IEEE Transaction in Medical Images (accepted)

Lianghao Han has also recently had a paper accepted by IEEE Trans Medical Imaging: 'A Non-linear Biomechanical Model Based Registration Method for Aligning Prone and Supine MR Breast Images'



Emma Malone : "Multifrequency Electrical Impedance Tomography using spectral constraints" -  IEEE Trans Med Im


Matthias Ehrhardt : "Vector-Valued Image Processing by Parallel Level Sets" -  IEEE Trans Image Processing





July 2013:


Papers accepted at IPMI:


Matt Rowe oral Beyond crossing fibers: Tractography exploiting sub-voxel fibre dispersion and neighbourhood structure

Enrico Kaden poster Can $ T_2 $-Spectroscopy Resolve Submicrometer Axon Diameters?


 April 2013:


Papers accepted:

James Martin’s PMB paper accepted on motion compensation in cone beam CT

Holger Roth et al’s paper in Radiology accepted on prone/supine CT colonography registration



L. Maier-Hein, P. Mountney, A. Bartoli, H. Elhawary, D. Elson, A. Groch, A. Kolb, M. Rodrigues, J. Sorger, S. Speidel, D. Stoyanov: Optical Techniques for 3D Surface Reconstruction in Computer-assisted Laparoscopic Surgery, Med Imag Anal, in press, 2013

Oliveira, L., Ladouceur, C.D., Phillips, M.L., Brammer, M., Mourao-Miranda, J., What does brain response to neutral faces tell us about major depression? Evidence from machine learning and fMRI. PLoS ONE (accepted)

Are recently joined the group:

We have a new PhD student in the group, Joao de Matos Monteiro, supported by the Portuguese Foundation for Science and Technology.

We also have a visiting PhD student from the Laboratory of Behavioral Neurophysiology at Federal Fluminense University (Brazil), Orlando Fernandes Junior, who will stay for 5 months.


Congratulations to Torben Schneider for his PhD.

Cognratulations to Ged and Lucy Ridgway on the birth of their daughter Iris!


March 2013:


Congratulations to Dr Holger Roth and to Dr Yipeng Hu for their PhD.

February 2013:


Congratulations to Pankaj Daga for his "Best Student Paper Award" at SPIE 2013.

Paper accepted:
Schrouff, J.*, Rosa, M. J.*, Rondina, J., Marquand, A., Chu, C., Ashburner, J., Phillips, C., Richiardi, J., Mourao-Miranda, J. PRoNTo: Pattern Recognition for Neuroimaging Toolbox, Neuroinformatics, 2013 (accepted). *co-first authors.
A.E. Rolls, C.V. Riga, D.V. Stoyanov, C. V. Shah, I. Van Herzeele, M. Hamady, N. J. Cheshire, C. D. Bicknell. A Pilot Study of Video-motion Analysis in Endovascular Surgery: Development of Real-time Discriminatory Skill Metrics. European Journal of Vascular and Endovascular Surgery
Jorge Cardoso: STEPS paper accepted (new image segmentation framework) in Medical Image Analysis
Natalie Ryan: BRAIN paper accepted about new diffusion imaging work revealing early changes in AD. Technical work of the paper entirely developed by CMIC (Danny, Gary, Seb's team are co-authors).
Abi: PLOS ONE paper accepted – title: "Atrophy rates in asymptomatic amyloidosis:  Implications for Alzheimer prevention trials"
Shiva/Gary and Seb's team: Longitudinal DTI pipeline (first of its kind) accepted to Neuroimage

ISMRM abstracts accepted as oral presentations for Simon Richardson and Matt Rowe.  Lots of others accepted as poster presentations.
Oral presentations for 5 of 7 NODDI abstracts at ISMRM (Gary  Hui Zhang)
David Atkinson team: 3 posters (Valentin Hamy, Rachel Chan, Nikos Dikaios), 2 oral (Alex Menys, Nikos Dikaios)
Alexandra Tobisch: Her MSc work with with Gary Hui Zhang  also accepted as an oral presentation at ISMRM
Adrienne Campbell (a recent PhD graduate from CABI): Her recent paper reporting a first-of-its-kind myocardial perfusion imaging technique (multi-slice cardiac arterial spin labelling) is one of the three finalists for the prestigious I.I. Rabi award at ISMRM this year. Contributions with Gary Hui Zhang and Bernard Siow.

Cancer Centre Imaging Award

Congratulations to Ivana Drobnjak for two more additions to the family

January 2013:


Congratulations to Dr Gemma Nedgati-Gilani for her PhD.

A series of new grants awarded to CMIC Principal Investigators is the following areas: PET/MRI (Simon Arridge and Sebastien Ourselin), with MND Association (Daniel Alexander)

Papers' acceptance:
In JMR (Andrada Ianus)
In PLOS ONE (Shiva Keihaninejad), "TBSS analysis using cohort specific group-wise atlases"
In European Urology (Yipeng Hu, Dean Barratt), on cancer risk stratification following targeted prostate biopsy
In IEEE TMBE (Max Allan)

Congratulations to Andrew and Jenny Melbourne on the birth of their son Oliver Henry.

December 2012:


Welcome to Ilias Sioutis, new PhD student with Dan Stoyanov.


The Engineer published an article about Dan Stoyanov;s work:

The Engineer published an article about Dan’s work:

November 2012:


Congratulations to Jamie McClelland for getting his review paper accepted into MedIA

Congratulations to Jorge Cardoso and Andrew Melbourne for getting their pre term segmentation work accepted to Neuroimage.

Great news about Danny Alexander's CONNECT project and the first micro-struture atlas of the human brain.

Congratulations to Pankaj Daga for getting his registration and distortion correction pipeline integrated into the operation room (iMRI neurosurgery). "First-in-man" (or in woman in this case!) was achieved on Thursday, while a second case was done on Monday. For the first time, per-operative information of the optic radiation location can be propagate from pre-op high-res DTI into intra-op DTI, compensating for brain shift and EPI distortion, in less than 5 minutes.

Good luck to Max Allan, PhD student, who is joining Siemens Corporate Research (Princeton) for six months.

SPIE Medical Imaging 2013 -accepted papers:

1. Surface based prostate registration with biomechanical regularization (Paper 8671-62)
Wendy J.M. van de Ven, Yipeng Hu, Jelle O. Barentsz, Nico Karssemeijer, Dean Barratt, and Henkjan J. Huisman

2. Fully Automated Prostate Magnetic Resonance Imaging and Transrectal Ultrasound Fusion via a Probabilistic Registration Metric
(Paper 8671-10)
Rachel E. Sparks, Ernest Feleppa, B. Nicholas Bloch, Dean Barratt, and Anant Madabhushi.

October 2012 -  congratulations to Dr Jorge Cardoso for being awarded his PhD.   September 2012 - CMIC prizes at MICCAI 2012 (Nice, France):


Holger Roth: Abdominal Workshop prize

Sebastien Ourselin et al: Ventricle Segmentation challenge

September 2012 - welcome to new members of staff and students:


Welcome to Neil Oxtoby, Enrico Kaden and Matt Hall who joined Daniel Alexander's group recently.

And also to the new Mres/PhD students who enrolled Sept 2012: Eliza Orasanu, Angela D'Esposito, Felix Bragman, Zachary Eaton-Rosen, Laurence Jackson, Yanan Zhu, Alexandra Young, Martin Kochan, Lebina Shrestha, Ninon Burgos, Arun Niranjan.

August 2012 - congratulations to Dr Thomy Mertzanidou for being awarded her PhD.

FIMH 2013


CMIC, in collaboration with KCL and Imperial College, is organising the 7th International Conference on Functional Imaging and Modeling of the Heart.

June 2012:


CMIC is awarded 3 Smart Surgery Grant (for a total of £ 5M).

April 16th was a good week for CMIC:


 James Martin was awarded an Industrial Fellowships from the Royal Commission for the Exhibition of 1851 Celebrations next week. James gets an uplift to his stipend and funds to continue his research for a year after completion of his EngD.  

 After Marc Modat's recent CNT award, he was contacted by a freelancer from Nature and this resulted in a profile in Nature, see:

 Finally Hash Ahmed of the MIPI Group got the front page of the Daily Telegraph and BBC News on Monday for their latest clinical trial of High Intensity Focussed Ultrasound of the Prostate, just published in Lancet Oncology. MIPI (Minimally Invasive Prostate Interventions) includes Dean Barratt and Yipeng Hu from CMIC.

Computer Science Inaugural Alumni Dinner - Wedn. 16th November 2011 - UCL.

More on this event on by clicking on the link  

IPMI Erbsman Prize.

Hubert Fonteijn won the Erbsmann prize at the IPMI conference last week for his disease progression modelling work that he did while here at CMIC.  Fantastic news for Hubert, but also for all of us at CMIC.  The award is genuinely prestigious, because the IPMI conference itself is exclusive, and there is only one such award every two years dating back to the 80s. It is sort of a best-paper-at-conference award, although only first-time presenters under the age of 35 are eligible. The judges also consider the presentation quality, question handling and general contribution to the conference, so this is really a personal award to Hubert. Congratulations Hubert!

CMIC In The Engineer

The engineer recently ran an article on the collaborative programme grant awarded by the EPSRC.  the Engineer is a magazine covering the latest developments and business news and technology in the UK.  the article is available on The Engineer's website.  James Marti, a PhD student also had an article in the same magazine on a non medical imaging related subject.

EPSRC Programme Grant. Intelligent Imaging: Motion, Form and Function Across Scale.

Professor Dave Hawkes of the Centre for Medical Image Computing has been awarded £5.8M for a Programme Grant from EPSRC  with the title "Intelligent Imaging: Motion Form and Function across Scale". This will allow him and his team together with co-investigators at King's College London, Imperial and the Institute of Cancer Research to explore a new paradign in medical imaging in which computational models of anatomy, motion and microstructure are used to guide image acquisition to compute relevant visualisations and quantitative clinical parameters directly from acquisition data.

 This programme will be devising new ways to extract information which can be used to inform diagnosis and guide therapy directly from the measurements of the imaging device. The derivation of clinically-relevant information will drive the entire imaging process, unlike the current paradigm in which an image is acquired to a fixed protocol and then as a separate process that image is interpreted or processed to extract the relevant information. This will enable much closer coupling of acquisition and interpretation, speeding up the imaging process, allowing much more accurate information to be gathered from moving structures in the chest and abdomen, and potentially reducing radiation dose and cost. MR and CT image acquisition will be our main technology platform although the principles can be applied across the technology spectrum. We will be applying this methodology to better detect cancer and charaterise response to therapy of some of the most common and lethal cancers (lung, liver, breast, prostate, colon), cardiovascular disease and the health of the foetus and new born infant.

 This new Programme brings together researchers in medical imaging from KCL, Imperial and the Institute of Cancer Research to form an exceptionally strong London wide consortium. The Programme has close links with clinical researchers in London as well as excellent links with industry including large multinationals such as Philips and GSK and a number of SMEs in order to hasten translation of these opportunities to healthcare for the benefit of patients. This Programme will place London at the forefront of international activity in this competitive field.


Congratulations to Andrew and Jenny Melbourne on the birth of their daughter Isabel Katherine.  Andrew reports both are doing well.

EPSRC post Doctoral Fellowship

We are delighted to announce that Dr Marta Betcke won a prestigious EPSRC Post-doctoral Fellowship in Mathematical Sciences on Image Reconstruction: the Sparse Way.  Many congratulations to Marta.

Mark Lythgoe on the radio

A new 5 part series - Images That Changed The World -  on BBC Radio 4 presented by Dr Mark Lythgoe, Director for the Centre for Advanced Biomedical Imaging, UCL.

Mark tells the untold story of medical imaging and why uncovering our inner selves changed the world

Monday 25 to Friday 29 January at 15:45 and then downloadable on BBC iplayer at

Synopsis: Medical imaging has had a profound impact on all our lives. In this new five part series, I'll be exploring how techniques such as xrays, ultrasound, microscopy and magnetic resonance imaging (MRI) scans have allowed us to see deep inside our bodies, right to our broken bones and dividing cells. I'll be asking how imaging has impacted not only on healthcare but also on philosophy, art, literature and the general public consciousness, radically influencing the way we think about ourselves as human beings.

CMIC in the Newspaper

Sept 2009 Danny Alexander's diffusion group recently made the headlines in a Cretan newspaper.  See here for the article and here for a rough translation.

CASE studentships

CMIC has recently been awarded two industrial CASE studentships: one for the devlopment of novel imaging biomarkers in oncology and inflammation (with Ixico Ltd) and the other for the development of a visualisation system for integrating colonoscopy and microendoscopy (with Medicendo).

Comprehensive Cancer Imaging Centre

CRUK have awarded a significant grant to a joint Comprehensive Cancer Imaging Centre jointly to KCL and UCL, one of 4 UK Centres recently announced. The UCL component is led by Professors Richard Begent (Cancer Institute) with David Hawkes of CMIC as co-PI. More details can be found here.

SEPTEMBER 2008 UCL engineering at the BA Festival of Science

CMIC researchers took part in the BA Festival of Science last week as part of an exhibition to highlight the critical role that engineering and physical sciences play in healthcare. More information can be found here.

July 2008 EPSRC Fellowship

Dr Daniel Alexander has been awarded a prestigious EPSRC Leadership Fellowship. EPSRC Leadership Fellowships provide up to five years funding to talented early or mid-career researchers with the most potential to develop into the UK’s international research leaders of tomorrow. They provide an opportunity to concentrate on research for the period of the award, as well as supporting the cost of associated research for the full duration of the fellowship. The expectation is that fellows will have established themselves as leading researchers of international standing in their area by the end of the award, as well as demonstrating leadership within their institution and research community. More.


CMIC has had an outstanding 8 papers - 5 oral and 3 poster - accepted for the MICCAI 2008 conference, which will be held in New York this September.


Jamie McClelland has successfully defended his PhD thesis on 'Registration Based Respiratory Motion Models for use in Lung Radiotherapy'


Bea Sneller has successfully defended her PhD thesis


Dr. Sebastian Ourselin has recently joined CMIC as a Reader in Medical Image Computing. Sebastien previously led the BioMedIA Lab at CSIRO in Australia, where he held the posts of Associate Professor at the University of Queensland, Brisbane and University of New South Wales, Sydney.


Irina Waechter has won the MICCAI Young Scientist Award at the 10th Medical Image Computing and Computer Assisted Intervention conference. Her paper, entitled "Quantification of Blood Flow from Rotational Angiography", was selected as the best submission in the Innovative Clinical and Biological Applications category on the basis of its score following peer review. Zeike Taylor was also shortlisted for a prize in the Simulation and Visualization category, but was unfortunately pipped to the post.

CMIC researchers presented 5 papers at this year's MICCAI conference (3 oral presentations and 2 posters):

Methods for inverting dense displacement fields: evaluation in brain image registration. W. Crum, O. Camara, D. Hawkes3D Reconstruction of internal organ surfaces for minimal invasive surgery. M. Hu, G. Penney, P. Edwards, D. HawkesQuantification of blood flow from rotational angiography. I. Waechter, J. Bredno, D. Barratt, J. Weese, D. HawkesReal-time nonlinear finite element analysis for surgical simulation using graphics processing units. Z. Taylor, M. Cheng, S. OurselinAnisotropic wave propagation and apparent conductivity estimation in a fast electrophysiology model: application to XMR interventional imaging. P. Chinchapatnam, K. Rhode, A. King, G. Gao, Y. Ma, T. Scaheffter, D. Hawkes, R.S. Razavi, D. Hill, S. Arridge, M. Sermesant. OCTOBER 2007: CMIC RESEARCHERS AWARDED £5M EPSRC GRANT FOR RESEARCH INTO HIFU THERAPY

Dr. Dean Barratt and Prof. David Hawkes, together with colleagues from UCL Mechanical Engineering (Dr. Nader Safari and Dr. Eleanor Stride), The Institute of Cancer Research (Prof. Gail ter Haar and Dr. Ian Rivens), and Oxford University (Dr. Constantin Coussios), have been awarded a 5 year grant by the EPSRC to carry out research into image-guided, high-intensity focused ultrasound (HIFU) therapy of liver tumours.

The grant, worth approximately £5M in total (£1.5M of which is allocated to UCL researchers), aims to develop methods for accurate delivery of HIFU through the rib cage through the development and application advanced imaging, mathematical modelling, and microbubble techniques.

Further details can be found at: and


CMIC researchers, Oscar Camara-Rey, Bill Crum, Julia Schnabel, Ged Ridgway, and Derek Hill, together with Rachael Scahill and Nick Fox from the UCL Dimentia Research Centre, have won the best paper prize at this year's Medical Image Understanding and Analysis conference. 

Their paper is entitled: "Evaluation of local and global atrophy measurement techniques with simulated Alzheimer's disease images" Oscar Camara, Rachael I Scahill, William R Crum, Julia A Schnabel, Gerard R Ridgway, Derek LG Hill and Nick C Fox

The full proceedings can be found at:

JUNE 2007: Wateraid Munro Challenge

On the 9th June a team from CMIC successfully completed the Munro Challenge by climbing Sgurr Fhuaran and the other 5 Sisters of Kintail, on the Road to the Isles, NW Scotland. The weather was perfect and with no broken bones and only one twisted ankle! They raised £1212.57 for Wateraid (


(From left) David Atkinson, Xiahai Zhuang, Philip Batchelor (ex CMIC), Steve Thompson, Dave Hawkes, Dong-Ping Zhang (Imperial College London/honorary CMIC!), Dean Barratt and Mark White


Dave Hawkes, helped significantly by Christine Tanner and John Hipwell, has just been awarded an EPSRC grant to work with groups in Manchester, Oxford and the Institute of Cancer Research on a model based approach to comparing breast images.

INVERSE PROBLEMS - SIMON ARRIDGE IN "highlights of 2006" - MARCH 2007

Two articles by Simon are cited:
"Approximation errors and model reduction with an application in optical diffusion tomography", S R Arridge, J P Kaipio, V Kolehmainen, M Schweiger, E Somersalo, T Tarvainen and M Vauhkonen - Inverse Problems 22 No 1 (February 2006) 175-195. This one formed part of Simon's CMIC Open day talk

"Three-dimensional reconstruction of shape and piecewise constant region values for optical tomography using spherical harmonic parametrization and a boundary element method", Athanasios D Zacharopoulos, Simon R Arridge, Oliver Dorn, Ville Kolehmainen and Jan Sikora - Inverse Problems 22 No 5 (October 2006) 1509-1532. This one was by IRC PhD student (now a post doc in CMIC)

(More on:


Andrew Todd-Pokropek, Dave Hawkes, Damien Buie and Ron Gastion went to Vienna for CMIC and manned the CMIC stand in the Imagine Exhibition. See pictures here and here. More on the ESR.


Dave Hawkes, helped significantly by Christine Tanner and John Hipwell, has just been awarded an EPSRC grant to work with groups in Manchester, Oxford and the Institute of Cancer Research on a model based approach to comparing breast images. More


CMIC members entered images. Where art meets research... See for yourself: The Glass Skull (by Dean Barratt).


Dean Barratt and Tim Carter win the "Post-Graduate, Staff and Alumni" category of the Idea Assessment stage of the London Entrepreneur's Challenge 2006/7. Congratulations to them both!


Tim Carter walks off with the 2nd prize for his presentation A Framework for Image-Guided Breast Surgery. Congratulations to him!


The 3rd Prize of the Young Investigator Competition goes to Irina Waechter for her presentation Using Flow Information to support 3D Vessel Reconstruction. Congratulations to her!


Dean Barratt has been awarded one of the eight research fellowships presented by the Royal Academy of Engineering this year. Congratulations to him! More.


To celebrate the opening of the Centre for Medical Image Computing (CMIC) at UCL we held a workshop on  April 3rd 2006 from 10:00am at the Darwin Lecture Theatre, UCL, Gower Street, London, followed by presentations and demonstrations in the Malet Place Engineering Building. Professor Sir Michael Brady gave our keynote presentation. more. An online version of the CMIC Opening Workshop brochure is available.


CMIC's Research Fellow Dean Barratt was invited to present a poster on his research at the House of Commons on 13 March 2006 as part of the UK National Science Week. More information can be found at


Professor David Hawkes has been invited to give the Wilhelm Roentgen Lecture at the European Congress of Radiology on Saturday 4th March 2006


Congratulations to the following for successfully defending their PhD theses

Christine Tanner - 11 Jan 06 Carolyn Chan - 21 Dec 05 Adam Chandler - 14 Dec 05

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