2nd International Training School on PET-MRI Engineering

April 27-30, 2015, 2015, University of Leeds, United Kingdom

General DescriptionApplication ProcessStudents SupportAccomodationVenue | Committees | Contact | Tentative program | Detailed program | School Events

General Description

The COST Action TD1007: "Bimodal PET-MRI molecular imaging technologies and applications for in vivo monitoring of disease and biological processes" and the EPSRC Computational Collaborative Project (CCP) “Synergistic PET-MR Reconstruction” co-organise the "2nd International Training School on PET-MRI Engineering". The School will focus on the Software aspects of PET-MRI technology and is open for early stage researchers (ESRs) without or with a PhD (less than 3 years) interested in this interdisciplinary, emerging topic. 
The training school will take place in Leeds (UK), from the 27th to 30th April, 2015. Members of the COST Action TD1007, CCP on “Synergistic PET-MR Reconstruction”, young lecturers and invited speakers will share their experience on PET-MRI basics and detailed aspects of: Multimodality Image Processing, Simulation tools, Reconstruction & Corrections, Acquisition Protocols and Kinetic Modelling as well as Quantitative Imaging. 
The Training School will be held only a few weeks before the annual International Conference:  4th Conference on PET/MR and SPECT/MR, which will take place between the 18th and 20th May 2015 in Elba island, Italy and Training School participants are encouraged to attending this event as well.

Application Process
At least 25 studentships will be available. ESRs interested to apply for attending the school should send i) a short motivation letter and ii) a short CV to  gloudos[at]teiath[dot]gr.
The deadline for applications is March 20th, 2015.
The aim of the school organizers is to have a fair geographical distribution, thus the selection process will take into account the participation of students from different countries and laboratories, as well as gender balance issues.

Student Support
There will be
no registration fee and the COST Action and the CCP on “Synergistic PET-MR Reconstruction” will support at least 25 students, including travel and accommodation expenses. For international (non UK) students, this support will be in the form of a fixed grant of 600€.
To be eligible for this grant, students must be affiliated  with one of the 35 COST Member Countries (excluding UK) which are: Austria, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Iceland, Ireland, Italy, Latvia, Lithuania, Luxembourg, Malta, The Netherlands, Norway, Poland, Portugal, Romania, Serbia, Slovakia, Slovenia, Spain, Sweden, Switzerland, Turkey and the former Yugoslav Republic of Macedonia.
Some additional student support will be possible for UK students as well.

The proposed accommodation will be at IBIS Leeds Centre Hotel, which has offered room availability for all at good prices. The hotel is very close to the train station, which connects Leeds to other cities such as London (a little longer than 2 hours), Manchester (less than an hour) and York (20mins). Also the area around Leeds City Centre is rather alive in the night for a "last drink"!

The School this year will take place in Leeds. Leeds is the third largest city of the UK and the financial centre of Yorkshire, the largest county of England. The event is held at the University of Leeds campus. The University of Leeds is the second largest university in the UK and its campus is located at the heart of Leeds city. More directions on how to reach the University can be found here. For directions within campus you can check the campus interactive map. The school will take place at the Fairbairn House Main Building Lower Chapel LR. Entrance is on the outside left of the building. There are some stairs and then on the right we reach the entrance to the Lower Chapel.

Organizing Committee
Charalampos Tsoumpas, University of Leeds, United Kingdom
George Loudos, Technological Educational Institute of Athens, Greece
Steven Sourbron, University of Leeds, United Kingdom
Kris Thielemans, University College London, United Kingdom

Advisory Committee
Brian Hutton, University College London, United Kingdom
Dimitris Visvikis, LaTIM, INSERM UMR1101, France

For application to the school or questions, you can send an e-mail to
George Loudos at gloudos[at]teiath[dot]gr.

Tentative Programme

Monday 27 April 2015

Introduction to the Training Course: Charalambos Tsoumpas, Athens (10 minutes)

Basics of PET & MRI - Image formation & hardware (3 hours)

PETMattia Veronese, London
MRIKaveh Vahedipour, New York

Hardware and engineering solutions: George Loudos, Athens

Changing the contrast (2 hours)

PET: Tracers, SUV & Pharmacokinetics: Mattia Veronese, London
MRI: Pulse sequences & image contrast: Nikos Dikaios, London

Research Communication (2 hours)

Introduction to the hot topic question: PET/MRI or PET+MRI? Steven Sourbron & David Buckley & Harry Tsoumpas, Leeds

Communicating your research: Steve Smye, Leeds

Tuesday 28 April 2015

Data simulation: the forward problem

Digital Anthropomorphic phantoms: Panagiotis Papadimitroulas, Athens (1 hour)

Simulation Theory on PETJulien Bert, Brest (1.5 hours)

PET simulation software demonstrationJulien Bert, Brest & Panagiotis Papadimitroulas, Athens (1.5 hours)

Simulation Theory on MR: Kaveh Vahedipour, New York (1.5 hours)

MR simulation software demonstrationKaveh Vahedipour, New York (1.5 hours)
The COST Action TD1004 on PET/MR: George Loudos, Athens (0.5 hours)

Wednesday 29 April 2015

Data post-processing: the inverse problem

PET Image Reconstruction & CorrectionsKris Thielemans, London, Hadi Fayad, Brest & Nikos Efthimiou, Athens (2 hours)

Demonstration of STIRKris Thielemans, London & Harry Tsoumpas, Leeds (1.5 hours)

MRI Image Reconstruction: Claudia Prieto, London (1 hours)

Software Demonstration of MRI undersampled reconstructionClaudia Prieto & Christoph Kolbitsch, London (1.5 hours)

Multimodality Image Processing (localisation and segmentation): Mathieu Hatt, Brest (1 hour)

Thursday 30 April 2015

PET-MRI: Pitfalls, opportunities & open problems

The clinician’s perspective on patient benefit: Prakash Manoharan, Manchester (1 hour)

The clinical scientist’s perspectiveAnna Barnes, London (1 hour)

PET/MR: A Commercial Success Story?: Antonis Kalemis, London (1 hour)

Current Research & Open Problems: Hadi Fayad & Mathieu Hatt, Brest (1 hour)

Hot Topic Discussion: Students & Panel (2 hours)

Closing (15 minutes)

Detailed Program

Monday 27


Introduction to the Training Course
Charalambos Tsoumpas, Athens


General Introduction to PET
Mattia Veronese, London


General Introduction to MRI 
Kaveh Vahedipour, New York


Coffee Break


PET: Tracers, SUV & Pharmacokinetics
Mattia Veronese, London


Pulse Sequences & Image Contrast
Nikos Dikaios, London


Lunch break (Refectory)


Communicating your research
Steve Smye, Leeds


Introduction to the hot topic question: PET/MRI or PET+MRI?
Steven Sourbron, David Buckley & Harry Tsoumpas Leeds


Tuesday 28


Digital Anthropomorphic Phantoms
Panagiotis Papadimitroulas, Athens


Simulation Theory on PET
Julien Bert, Brest


Coffee Break


PET Simulation Software DemonstrationJulien Bert, Brest & Panagiotis Papadimitroulas, Patras & Nikos Efthimiou, Athens


Lunch break (Refectory)


Simulation Theory on MR
Kaveh Vahedipour, New York


MR Simulation Software Demonstration 
Kaveh Vahedipour, New York

 17:00-17:30  The COST Action TD1007 on PET/MR 
  George Loudos, Athens


Wednesday 29



Reconstruction & Corrections for PET
Kris Thielemans, London & Hadi Fayad, Brest
& Nikos Efthimiou, Athens


Demonstration of STIR
Kris Thielemans, London & Harry Tsoumpas, Leeds & Nikos Efthimiou, Leeds


Coffee Break


MRI Image Reconstruction
Claudia Prieto, London


Lunch break (Refectory)


Software Demonstration of MRI undersampled reconstruction
Claudia Prieto & Christoph Kolbitsch, London


Multimodality Image Processing (localisation and segmentation): Mathieu Hatt, Brest




The Clinician’s Perspective on Patient Benefit
Prakash Manoharan, Manchester

Thursday 30


The Clinical Scientist’s Perspective
Anna Barnes, London


Coffee Break & Pre-lunch


PET/MR: A Commercial Success Story?
Antonis Kalemis, London


Current Research & Open Problems
Dimitris Visvikis, Brest


Late Lunch break


Hot Topic Discussion



School Practical Exercises

The school courses will include practical training and/or demonstration on reconstruction and simulation techniques. The students are expected to come with their laptops (please, do not forget your charger and a UK adapter) and have preinstalled and pretested the following software libraries: 


MR Simulations
For this course we will use JEMRIs. The library can be downloaded and installed following the instructions:


PET Simulations

For this exercise we will use GATE software. Students will need to install the latest VirtualBox version on their machines, and download the Virtual Gate 3.0 (1.7 GB). The link is:


PET Reconstructions
In this practical we will use STIR library. Follow the instructions in the link below to download an enhanced STIR version which will be necessary for the exercises:


We are planning to use similar datasets for the tutorials and if you wish you can download and use brain datasets are already available at the following website: http://brainweb.bic.mni.mcgill.ca/brainweb/selection_normal.html

School Events
First meeting on Sunday evening
Since most of the School attendants will be in Leeds on Sunday, we will meet for a drink at a local traditional Public House: Fox & Newt, 9 Burley Street, LS3 1LD at 19:00, so that we will have the chance to get to know each other. This pub is located only 3’ walk from the IBIS hotel.

School Dinner on Tuesday evening
We have arranged the official dinner, which will be covered by the COST action. This is a local restaurant at the foot of Leeds University campus.

Other evenings
We have also some suggestions for all evening of the School, so that tutors and students can spend more time together.

Friday excursion to York
We are planning to visit the historic town of York on Friday, 1st of May 2015.


As suggested, we have booked for the central IBIS hotel: http://www.ibis.com/gb/hotel-3652-ibis-leeds-centre/index.shtml. There you will find the location of the hotel and other information. The hotel will be a short walking distance from the train station. If you arrive at the Leeds airport, you can take from Leeds Bradford Airport, Bus Point: Stand 1, the Bus Number 757 (Yorkshire Tiger) towards Leeds and you can get out at West Street Westgate stop (two stop before the last). The bus journey takes approximately 35’ and there is one bus in about every 30’. For more details on the timetable: http://www.wymetro.com/BusTravel/bustimetables/


In the UK we have GB pounds. To get a good deal it’s advisable to bring some cash with you before hand and ensure your credit/debit cards are going to work in the UK or you bring a pre-paid card. It is generally best to come to the UK with a passport rather than your country’s ID. Ensure well in advance that you will get any Visa’s document because they can be delayed significantly and as far as I understand if you have received the studentship, you will have to attend to get it, which means that if you cannot come for any reason you will lose your funding; so maybe it is not a bad idea to include some kind of travel insurance if your university doesn’t cover this exclusively.  


Here are some details: http://www.leeds.ac.uk/info/20014/about/157/how_to_find_us