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International MRIlab Module III - A One Year Journey From The Basics To Advanced Methodologies of MRI

International MRIlab Module III - A One Year Journey From The Basics To Advanced Methodologies of MRI
  • Neurology
  • Multiple sclerosis
Webinar by Excemed
Tuesday, Apr 12 2022



Event format

Learning Journey
Workshop session



Registration status

To register for this event, contact

Registration fee


- Module I: Live Virtual Course, 7–8 Jul 2021

- Module II: Siena, 13–15 Jan 2022

- Module III: Final Webinar, 12 April 2022


All applications will be reviewed by the scientific committee members who will select the best candidates according to their profiles. The successful candidates will participate in both Module I, II and III.

The following requirements are needed to apply:

  • An abbreviated curriculum vitae of the applicant including bibliography of any relevant publication
  • An applicant’s letter of intent
  • A letter of reference from the applicant’s mentor

The Comprehensive Registration fee is €600.

A reduced registration fee for academic applicants will be €400.

The registration fee includes: 

  • Modules I,II & III
  • Online tutorials
  • Live interventions
  • Coffee breaks and lunch
  • Educational materials
  • Certificate of attendance


This collaborative EXCEMED multi-format programme, includes a series of international MRILab Workshops designed for young neurologists/ neuroradiologists or other professionals with a particular interest in quantitative MRI applied to research in Multiple Sclerosis.


In demyelinating and neurodegenerative disorders such as multiple sclerosis (MS), magnetic resonance imaging (MRI) supports diagnostic and therapeutic decisions, assesses prognosis, and improves understanding of the disease. Standardisation and optimisation of MRI acquisition protocols and analysis are therefore critical, both in clinical and research settings. Quantitative methods assessing lesions and atrophy are far less subjective for measuring disease burden in MS, compared with visual inspection, and are moving from research into clinical settings. Structural damage is predictive of motor and cognitive disability and needs to be accurately quantified, also in order to measure response to treatment. Several methods for imaging post-processing have been developed over time with different strengths, limits and scopes. However, whereas quantitative MRI measures have been extensively used in clinical studies and as endpoints in clinical trials, their introduction in the clinical setting has been difficult due to a number of methodological issues.

EXCEMED together with the team of the University of Siena - Experimental Neurology Unit, Department of Medicine, Surgery and Neurosciences - and with the Vall d’Hebron University Hospital in Barcelona - Section of Neuroradiology and MRI Unit, Department of Radiology designed the MRILab - an international 12-month-training period for young neurologists and neuroradiologists particularly interested in quantitative neuroimaging applied to research in demyelinating and neurodegenerative disorders. The Lab is structured as follows:

  • The first module will be performed on-line and will include lectures that review the relevance of different MRI features and metrics in multiple sclerosis, and on technical aspects on brain andspinal MRI acquisition. The last part of this first module will include an introduction on how to use different academic tools for quantitative assessment of MR images. After this first module, the attendees should write (in pairs) a research study proposal using quantitative MRI data, which will be evaluated by the course faculty.
  • The second module, that will take place in 6 months from the first one, will be organized in Siena, and will consist of a hands-on workshop in which all the attendees will have the possibility to learn and use different post-processing tools. After this module, the attendees will have access to a sample of MRI studies from multiple sclerosis patients, from which they will have to perform a quantitative analysis (in pairs) based on a common research project, which will be evaluated by the Surgery and Neuroscience course faculty. 
  • Final Webinar will be organized in which the attendees and course faculty will analyse the studies performed by the attendees.
  • A remote tutoring programme provided by the members of the scientific committee and their teams will support the trainees in their research activities between the two modules and before the Final Webinar by a message board on the MRILab dedicated page which will be accessible to all the participants to post questions and doubts.


Learning objectives

Through a series of different educational formats - both live and online - the MRI-Lab, facing basic and advanced methodological key aspects related to the use of quantitative measures of lesions and atrophy, aims to achieve the following learning objectives:

  • Illustrate the main issues in the standardisation and optimisation of MRI acquisition protocols
  • Describe how to facilitate image post-processing
  • Discuss strengths and limits of currently used software packages for image quantification
  • Deliver full analysis of lesion burden and atrophy in MRI samples.


Pre-Event Tutorials

These preparatory tutorials provide an overview of the course for both modules focusing on the main goals that attendees will achieve through their learning journey in the field of quantitative MRI. The video scribing format facilitates the understanding of the entire learning path, translating scientific concepts into graphic maps. The tutorials will: 

  • Define the importance of quantitative imaging in the evaluation of structural damage in MS
  • Explain the main advancements and pitfalls in this field and how to approach quantitative MRI in a critical way


Post Event Tutorials

The post-course tutorials aim to summarise the main topics delivered in the modules. It will provide attendees with tips and practical exercises to help them develop original research projects building on the information gathered during the course. The tutorials will:

  • Simplify complex concepts into manageable information
  • Efficiently translate the theory of quantitative MRI into working knowledge



In order to get a full benefit of attending the course, attendants need to have some knowledge in the analysis of brain and spinal cord MRI studies, and ensure that the basic tools required to perform basic quantitative analysis of brain and spinal cord MRI studies will be available at their host institution (or on a personal laptop). Instructions on how to install the tools will be given on module I, and thy should be installed before the module II. Requirements: MIPAV (, Matlab (basic license), Statistical Parametric Mapping (; free software but needs Matlab to run), FSL ( and Spinal Cord Toolbox (, which run over a Linux/Unix system (in case you work with PCs, a Virtual Machine should be installed).

Accreditation details

The International MRI Lab, Siena, Italy, 13/01/2022 - 15/01/2022, has been accredited by the European Accreditation Council for Continuing Medical Education (EACCME®) with 14 (fourteen) European CME credits (ECMEC®s). Each medical specialist should claim only those hours of credit that he/she actually spent in the educational activity.

Through an agreement between the Union Européenne des Médecins Spécialistes and the American Medical Association, physicians may convert EACCME® credits to an equivalent number of AMA PRA Category 1 CreditsTM. Information on the process to convert EACCME® credit to AMA credit can be found at

Live educational activities, occurring outside of Canada, recognised by the UEMS-EACCME® for ECMEC®s are deemed to be Accredited Group Learning Activities (Section 1) as defined by the Maintenance of Certification Program of the Royal College of Physicians and Surgeons of Canada.

The other module will be submitted for CME accreditation to the EACCME®.


Scientific programme


DAY 1 - Wednesday, 7 July 2021 

14.00           Opening and Welcome 

                    N. De Stefano (Italy) - À. Rovira (Spain) 

14.15  L1:    MRI acquisition protocols and characteristics of MRI sequences for brain lesion load and volume assessment 

                    À. Rovira (Spain) 

14:35  L2:    Clinical relevance of white matter lesions 

                    N. De Stefano (Italy)

14.55           Q&A

15.15           Break  

15.25  L3:    Pathology of grey matter in multiple sclerosis

                    M. Schoonheim (The Netherlands)

15.45  L4:    Clinical relevance of grey matter lesions

                    N. De Stefano (Italy)

16.05  L5:    MRI acquisition protocols for grey matter lesions assessment

                    À. Rovira (Spain) 

16.25           Q&A

16.45           Wrap-up day 1

17.00           End day 1  


DAY 2 - Thursday, 8 July 2021 

14.00  L6:     MRI markers of disease progression

                     À. Rovira (Spain) 

14.20  L7:     Clinical relevance of brain and spinal cord atrophy

                     N. De Stefano (Italy)

14:40  L8:     Artificial intelligence for creating predictive models in multiple sclerosis

                     M. de Bruijne (The Netherlands)

15.00            Q&A

15.20            Break  

15.30            Introduction to hands-on training (module II)

                     Installation of the tools required for the hands-on session on module II

                     M. Battaglini (Italy) - D. Pareto (Spain)

17.30            Homework: Install the required toolboxes (MIPAV, Matlab, SPM, FSL and SCT)                  

18.00            Final wrap-up day 2                

18.15            Module I conclusion



DAY 1 - Thursday, 13 January 2022 

08.45             Opening and Welcome 

                      N. De Stefano (Italy) - A. Rovira (Spain) 

09.00 L1:       MRI acquisition issues influencing the accuracy of quantitative measurements 

                      M. Battaglini (Italy) - D. Pareto (Spain) 

09.30 L2:       Practical Issues with brain lesions segmentation and brain lesions segmentation

                      M. Battaglini (Italy) - D. Pareto (Spain)

10.00             Q&A

10.15             Coffee break           

10.30             Hands on practice training: brain lesions (lesion load)

                      M. Battaglini (Italy) - D. Pareto (Spain)

                      Learn the Tools: how to use JIM to perform manual lesion load

                      • Case 1: T2-W lesion load

                      • Case 2: T1-W lesion load (or black-holes) 

                      • Case 3: Gadolinium enhancing lesion load  

13.00             Lunch

14.00             Hands on practice training: brain lesions (lesion load)

                      M. Battaglini (Italy) - D. Pareto (Spain)

                      How to measure lesion load segmentation with "Lesion Segmentation Toolbox"

16.00 L3:       How to recognize and differentiate spinal cord lesions

                      À. Rovira (Spain)

16.30             Q&A

17.00             End of day 1


DAY 2 - Friday, 14 January 2022 

09.00 L4:       Practical issues with global brain volume segmentation

                      N. De Stefano (Italy) 

09.30 L5:       Methods to quantify global brain volumes /changes: pros and limits 

                      M. Battaglini (Italy) - D. Pareto (Spain) 

10.00 L6:       Methods to quantify regional brain volumes: pros and limits

                      M. Battaglini (Italy) - D. Pareto (Spain)

10.30             Q&A

10.45             Coffee break           

11.30             Hands on practice training: brain volume

                      M. Battaglini (Italy) - D. Pareto (Spain)

                      Learn the Tools: how to use SIENAx/SIENA to assess brain volume/change estimation

                      • Cross-sectional cases: SIENAx

                      • Effect of filling on calculated GMF, WMF, BPF

                      • Longitudinal cases: SIENA

13.00             Lunch

14.00             Hands on practice training: Cortical GM volume

                      M. Battaglini (Italy) - D. Pareto (Spain)

                      Introduction to VBM
                      • VBM analysis of grey matter

15.30             Coffee break

15.45             Hands on practice training: deep grey matter volume

                      M. Battaglini (Italy) - D. Pareto (Spain)

17.00             Difficulties faced during hand-on sessions


17.30             End of day 2


DAY 3 - Saturday, 15 January 2022 

09.00 L7:       Methods to quantify spinal cord volumes: pros and limits

                      M. Battaglini (Italy) - D. Pareto (Spain)

09.30             Hands on practice training: spinal cord volume

                      M. Battaglini (Italy) - D. Pareto (Spain) 

                      • MIPAV
                      • Spinal cord toolbox

11.30             Coffee break           

11.45             Homework. Attendees will be instructed to perform a real research study based on quantitative assessment of MRI studies (a data set will be provided)

12.30             Final discussion and wrap-up

12.45             Module II conclusion



Final Webinar - Tuesday, 12 April 2022

15.00             Revision of homework and final discussion of problems encountered

18.00             End of the webinar



Nicola De Stefano

Department of Medicine, Surgery & Neuroscience
University of Siena
Siena, Italy

Alex Rovira

Department of Radiology
Unit of Magnetic Resonance
Vall d’Hebron University Hospital
Barcelona, Spain

Deborah Pareto

Vall d’Hebron University Hospital
Section of Neuroradiology Department of Radiology
Barcelona, Spain

Marco Battaglini

Department of Neurological and Behavioral Sciences
University of Siena
Siena, Italy

Marco Battaglini

Department of Neurological and Behavioral Sciences
University of Siena
Siena, Italy

Nicola De Stefano

Department of Medicine, Surgery & Neuroscience
University of Siena
Siena, Italy

Deborah Pareto

Vall d’Hebron University Hospital
Section of Neuroradiology Department of Radiology
Barcelona, Spain

Alex Rovira

Department of Radiology
Unit of Magnetic Resonance
Vall d’Hebron University Hospital
Barcelona, Spain

Menno Schoonheim

Department of Anatomy & Neurosciences
VU University Medical Center