jMRUI course March 2020

Magnetic Resonance Spectroscopy (MRS) data processing in the time-domain with jMRUI

16-18 March, 2020 – Brno, Czech Republic

Course overview

The H2020-MSCA-ITN INSPiRE-MED European organizes the course “MRS data processing in the time-domain with jMRUI” as a training event for the early-stage researchers of the INSPiRE-MED project funded by a Marie Sklodowska-Curie action grant of the European Union Horizon 2020 research and innovation programme.

We also offer 20 free places in the jMRUI training course that will be held from Monday, March 16 to Wednesday, March 18, 2020 in Brno, Czech Republic.

If you wish to attend the course, please register as soon as possible because, once the course capacity is filled, the registration will be closed. We will confirm your registration and give you full information promptly after you register. If you register after the capacity has been filled, you will be notified.

In this course you will learn how to apply the many algorithms available in jMRUI to process biomedical MRS data in the time-domain. For instance, you will apply HLSVD and related tools to filter unwanted signals, e.g. to remove a large residual water peak; and you will use fitting tools like AMARES and QUEST to quantitate the metabolites in the spectrum. One session will be devoted to learn and practice the use of NMRSCOPE-B to simulate the metabolite spectra required to build a basis-set for quantitation with QUEST/AQSES, and two additional sessions will be dedicated to master the use of the advanced features available in NMRSCOPE-B. Additional sessions will teach you how to code plug-ins to extend and customize the jMRUI software.

At the end of this three day training course, you should be able to use the tools available in jMRUI to process biomedical MRS data in the time-domain and to assess the results obtained. Additionally, you will have a basic knowledge of the concepts involved in signal processing and fitting in general, and in time-domain processing in particular, so that you can keep up with future developments in this field applied to MRS processing.

Target audience

This course is aimed at PhD students or junior postdocs researchers working on Magnetic Resonance Spectroscopy (MRS) and interested in learning how to apply time-domain algorithms to process MRS data, in particular biomedical, preclinical and clinical MRS data.


We have two requests for all participants member and non-members of the INSPiRE-MED EU project:

  • Bring your own laptop (preferably with Windows, on-site installation support and hands on plug-ins will be provided for Windows). Keep in mind that this is mostly a practical course on how to use the jMRUI software and that the best way to learn it is to use it.
  • It is highly recommended to license, download and install jMRUI 6.0 beta in advance (or at least to try so). Although we have allocated time early on the first day to install the software, it will be more productive if you do it at home before the course.


Due to space constrains, we can only offer 20 free places to non-members of the INSPiRE-MED project. Every registration will be booked subject to the number of places still available, and they will be confirmed by email to participants upon registration.

All course participants (*) are responsible for arranging and paying their own travel and accommodation and meals.

Coffee break refreshments will be provided for free.

(*) INSPiRE-MED members should check their email box for additional instructions.

Please submit your online registration here.

Programme at a glance

Day 1 - 16th MarchDay 2 - 17th MarchDay 3 - 18th March
jMRUI installation, overview & history
09:00Quantifiying with AMARES & AMARES applications09:00Hands on plugins
10:30coffee break10:30coffee break
11:00Basis set simulation with NMRSCOPE-B11:00Quantifiying with QUEST
12:30lunch12:00lunch12:00Closing session
14:00NMRSCOPE-B advanced usage (I)13:30Clinical examination (SV MRS + MRSI) & Monte-Carlo with jMRUI
15:30coffee break15:30coffee break
16:00NMRSCOPE-B advanced usage (I)16:00Plugins overview & hands on

A more detailed programme is available on a separate page.



Hotel Continental Brno
Kounicova 6
602 00 Brno
Czech Republic
T: +420 541 519 111
E: info@continentalbrno


Institute of Scientific Instruments of the Czech Academy of Science
Královopolská 147
612 64 Brno
Czech Republic

Local organizers


This course is funded by the European Union Horizon 2020 Framework Programme for Research and Innovation, through the Marie Skłodowska-Curie actions, with grant agreement No 813120.