All posts by Miquel

About Miquel

I am a senior NMR spectroscopist at Universitat Autonoma de Barcelona since 1994. That same year I learned about jMRUI and started collaborating with the project. Since 1997, I am responsible of the project web services and software distribution.

TRANSACT-ITN final software survey

TRANSACT-ITN 2017 software survey

If you are a user of either the jMRUI software, the INTERPRET Decision Support System or the SpectraClassifier tool, we would like to know how you use these software tools and your opinion about them, so that we can keep improving our software to better serve your needs.

For that purpose, we ask you to participate in the TRANSACT-ITN final software survey by answering few questions about your training, your working environment, the data you process, and how you use and rate the software. Although most questions are mandatory, many are so trivial that you will answer them in a blink, and the full questionnaire should take you less than 15 minutes to complete, and less than 10 minutes if you only use the jMRUI software. The questionnaire has been tested with the most popular web browsers running on desktop computers and mobile phones and tablets, and you should be able to answer it from elsewhere.

The survey is brought to you by TRANSACT, the EU-funded FP7-PEOPLE Marie Curie Initial Training Network (ITN) project that has been fostering the development of the jMRUI software from March 1, 2013 to February 28, 2017. The aim of the project was to Transform Magnetic Resonance Spectroscopy into a Clinical Tool, and two of the main objectives of the project were:

Once the survey is over, a report summarizing all collected answers will be written and made available through the TRANSACT web site and/or this site.

We thank you in advance for your cooperation!

Picture “Survey” by NY, used under CC-BY-SA 3.0 / Cropped from original

ISMRM - MR Spectroscopy Study Group

Virtual meeting: SpectrIm, a tool for the combined analysis of MR Spectroscopy and Imaging

Take note of the incoming virtual meeting “SpectrIm –  a tool for the combined analysis of MR Spectroscopy and Imaging” presented by Dr. Johannes Slotboom and Nuno Pedrosa de Barros, from the swiss Support Center for Advanced Neuroimaging (SCAN, Inselspital, University of Bern). This meeting is part of a series of planned virtual meetings on the topics: preprocessing,  quantification, and simulation software for MRS/MRSI.

SpectrIm 1.0 beta screentshot
SpectrIm 1.0 beta screentshot

This virtual meeting is organized by the ISMRM Study Group on MR Spectroscopy and it will be held on Thursday 23 February at 07:00 PST, 10:00 EST, 16:00 CET. The meeting will start with a short introduction by Dr. Slotboom followed by a software demonstration by Nuno Pedrosa de Barros.

Note: This activity is restricted to members of the ISMRM MR Spectroscopy Study Group and requires prior registration. To register, please go to the meeting registration page at ISMRM website. The login information will be sent to registered attendees on Wednesday, 22 February 2017.


New atlas of mouse anatomy: from classical anatomical techniques to correlative X-ray, CT, MRI and Ultrasound images

If you use mice as animal model in research projects, make sure not to miss this new atlas of mouse anatomy:

Morphological Mouse Phenotyping: Anatomy, Histology and Imaging. 1st ed. Editorial Médica Panamericana S.A., 2016.
Morphological Mouse Phenotyping: Anatomy, Histology and Imaging. 1st ed. Editorial Médica Panamericana S.A., 2016.

París, Jesús Ruberte, Romay Ana Carretero, and Beltrán Navarro. Morphological Mouse Phenotyping: Anatomy, Histology and Imaging. 1st ed. Editorial Médica Panamericana S.A., 2016.

From the back cover of the book: Animal models of disease are fundamental in research to improve human health. The success of using genetically engineered mice to evaluate molecular disease hypotheses has encouraged the development of massive European and global projects making the mouse the most used animal model. Consequently, laboratory mouse populations are straining the housing capacity of pharmaceutical and biotechnology companies, as well as public research institutions. However, the scientific community often lacks sufficient expertise in morphological phenotyping to effectively characterize and validate these animal models.

Although the mouse displays fundamental morphological similarities to humans, a mouse is not a man. Here we present a complete and integrative description of normal mouse morphology. The main characteristics of this book are:

  • More than 2.200 original images have been specifically produced for this book in the Mouse Imaging Platform (Center for Animal Biotechnology and Gene Therapy, Universitat Autònoma de Barcelona).
  • These images show the anatomy, histology and cellular structure of mouse organs.
  • In addition, correlative X-ray, Computed Tomography, Magnetic Resonance (*) and Ultrasound images complete this integrative vision of the mouse morphology.
  • Classical anatomical techniques such as conventional dissection, skeletal preparations, vascular injections, as well as histological, immunohistochemical and electron microscopy techniques have been employed to characterize the mouse morphology.

This book, essentially an atlas, also contains explanatory diagrams and text that guides the reader through normal mouse anatomy, histology and imaging, and is aimed for mouse researchers as well as veterinarian and human pathologists.

The book is available from the publisher, from (check also your country website if available), and from other places.

(*) all Magnetic Resonance images in this book were acquired by Dr. Silvia Lope-Piedrafita at the  at the NMR service (SeRMN) of Universitat Autònoma de Barcelona, in a 7 Tesla Bruker BioSpec 70/30USR spectrometer. SeRMN has been an active partner of the jMRUI community since many years.

Teching at Paris (Wikipedia)

Non-commercial use of jMRUI in teaching-training activities

Few weeks ago we were contacted by Dr. Adam Liston, Course Director on the MSc in Advanced Neuroimaging at University College London, who wanted to know whether they could use the jMRUI software at the MSc in Advanced Neuroimaging for educational purposes. Although we knew from the very first moment that our answer would be “yes”, we decided to use his request to establish a set of general conditions the teaching and/or training activity would have to fulfil to be regarded as a non-commercial activity.

The use of the jMRUI software in teaching and/or training activities (e.g. postgraduate courses, workshops, etc.) does not constitute a commercial purpose as long as all these conditions are fulfilled:

  1. The jMRUI software is preferably installed on computers managed by the organising institution.
  2. If the jMRUI software is installed on student personal computers, students will be instructed that they must apply for a license if they want to keep the software after the course ends, and that otherwise they must delete it from their personal computers.
  3. The jMRUI software must be made freely available to the course attendees, and no fee can be charged to them for the distribution and/or the use of the software. Nevertheless, you can recoup the cost of the media: pendrive, cdrom, etc., used to distribute the software.
  4. The European Union research project currently funding the development of the jMRUI software must be acknowledge in the course brochure and/or website (if any) and in the teaching materials, at least in the part devoted to the jMRUI software. For that purpose you can use the text below or a similar sentence:

The current development of the jMRUI software is funded by TRANSACT – Transforming Magnetic Resonance Spectroscopy into a Clinical Tool (PITN-GA-2012-316679,, an EU-funded FP7-PEOPLE Marie Curie Initial Training Network running from 1st March 2013 till 28th February 2017. 

Last, although it is not a requirement, we would appreciate from you sending us a brief description of the course so that we can mention it on our TRANSACT project reports. Additionally, we may ask you for permission to publish a short post about the course on this jMRUI blog.

Institute of Neurology, University College London

Using jMRUI for training at IoN-UCL Advance Neuroimaging MSc

We are delighted to report that the jMRUI software will be used for training purposes at the Advanced Neuroimaging MSc Programme of the Institute of Neurology (IoN) and the National Hospital for Neurology and Neurosurgery of the University College London (UCL).

UCL Institute of Neurology and the National Hospital for Neurology and Neurosurgery
UCL Institute of Neurology (left) and the National Hospital for Neurology and Neurosurgery (right) in Queen Square, London (Source: Wikipedia).

The MSc in Advanced Neuroimaging is a multidisciplinary programme which aims to give students a strong working knowledge of neuroanatomy and an in-depth understanding of standard and advanced neuroimaging techniques for image acquisition, processing and analysis in the diagnosis, treatment and study of a full range of neurological diseases. During their time at Queen Square, students will have the opportunity to contribute to world-leading research and have access to cutting edge neuroimaging facilities.

You are welcome to follow their initiative, but keep in mind that some rules must be fulfilled if you want to use and distribute the jMRUI software for free.

New jMRUI website screenshot

Welcome to the new jMRUI website!

It has been a long while since we deployed the jMRUI website and after years of ageing it was intensely pleading for a thorough update. The work began under the FAST European Project, but it has finally come to light with the current TRANSACT European Project.

The new website runs on WordPress, a free and open source blogging and content-management software running on PHP and MySQL. According to Wikipedia, WordPress is used by more than 23.3% of the top 10 million websites as of January 2015, and it is the most popular blogging system in use on the Web at more than 60 million websites.

It is our hope that this new website will foster the development of a virtual community that will work towards spreading the use of MR spectroscopy in the pre-clinical and clinical worlds.