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

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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.

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jMRUI 6.0 beta

jMRUI 6.0 beta released

A new version of jMRUI is available!

We are happy to announce the beta release of the new jMRUI version 6.0 for testing purposes.

Before releasing the final version, we would like to ask you to help us to test this beta version. If you decide to help us, please, download the installation file for Microsoft Windows and/or GNU/Linux from the beta version download page, and  test all the functionalities you usually use, but also try the new features, and report any problems encountered and/or send suggestions either to the jMRUI forum or by email to zc.on1498720137rbisi1498720137@iurm1498720137j1498720137 with the subject “jmrui 6.0 beta report”.

This new version comes loaded with many improvements and new features, amongst the most important:

  • Combined analysis of MR Spectroscopy and Imaging (SpectrIm), currently available for Siemens Advanced DICOM format. Philips DICOM data format is being implemented, but not yet included in this version. For testing purposes you can download some example data sets from the jMRUI download web page.
  • QuasarX (Quest with some new constraints, such as common damping for selected metabolites, fixed frequency shift of selected metabolites, shape peak selection);
  • New history-tracking mode that allows (1) to retrieve all processing steps that led to the creation of a particular data/result, and thus increases the reproducibility and documentability of all processing steps; and (2) to run macros in the interactive mode.
  • New plugins SpectraClassifier and INTERPRET Decision-Support System for spectra classification and pattern recognition. These plugins are compatible with jMRUI v. 5.2 and they are distributed separatedly under their own license terms.
  • New plugin jMRUI2XML for automating MRS processing and for exchanging data. This plugin is compatible with jMRUI v. 5.2 and it is distributed separatedly under its own license terms.
  • Improved version of the spin system simulator NMRScopeB – new protocols (SPECIAL, MEGA-PRESS, semi-LASER), possibility to choose a pulse shape directly in the protocol window (no more need to modify the Python script) and many other improvements;

We thank you for helping us to make the code better.

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morphological-mouse-phenotypig-featured-image

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 Amazon.com (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.

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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, http://www.transact-itn.eu), 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.

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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.

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Improved import plug-ins of GE and Siemens data-sets

GE and Siemens format update

Updated plug-ins for loading GE and Siemens data sets are now available. If you experienced any problems with any of those two data types, please download and update the plug-ins in your jMRUI installation.

Installation

  1. Before proceeding please make a copy of GE and Siemens plug-ins in any external directory
  2. Copy the plug-ins to “<jmrui_root>\plugins” folder; in case of the ge.jar file replace the original one by the new one. Note: you must not leave the copy of the original ge.jar file in the  “<jmrui_root>\plugins” folder together with the new one.

Download 

Download GE_Siemens_Update-1.zip (25.4 KB)

Troubleshooting

If the problem with Siemens Dicom persists, please load the data file using “File/Open As” and select “Siemens DICOM”.

jMRUI Development Team

 

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jmrui2xml plugin

The jMRUI2XML plugin is reported in BMC Bioinformatics

From raw data to data-analysis for magnetic resonance spectroscopy – the missing link:  jMRUI2XML.

Victor Mocioiu, Sandra Ortega-Martorell, Iván Olier, Michal Jablonski, Jana Starcukova, Paulo Lisboa, Carles Arús and Margarida Julià-Sapé.

BMC Bioinformatics 2015, 16:378  DOI: 10.1186/s12859-015-0796-5

Abstract

Background

Magnetic resonance spectroscopy provides metabolic information about living tissues in a non-invasive way. However, there are only few multi-centre clinical studies, mostly performed on a single scanner model or data format, as there is no flexible way of documenting and exchanging processed magnetic resonance spectroscopy data in digital format. This is because the DICOM standard for spectroscopy deals with unprocessed data.

The paper proposes a plugin tool developed for jMRUI, namely jMRUI2XML, to tackle the latter limitation, given that jMRUI has evolved into a plugin platform allowing for implementation of novel features.

Results

jMRUI2XML is a Java solution that facilitates common preprocessing of magnetic resonance spectroscopy data across multiple scanners. Its main characteristics are: 1) it automates magnetic resonance spectroscopy preprocessing, and 2) it can be a platform for outputting exchangeable magnetic resonance spectroscopy data. The plugin works with any kind of data that can be opened by jMRUI and outputs in extensible markup language format. Data processing templates can be generated and saved for later use.

The output format opens the way for easy data sharing- due to the documentation of the preprocessing parameters and the intrinsic anonymization – for example for performing pattern recognition analysis on multicentre/multi-manufacturer magnetic resonance spectroscopy data.

Conclusions

jMRUI2XML provides a self-contained and self-descriptive format accounting for the most relevant information needed for exchanging magnetic resonance spectroscopy data in digital form, as well as for automating its processing. This allows for tracking the procedures the data has undergone, which makes the proposed tool especially useful when performing pattern recognition analysis. Moreover, this work constitutes a first proposal for a minimum amount of information that should accompany any magnetic resonance processed spectrum, towards the goal of achieving better transferability of magnetic resonance spectroscopy studies.

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