Category Archives: Plugins

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.

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



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.


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.


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.