Marie-Curie Fellow
Research & Training Network
D. R. Amariei (ESR)

Marie Curie Fellow (ESR) of the FAST project
Universitat Autònoma de Barcelona, Spain
Contact    

• eMRUI Software package
  Task 5 assures that the algorithms FAST shall devise,can be used in Clinics and Research Laboratories with minimal effort in an Information System. To this end, the algorithms are packaged in an innovative, collaborative, object-oriented, Java-based graphical user-interface (GUI) to be developed by the SME ALTER-Systems. Combination of both will result in the eMRSI software package. 
• The software package jMRUI with Java-based Graphical User Interface [1] is being developed for user-friendly time-domain analysis of medical Magnetic Resonance Spectroscopy (MRS), Spectroscopic Imaging (MRSI), and HRMAS-NMR signals. The beta version 4.0 has been distributed in1800 research groups and hospitals world-wide, see Fig.1. The new version 4.1 resulting from the efforts of the European Marie Curie project FAST is an enhanced plug-in platform, offering new important functionalities.
• Plug-ins can be implemented using Eclipse (http://www.eclipse.org) and the jMRUI Plug-in template project enabling users to extend the software
• Partner 8 (UAB) is involved in:
  • distribution of eMRSI, handling of automatic license requests, development of the eMRSI licensees database, porting to a secure web server, development of the eMRSI website
  • creation (SQL-based) of a database of spectra/images with PHP/HTTP interfaces
  • quantum-mechanical simulation of HR-NMR signals
  • investigation of JSDT-based distance learning and teaching
  • implementation of moodle-base course management system for eTeaching
  • contribution to the eMRSI GUI

• Kernel and plug-in jMRUI contribution
  

The software package jMRUI with Java-based Graphical User Interface is being developed for user-friendly time-domain analysis of medical Magnetic Resonance Spectroscopy (MRS), Spectroscopic Imaging (MRSI), and HRMAS-NMR signals. The beta version 4.0 has been distributed in 1800 research groups and hospitals world-wide. The new version 4.1 resulting from the efforts of the European Marie Curie project FAST is an enhanced plug-in platform, offering new important functionalities.

• Mice heart segmentation using MR images

Mouse animal models are a valuable biomedical tool for specialists studying Cardiovascular Diseases (CVD) like hypertension, coronary heart disease, heart failure, and stroke. Cardiac MRI may provide them with an accurate, non-invasive technique for their research, but MRI studies result in the acquisition of large image data-sets that must be processed and carefully analyzed. Currently, the standard procedure for the analysis of images requires that an expert with anatomical knowledge delineates the structures of interest on each slice of the image data set. This procedure is time consuming and subject to inter- and intra-operator variability. Thus, because of the lack of an available tool that could alleviate and speed up theimage processing task, we decided to develop a method that would delineate the structures of interest with as little human intervention as possible in each slice of the mouse heart.  

• Acoustic frequency of proton echo planar spectroscopic imaging
  Visualization of acoustic frequencies caused by switching of gradients during an echo planar sequence as secondment with ULeipzig ER C. Labadie.

Simulation of single-shot PEPSI readout (S. Posse et al. 2009 MRM 61:541-547)

Corresponding acoustic frequency spectrum

• Segmentation of short axis view mouse heart images acquired with an IntraGate FLASH MRI pulse sequence

Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), Canada, Montreal, May 2011.

D. Amariei¹, S. Lope-Piedrafita^2,3, E. Dominguez⁴, M. Navarro⁴, J. Ruberte⁴, M. E. Cabañas^2,3, A. Hernandez Sabate⁵, and D. Gil⁵

¹SeRMN, Universitat Autonoma de Barcelona, Cerdanyola del Valles, Barcelona, Spain, ²SeRMN, Universitat Autonoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain, ³CIBER-BBN, Cerdanyola del Valles, Barcelona, Spain, ⁴CBATEG, Universitat Autonoma de Barcelona, Cerdanyola del Valles, Barcelona, Spain,⁵Centre de Visio per Computador (CVC), Universitat Autonoma de Barcelona, Cerdanyola del Valles, Barcelona

• The version 4.1 of jMRUI: a state-of-the-art plug-in platform for medical MRS

Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), Canada, Montreal, May 2011.

D. Stefan^1, D. Amariei^2, F. Di Cesare^3, R. Guimaraes^4, A. Lazariev^3, G. Oppedisano^3, O. Strbak^5, M. Uberti^3,6, E. Vescovo^7, A-R. Allouche^8, M. Aubert-Frécon^8,M. Cabanas^2, R. de Beer^9, M. D. Boska^6, D. Sima^10, J. Slotboom^11, Z. Starcuk^5, J. Starcukova^5, S. Williams^7, D. van Ormondt^{9, and} D. Graveron-Demilly³

¹Alter Systems, Lyon, France, ²Universitat Autonoma de Barcelona, Barcelona, Spain,  ³Creatis-LRMN, Université Claude Bernard Lyon ¹, Villeurbanne, France, ⁴Institute for Language and Speech Processing, Athens, Greece, ⁵Institute of Scientific Instruments, AS CR, Brno, Czech Republic, ⁶Department of Radiology, University of Nebraska Medical Center, Omaha, United States, ⁷University of Manchester, Manchester, United Kingdom, ⁸LASIM, Université Claude Bernard Lyon ¹, Villeurbanne, France, ⁹Delft University of Technology, Delft, Netherlands,  ¹⁰Katholieke Universiteit Leuven, Leuven, Belgium, ¹¹University Hospital and Inselspital, Bern, Switzerland

 

• Double-Shot Center-Out Echo Planar Spectroscopic Imaging at 3 Tesla ePoster, Proc. 18th Scientific Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), Stockolm, Sweden, 1-7 May 2010

  C. Labadie^1,2, S. Hetzer¹, T. Mildner¹, D. R. Amariei³, M. Frécon⁴, and H. E. Möller^1,2

  ¹Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany, ²Faculty of Physics and Earth Science, University of Leipzig, Germany, ³Servei de Ressonància Magnética Nuclear, Universitat Autònoma de Barcelona, Spain, ⁴Laboratoire de Spectrométrie Ionique et Moléculaire, Université Claude Bernard Lyon 1, France