jMRUI : I. Installing on Windows II. Launching on Windows III. Installing on Linux IV. Launching on Linux V. License terms summary VI. Acknowledgements ____________________________________ WINDOWS _____________________________________________ I. Installation (Windows) -------------------------- 1. Download from the jMrui ftp server the .zip file 2. Uncompress the .zip file in the directory of your choice. Set the Keep PATH option, if necessary, in the uncompress software used. 3. If you decide to create a desktop shortcut to the starter batch (jmrui.bat or jmruicl.bat - see below), you may associate it with the jMRUI icon jmrui.ico. 4. Make sure that 32-bit (even on 64-bit computers!) Java Runtime Environment (JRE) or optionally JDK version 1.5 or higher has been installed. E.g. a free 32-bit installation package (OpenJDK) can be obtained at https://adoptopenjdk.net. Download the built architecture x86 !!! and install it (.msi) or uncompressed the zip file (.zip). 5. Specify the full path to 32-bit java.exe file in jmrui.bat and jmruicl.bat files i.e. modify the first line set javaFile="\java" where = is the full path name to 32-bit java e.g. "C:\Program Files (x86)\AdoptOpenJDK\jre-13.0.2.8-hotspot\bin\" then the first line would be set javaFile="C:\Program Files (x86)\AdoptOpenJDK\jre-13.0.2.8-hotspot\bin\java" 6. To be able to use plug-in NMRSCOPE-B, please see readme_nmrscopeb.txt file to learn how to install the plug-in II. Launching on Windows ----------------------------------- 1. Interactive mode Launch the jmrui.bat or jmruicl.bat file in the root directory of jMRUI. - jmruicl.bat displays information about jMRUI status in the console window - jmrui.bat stores it in a text file in the log directory. 2. Batch mode Launch a user defined macro (your own batch file) calling jmruicl.bat file with parameters Examples: - call_jmruicl.bat shows an example of calling jMRUI batch mode for data processing and quantitation - call_jmruicl_nmrscopeb.bat shows an example of calling jMRUI batch mode for spectra simulation in NMRScopeB _________________________________ LINUX _____________________________________________________________ III. Installation (Linux) ------------------------- 1. Download from the jMrui ftp server the .zip file 2. Uncompress the .zip file in the directory of your choice. 3. Make sure that 32-bit (even on 64-bit computers!) Java Runtime Environment version 1.5 or higher has been installed. To install 32bit Java (OpenJDK !) type: On Debian, Ubuntu, etc. sudo apt-get install openjdk-8-jdk:i386 On Fedora, Oracle Linux, Red Hat Enterprise Linux, etc. sudo dnf install java-11-openjdk.i686 or su -c dnf install java-11-openjdk.i686 4. Adapt the full path to 32-bit java file in your jmrui.sh command. REPLACE the path to the java-excutable bin/java in a given jmrui.sh, for instance, /usr/lib/jvm/java-8-openjdk-i386/jre/bin/, with the location of _your_ bin/java. For instance, if the path to your bin/java is /usr/lib/jvm/java-11-openjdk-i386/bin/java , your jmrui.sh command should be /usr/lib/jvm/java-11-openjdk-i386/bin/java -Xss2m -mx1200m -Dsun.java2d.pmoffscreen=false -Djava.library.path=lib -jar lib/mrui.jar NB. Following ’sudo dnf install java-11-openjdk.i686’, find the location of the resulting bin/java with the command ’locate’. But first update the filename-database with the command ’sudo updatedb’, and only then search with the command locate -i bin/java , where -i serves to make the search case-insensitive. This yields an overview of all existing bin/java in your system. 5. In some distributions you may need to manually install the package libg2c0. For Ubuntu you will need to download the package libg2c0_3.4.6-6ubuntu3_i386.deb wget http://old-releases.ubuntu.com/ubuntu/pool/universe/g/gcc-3.4/libg2c0_3.4.6-6ubuntu5_i386.deb and type on the command line sudo dpkg -i --force-all libg2c0_3.4.6-6ubuntu5_i386.deb 6. To be able to use plug-in NMRSCOPE-B, please see readme_nmrscopeb.txt file to learn how to install the plug-in IV. Launching on Linux --------------------------------- 1. Interactive mode Launch the jmrui.sh file in the root directory of jMRUI. - Type sh jmrui.sh or ./jmrui.sh - If you have any troubles with running the script allow to execute it: chmod +x jmrui.sh 2. Batch mode Launch a user defined macro (your own batch file) calling jmruicl.sh file with parameters. _________________________________ LICENSE ___________________________________________________________ V. LICENSE TERMS SUMMARY jMRUI is proprietary software, available for free for non-profit use, and which cannot be redistributed or/and modified. The software will at no time be used for commercial or industrial purposes (see http://www.mrui.uab.es/mrui/license/ for details). jMRUI uses some third party libraries for which different licences may apply (notice.txt). ______________________________ ACKNOWLEDGEMENTS ____________________________________________________ 4. ACKNOWLEDGEMENT LICENSEE WILL CITE THE FOLLOWING REFERENCES IN ANY ACADEMIC PUBLICATION OF RESEARCH THAT INVOLVES USE OF THE SOFTWARE: D. Stefan, A. Andrasescu, F. Di Cesare, E. Popa, A. Lazariev, E. Vescovo, O. Strbak, Z. Starcuk, M. Cabanas, D. van Ormondt and D. Graveron-Demilly, Quantitation of magnetic resonance spectroscopy signals: the jMRUI software package. Meas. Sci. Technol. 20:104035, (9 pp), 2009. A.Naressi, C. Couturier, J.M. Devos, M. Janssen, C. Mangeat, R. de Beer and D. Graveron-Demilly , 'Java-based Graphical User Interface for the MRUI Quantitation Package', MAGMA, 12, 141-152, 2001. AS WELL AS THE REFERENCES OF THE USED ALGORITHMS and the MRUI HomePage: http://www.jmrui.eu/technical-documentation/scientific-technical-literature/ The “CONSORTIUM” developed the Java-based MRUI software in the context of EU projects: - This project has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 813120. 2018-2022, 'Integrating Magnetic Resonance Spectroscopyand Multimodal Imaging for Research and Education in MEDicine (INPSIRE-MED)' - TMR, FMRX-CT97-0160, 1998-2001 ‘Advanced Signal Processing for Medical Magnetic Resonance Imaging and Spectroscopy’ - MRTN-CT-2006-035801, 2006-2010 ‘Advanced Signal Processing for Ultra-Fast Magnetic Resonance Spectroscopic Imaging, and Training, ‘FAST’ - PITN-GA-2012-316679, 2012-2017,‘Transforming Magnetic Resonance Spectroscopy into a Clinical Tool‘,‘TRANSACT‘. - European Regional Development Fund (MEYS CZ.02.1.01/0.0/0.0/16_013/0001775)