NMRSCOPEB: I. Installing on Windows II. Launching on Windows III. Installing on Linux IV. Launching on Linux V. License terms summary VI. Acknowledgements NMRScope-B is a plugin for program jMRUI, recommended for version 7.0 or later. It provides the functionality useful for the simulation of coupled spin systems during the NMR experiment. In the simulation, such properties as chemical shifts, spin-spin coupling, relaxation, spatial and/or spectral excitation selectivity, and customized pulse sequences are accounted for. The primary target is to support simulation of metabolite FIDs in biomedical MR spectroscopy, as needed for spectroscopic quantitation, but many functions are meant to support the development of methods for MR spectroscopic imaging. It is accessible either from the jMRUI wizard or from the jMRUI’s menu item “Custom” by selecting item “NMRScope-B”. ____________________________________ WINDOWS _____________________________________________ I. Installation (Windows) -------------------------- NMRScope-B can run as a 32-bit or 64-bit application. NMRScope-B requires Python installed on your computer. To install NMRScope-B: 1. Make sure that jMRUI jmrui_v7.0 or later is installed (see readme.txt) 2. Install Python 3, SciPy and NumPy on your computer. Note: you may obtain Python+SciPy+NumPy in many freely available scientific packages. We recommend downloading WinPython (free Python scientific package) from https://sourceforge.net/projects/winpython/files/ e.g. https://sourceforge.net/projects/winpython/files/WinPython_3.10/3.10.8.0/Winpython64-3.10.8.0.exe 3. If you have not modified nmrscopeb.bat file during jMRUI installation - modify the path to python.exe in /lib/nmrscopeb.bat file to correspond to your python 3 installation directory i.e. modify the first line set pythonPath="C:\Programs\WPy64-31080\python-3.10.8.amd64" to set pythonPath= where is the path to your python.exe e.g. set pythonPath="C:\Programs\WPy64-31080\python-3.10.8.amd64" ------------- Important !!!!!!!!! ------------- Make sure you will choose protocols from \work\NMRSCOPEB\ProtocolsPy3 folder. Note for users of old nmrscopeb version If you have used previous version of nmrscopeb (in jMRUI 6 or 5.2) your old protocols will not work with the new nmrscopeb version. In case you customized some protocols (.py files) in the past (with older nmrscopeb version) you have to rewrite them to Python3 (see protocols in \work\NMRSCOPEB\ProtocolsPy3 for inspiration). Another option is to use old nmrscopeb and Python2. To do so copy all files from /lib/nmrscopeb_python_2 to /lib and modify the path to python.exe in /lib/nmrscopeb.bat file to correspond to your python2 installation directory. Be aware that you cannot use the protocols from \work\NMRSCOPEB\ProtocolsPy3 folder if you use nmrscopeb Python2 If you need help contact jana@isibrno.cz or zenon.starcuk.jr@isirbno.cz II. Launching NMRSCOPEB on Windows ----------------------------------- - Launch jMRUI. - Select NMRScope-B in the application launch wizard, or select Custom | NMRScope-B in the menu.Your Firewall program may ask you to allow connection with a socket. Allow the connection. If no secondary command windows appears, these are the probable causes: o jMRUI is not installed corectly (check if nmrscope (not nmrscopeb) can be started - if not, please see instruction how to install jMRUI with 32-bit Java (readme.text)). o Your Python is not properly installed, or the Python path is set improperly. o Your firewall software is preventing jMRUI and/or NMRScopeB from using sockets. As sockets are used for the communication between these two programs, permit such behaviour permanently. In case nmrscopeb is not executed within jmrui you can run the NMRSCOPE-B manually by double clicking nmrscopeb.bat file in jmrui lib directory (in Command window that is started you can check Python version that must be >3.0 and you should see message "Server is listening for incoming connections on port 42314"). Then select NMRScope-B in the application launch wizard. Note: If needed you can set port number in /lib/nmrscopeb.bat by extending the line 'python.exe %~dp0nmrscopeb_python_3\nmrscopeb_server.py' with a port number of your choice e.g. 'python.exe %~dp0nmrscopeb_python_3\nmrscopeb_server.py 12345' Batch mode Launch a user defined macro (your own batch file) calling call_jmruicl_nmrscopeb.bat file (in Windows) with parameters Examples: - call_jmruicl_nmrscopeb.bat shows an example of calling jMRUI batch mode for spectra simulation in NMRScopeB _________________________________ LINUX _____________________________________________________________ III. Installation (Linux) ------------------------- NMRScope-B can run as a 32-bit or 64-bit application. NMRScope-B requires Python3 installed on your computer. 1. Make sure that jMRUI jmrui_7.0 or later is installed (see readme.txt) 2. Install Python, SciPy and NumPy on your computer. To install Python, type in the console window sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose 3. Install also xterm by typing sudo apt-get install xterm 4. Give execution rights to the nmrscopeb.sh file in mrui directory lib by typing chmod +x nmrscopeb.sh IV. Launching NMRSCOPEB on Linux --------------------------------- - Launch jMRUI. - Select NMRScope-B in the application launch wizard, or select Custom | NMRScope-B in the menu. - If no secondary command windows appears, these are the probable causes: o Your Python is not properly installed o Your firewall software is preventing jMRUI and/or NMRScopeB from using sockets. As sockets are used for the communication between these two programs, permit such behaviour permanently. In case nmrscopeb is not executed within jmrui you can run the NMRSCOPE-B manually from command line. Type in the main jMRUI directory: cd lib sh nmrscopeb.sh and then select NMRScope-B in the application launch wizard _________________________________ LICENSE ___________________________________________________________ III. License terms summary The NMRScope-B plugin into jMRUI is distributed as a component of jMRUI and its use is subject to a valid jMRUI license. For more information see license_nmrscopeb.txt ______________________________ ACKNOWLEDGEMENTS ____________________________________________________ IV. Acknowledgements PLEASE, CITE THE SUITABLE REFERENCE IN ACADEMIC PUBLICATIONS OF RESEARCH THAT INVOLVES USE OF THE NMRSCOPEB Z Starcuk Jr, J Starcukova; Quantum-mechanical simulations for in vivo MR spectroscopy: Principles and possibilities demonstrated with the program NMRScopeB. Anal Biochem. DOI: 10.1016/j.ab.2016.10.007. [In Press] Z Starcuk Jr, J Starcukova, O Strbak and D Graveron-Demilly: Simulation of coupled-spin systems in the steady-state free-precession acquisition mode for fast magnetic resonance (MR) spectroscopic imaging. Meas. Sci. Technol. 20, 10, 104033 (2009). doi: 10.1088/0957-0233/20/10/104033 The NMRScope-B plugin to jMRUI was developed by Zenon Starcuk and Jana Starcukova, Institute of Scientific Instruments of the ASCR, v.v.i., Brno, Czech Republic. - 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)', and was also supported by the grants - 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‘ - MEYS CR (LO1212) together with EC (ALISI No. CZ.1.05/2.1.00/01.0017), AV0 Z20650511, AVCR (RVO:68081731) and MŠMT CZ.1.05/2.1.00/01.00.