Installing and Configuring VNMR for MATLAB

1. Decide upon a location for the VNMR files (for example 'c:\mymatlab' directory). If this directory does not exist, create it.
2. Save the attached vnmr_35.zip (or vnmr_35.tar.gz -- for Unix/Linux) file in a temp directory. Unzip/untar it and copy the folder VS to the location you have chosen (you can save space and effort by unzipping the zipped file directly into this directory). Please keep in mind that file vnmr_35.zip was compressed using WinZip (Windows); file vnmr_35.tar.gz (Unix) should be first unzipped using gunzip and then un-tarred. A properly unzipped and copied VS folder must contain the following (sub)folders and files:
   • vs_src -- a folder containing VNMR source code and the translator;
   • vs_pp -- a folder containing several examples of pulse programs;
   • components -- a folder containing GUI components;
   • config -- a folder containing configuration files;
   • helper -- a folder containing several common scripts;
   • readme -- a folder containing vs_help file and other user-oriented info;
   • save -- a folder used by VNMR to save/load data, including user-generated shapes (for shaped RF pulses and PFG);
   • xlatedir -- a folder used by Xlator to write the output files from reading/translating a pulse sequence; (IMPORTANT: Make sure you have the write permission for this folder!)
   • components -- a folder containing GUI components;
   • manuals -- user's manuals in html-format;
   • temp -- a temporary folded where the program stores a temporary version of the current pulse program; (IMPORTANT: Make sure you have the write permission for this folder!)
   • files vsnmr.m, vs_start.m, vs_exit.m, make_xlate.m, vs_findWorkDirectory.m, vs_defineGlobals.m, addUser.m, and readme.txt.
   
   
3. Now you have to make an executable for the VNMR TRANSLATOR. You will have to make it only once, when you install the VNMR package. Follow these steps:
   • Start Matlab
   • In the Matlab window, go to your VS directory. If you are using Matlab 6 and up, you can use the "Current Directory" pull-down menu in the top part of the Matlab window to navigate and select the desired VS directory. For earlier versions of Matlab or if the Matlab (Java-based) graphical user interface is not available, you will have to type the corresponding "change directory" commands directly from your Matlab shell. An alternative way, which will work for all matlab versions, is to create a start file that will automatically place your matlab session into the VNMR directory.
   • Type the following command (from the Matlab prompt):
     
     make_xlate
     
     This will start the C-compiler and create an executable file for the xlator. The program may ask you to select a version of the C-compiler you would like to use. I usually select the compiler that comes as an integral part of the Matlab package.
     
     Note #1: Norton Antivirus conflicts with the commands involved in making the executavle (ask folks at Matlab and/or Symantec why). If you have Norton Antivirus running on your computer, you will have to disable it for the make_xlate step. You can enable your antivirus software after this step is done.
     Note #2: Matlab will create a Matlab-executable file (e.g. vs_lex_bruker.dll in Windows) and write it in the vs_src directory. Make sure you have the write permission for this directory.
     Note #3: This distribution of the Virtual Spectrometer includes an excecutable for Windows that should work under Windows 98, 2000, and XP, so you might be able to skip this step.

That's it! Now you are ready to launch the simulator:

1. Launch MATLAB.
2. In the Matlab window navigate to your VS directory.
3. Launch the Virtual Spectrometer by typing: vsnmr at the Matlab prompt (>>). The VNMR Main Window will appear on the screen.
4. Enjoy VNMR!