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The aqsesGUI software is a software package for processing Magnetic Resonance Spectroscopy signals.

AqsesGUI Tutorial
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author: Bart De Neuter, Diana Sima
copyright: 	Katholieke Universiteit Leuven,
	 	Departement Electrical Engineering,
	 	ESAT-SCD, BioMed, Belgium


1. Requirements
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A Java Runtime Environment (JRE) has to be installed in order to use the software. It has to be the JRE version 1.5 or higher. To check which version you have:

For Windows:

	- Open a DOS-box or Command prompt and type: java -version 

For Linux:

	- Open a terminal and type: java -version 

If you don't have a JRE installed or you have to upgrade it, you can download the latest version from the website http://www.java.com.




2. Installation
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The software is packaged in the file aqsesGUI-xxx.tar.gz and runs on Windows and Linux. Installation is quite straightforward.

2.1 Installation on Windows
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	- Open the file with WinZip or another program to unpack the tar.gz archive. 
	- Unpack or extract the file to the installation directory. The installation directory is the directory where you want to install the software. 
	- The directory aqsesGUI-x.x is created in the installation directory and contains the software. We will refer to this directory as $AQSESGUI.
	- You can remove the file aqsesGUI-xxx.tar.gz.

2.2 Installation on Linux
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	- copy the file to the installation directory. The installation directory is the directory where you want to install the software. 
	- Unpack the file in the installation directory: tar -xvzpf aqsesGUI-xxx.tar.gz.
	- The directory aqsesGUI-x.x is created in the installation directory and contains the software. We will refer to this directory as $AQSESGUI.
	- if necessary, make the script aqsesGUI.run in $AQSESGUI executable: chmod u+x aqsesGUI.run
	- You can remove the file aqsesGUI-xxx.tar.gz.

3. Start the program
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When the program is started, it will locate, load and initialize all the available plugins. The software will also create the two following directories in the home directory from the user that runs the program:

	- .aqsesGUI: This directory is used to store the settings from the program.
	- aqsesGUI: This directory is used to store data.

3.1 Windows
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	- Go to the $AQSESGUI directory
	- Double click on the batch file aqsesGUI.bat 

Alternative:

	- Open a Command Prompt.
	- Go to the $AQSESGUI directory
	- Execute the batch file aqsesGUI.bat

3.2 Linux
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	- Open a terminal.
	- Go to the $AQSESGUI directory
	- Execute the script aqsesGUI.run

4. Notes
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	- The software has 2 modes: a clinical mode (minimal, just loading and executing from templates to get results) and a research mode in which you have all the options available.
	- Under linux, it can happen that you can not control the GUI with the mouse. This is due to a bug in the GTK-theme. If this happens, you can solve it by switching to the metal theme. You can switch the theme in options -> Look & Feel
	- You can pass options to the script file and the batch file. One option is to set the language -language=en. By default the software takes the language from the system it is running on. If the software is not translated in this language the GUI appears with mixed languages (English and the default language). You can set the language then to english by passing the option -language=en.
	- The following languages are available at the moment: english (en), dutch (nl)