In-house software of BioMed
AqsesGUI
How to
1. Requirements 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 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 - 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 - 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 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 - 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 - Open a terminal. - Go to the $AQSESGUI directory - Execute the script aqsesGUI.run
4. Notes - 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)
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Source
You can find the latest source code here: aqsesGUI-src-20060118.tar.gz
- At the moment the source code doesn't contain the code from Aqses or HLSVDPro.
- The source code is released under the Lesser GPL. This means you can use the code in your program and distribute your code and program under every license you want. All the changes you make to the code under the LGPL has to be released again under the LGPL. For more information see: http://www.gnu.org/copyleft/lesser.html.
You can find the java documentation from the available source code here: javadoc
SpidGUI
The goal of SPID is to provide the user with tools capable to simulate, preprocess,
process and classify
in vivo and ex vivo MRS signals. These tools are embedded in a
matlab graphical user interface (GUI). (Pre)processing and classification methods can also
be automatically run in a row using the matlab command line.
The latest build:
Spidv0.3_100715.zip
Manual: Manual.html , Manual.pdf
Contact: diana.sima@esat.kuleuven.be
Howto
1.
Readable format:
o .mat format from SPID (see manual)
o .mat format from the JAVA version of AQSES-GUI
o .txt format from jMRUI3.0
o sdat, spar from Philips
2. Preprocessing methods:
o signal alignment (frequency domain)
o resampling (increase or decrease the resolution)
o truncation of the begin or end points
o eddy current correction with Klose's method
o Lineshape correction with QUALITY method (slightly adapted)
o Water filtering (solvent suppression) with MP-FIR, MP-FIR0 or HLSVD-PRO
o Manual phase correction
o Automatic phase correction
o L2-normalization
o ERETIC normalization (using a reference ERETIC signal)
o Baseline correction using an apodization function
o Baseline offset correction
o Rolling baseline correction using an adapted version of Golotvin's method
o Zero filling
o SNR improvement using an apodization function
o Denoising using wavelets
o Denoising using moving average filter
2. Processing methods:
o Quantification with HLSVD-PRO
o AMARES (linux only)
o AQSES (with the QUEST Subtract method)
o AQSES
o Whole spectrum restricted to the frequency region of interest
o Peak integration
o Peak bucket
o Fisher Criterion
o Kruskall-Wallis
o Relief-F
o PCA
o Fast-ICA (http://www.cis.hut.fi/projects/ica/fastica/)
o Dimensionality reduction toolbox (http://www.cs.unimaas.nl/l.vandermaaten)
o Scale normalizing
2. Classification:
o LS-SVM (http://www.esat.kuleuven.be/stadius/lssvmlab/
o Kernel Logistic Regression
o LDA
o Multi Layer Perceptron (http://www.ncrg.aston.ac.uk/netlab/)
o Clustering Methods
Requirements:
Run on any platform with version of Matlab 7.0 or higher.
Installation:
No specific installation is required (only matlab files).
Available databases:
DB1: Measured database of metabolite profiles
The database is collected at the Philips NT Gyroscan 1.5
Acquisition method: PRESS
Echo time: 23 ms
Volume PRESS box: 2x2x2 cm (obtained from SPAR file):
DB2: Simulated database at 11.4T - 600 MHz - step=0.1392
Start the program:
Go to the installation directory that we call arbitrary here $SPID.
1. For the graphical user interface (GUI):
Run in matlab
>> cd Software
>> spid
2. For the matlab command line:
Run in matlab
>> cd Software
>> runTSPID(template,loadsignals,savepar)
The variables “template,loadsignals,savepar” are explained in the SPID_Manual .
User manual:
A user‘s manual is available in the directory “Readme_doc” under the name “ManualSPID.pdf” .
General info about the content of the different directories is available in the txt file “Readme.txt” (in $SPID).
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