CSItools - A Matlab toolbox for processing magnetic resonance spectroscopic images (MRSI)
B. M. Kelm
CSItools is a Matlab toolbox for the processing of mangnetic resonance spectroscopic images (MRSI). CSItools comes with the CLARET graphical user interface (GUI) that can be used in cinical research prototypes for evaluating new quantification and/or classification approaches. Since CSItools has a modular design it is most suitable for batch processing huge amounts of data with user-defined Matlab scripts. CSItools supports various input formats among which are DICOM, Siemens RDA and Phillips SDAT. It offers quantification using the HSVD method and NLS fitting (nonlinear least squares) using Voigt metabolite models as well as measured or simulated metabolite templates. Many more functions useful for the processing of MRSI are provided. For an overview type 'help Contents' in the CSItools installation directory. CSItools requires the Matlab optimization as well as the image processing toolboxes. In order to compile the included mex-files, a C/C++ compiler (MSVC, gcc) as well as the DCMTK library (https://dicom.offis.de/) are required.
Software Download | Tutorial data | License | Changelog
References
Automated Estimation of Tumor Probability in Prostate MRSI: Pattern Recognition vs. Quantification.Kelm, B.M.; Menze, B.H.; Zechmann, C.M.; Baudendistel, K.T. & Hamprecht, F.A.
Magn Reson Med, 2007, (57): 150 - 159
(doi: 10.1002/mrm.21112) (preprint)
CLARET: a tool for fully automated evaluation of MRSI with pattern recognition methods.
Kelm, B.M.; Menze, B.H.; Neff, T.; Zechmann, C.M. & Hamprecht, F.A.
In: Handels, H.e.a. (eds.), Bildverarbeitung für die Medizin 2006 - Algorithmen, Systeme, Anwendungen, Springer, Hamburg/Germany, 2006, Informatik Aktuell, pp. 51-55
(doi: 10.1007/3-540-32137-3_11) (preprint)
Mimicking the human expert: pattern recognition for an automated assessment of data quality in MRSI
Menze, B.H.; Kelm, B.M.; Weber, M.; Bachert, P. & Hamprecht, F.A.
Magnetic Resonance in Medicine, 2008, (59): 1457-1466
(doi: 10.1002/mrm.21519) (preprint)
Using Spatial Prior Knowledge in the Spectral Fitting of Magnetic Resonance Spectroscopic Images
Kelm, B.M.; Kaster, F.O.; Henning, ; Weber, M.; Bachert, P.; Boesiger, P.; Hamprecht, F.A. & Menze, B.H.
NMR Biomed, 2011
(doi: 10.1002/nbm.1704) (preprint)