Computing Resources

CEST Data Processing Tools


Description of the package

The package of CEST Data Processing Tools was developed for the display and analysis of in vitro and in vivo CEST imaging datasets using the commercially available Matlab program. There are three Matlab scripts which are included in this package:

The Matlab function preprocess.mhas been written for 1) SNR based thresholding and 2) manually defining regions of interest (ROI) that will be analyzed in the next steps.

The Matlab function B0map.mhas been written to produce a B0 map by pixelwise fitting the WASSR data sets collected.

The Matlab function CEST_processing.mhas been written to perform quantitative z-spectral analysis on frequency-swept CEST data sets. In particular, the following actions are performed: 1) correct B0 inhomogeneities pixelwise; 2) display plots of the z-spectrum and MTRasym for a defined ROI; and 3) display MTRasym maps.

In addition, example data sets are included for the purpose of testing, which was acquired on a phantom of myo-inositol solutions (31.2 mM in PBS) with pH ranging from 5.0 to 7.8. A PDF manual is also included.

Disclaimer

These Matlab functions have been developed at the Kennedy Krieger Institute and Johns Hopkins Medical School in Baltimore, Maryland, United States of America. They are used primarily by members of The F.M. Kirby Research Center and The Russell H. Morgan Department of Radiology and Radiological Science. The Matlab package is available publicly, in the hope that it will be useful, but without any warranty and without even the implied warranty of merchantability or fitness for a particular purpose. It is designed to help researchers in the field of Magnetic Resonance Imaging who may have interests of CEST imaging. It is not intended for use in a clinical setting.

Citation

If you process data using the package for any publication, please cite the following publication:

  1. Liu G, Gilad AA, Bulte JWM, Van Zijl PCM, Mcmahon MT. High-throughput screening of chemical exchange saturation transfer MR contrast agents. Contrast Media Mol Imaging 2010;5(3):162-170.

Additional publications which are related:

  1. Kim M, Gillen J, Landman BA, Zhou J, van Zijl PC. Water saturation shift referencing (WASSR) for chemical exchange saturation transfer (CEST) experiments. Magn Reson Med 2009;61(6):1441-1450.

  2. Liu G, Moake M, Har-el Y-e, Long CM, Chan KWY, Cardona A, Jamil M, Walczak P, Gilad AA, Sgouros G, van Zijl PCM, Bulte JWM, McMahon MT. In vivo multicolor molecular MR imaging using diamagnetic chemical exchange saturation transfer liposomes. Magn Reson Med 2012;67(4):1106-1113.

  3. Liu G, Chan K, Song X, Zhang J, Gilad AA, Bulte JWM, van Zijl PCM, McMahon MT. NOrmalized MAgnetization Ratio (NOMAR) Filtering for Creation of Tissue Selective Contrast Maps. Magn Reson Med 2012.

Download

Download the package.

Downloads as of 23 Feb 2016
Year Americas 50 Asia/Pacific 45 Europe 62
20125 3 3
201311 15 21
20148 14 20
201521 12 17
20165 1 1
Grand Total 160
(includes 3 with location unspecified)

For more information please contact the Kirby Center.

Thank you.