These are my personal tools for loading CEST data from 2dseq files (Bruker) and performing corrections and analysis on this data. It is still a WIP, but most features are working in some capacity. All image parameters are loaded from the method file and Lorentzian fitting is done with a two-step method.
For now, fitting only works on in vivo cardiac data.
You can use check_zspecs.py to draw ROIs and check the average z-spectrum in that region.
Run this file from the terminal using the command:
python3 main.py
This will walk you through the necessary selections and output fits to folders within the app directory (under /data/).
All of the required analysis files exist in this directory. They can be changed or modified for personal applications.
Note: This works well for my data and applications, but there is no guarantee it will work for other acquisition or data types. I have done my best to account for other use cases, but it is not comprehensive.
Required packages listed under requirements.txt file.
Install using pip by navigating to the directory and using the command:
pip install -r requirements.txt
2dseq loading and image reorganizing for CEST_RARE sequence (Martinos) adapted from code by Or Perlman.
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 Jun;61(6):1441-50. doi: 10.1002/mrm.21873. PMID: 19358232; PMCID: PMC2860191.
Zaiss M, Schmitt B, Bachert P. Quantitative separation of CEST effect from magnetization transfer and spillover effects by Lorentzian-line-fit analysis of z-spectra. J Magn Reson. 2011 Aug;211(2):149-55. doi: 10.1016/j.jmr.2011.05.001. Epub 2011 May 15. PMID: 21641247.