Open-source hardware and software for implementing a preclinical MRgHIFU system on a small-animal MRI scanner
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README.md

#smallAnimalMRgHIFU


Open-source plans for constructing and implementing a preclinical MRgHIFU/MRgFUS system on a small-animal MRI scanner.

DOI: 10.5281/zenodo.51633

ME Poorman, VL Chaplin, K Wilkens, MD Dockery, T Giorgio, WA Grissom, and CF Caskey

Vanderbilt University Institue for Imaging Science

Freely available for use and modification with citation of original distribution/article (https://jtultrasound.biomedcentral.com/articles/10.1186/s40349-016-0066-7). See license file for more information.


MRgFUS_software:

  • Matlab code to control sonication real-time with baseline subtraction thermometry and a PID feedback controller
  • V1: Single script version - intended for debugging purposes only
  • V2: Modular software and GUI commented and tested - intended for use and straightforward modification
  • ARFI folder: pulse sequence and recon code. C code must be compiled prior to use
  • calcCEM_vect.m: computes thermal dose given focal temperature
  • initFGEN.m: initializes waveform generator
  • offFGEN.m: stops all waveform outputs to transducer
  • parsepp.m: reads parameter file
  • pidUpdate.m: PID controller computation
  • readInFID.m: reads in next image from .fid data file
  • runControlSoftware.m: master script, contains GUI to set up execution, begins sonication
  • runExpGui.m/.fig: button to begin sonication
  • runTempRecon.m: computes thermometry, calls other modules for execution
  • userinterface.m/fig: optional GUI to set up sonication parameters

###MRgHIFU_hardware_pt#:

  • Solidworks files and parts list of all hardware components used to build the system
  • Split into 4 ".zip" files to comply with size requirements. Unzip into same folder for proper use.

Instructions for use:

  • See instructions file

License

  • See license file

Helpful tips:

  • On the Varian systems, the current acquisition file can be found in '~/vnmrsys/exp2/acqfil/fid'
  • Previously stored Varian data is found in'~/vnmrsys/data/studies/s_YYYYMMDD_##'
  • Can run software in recon mode to see past execution