MAGIQ

MAGIQ (MRS Analysis, Generation, and In-Vivo Quantification) is a software suite is used by the Bartha Lab to generate simulated prior-knowledge templates, post-process spectra, to fit spectra, and to quantify metabolite concentrations.

Project Details

About MAGIQ

MAGIQ stands for MRS Analysis, Generation, and In-Vivo Quantification. This software suite is used by the Bartha Lab to generate simulated prior-knowledge templates, post-process spectra, to fit spectra, and to quantify metabolite concentrations.

Included Tools

PINTS (Prior Information Templates)

PINTS is a program used to generate simulated semi-LASER and LASER 1H-MRS prior information templates (basis sets). With PINTS, you can:

  • simulate metabolites
  • visualize the basis sets
  • generate FITMAN compatible *.cst, *.ges, and *.dat files

APPS (Assorted Pre-Processing Tools)

APPS is a program used to perform a variety of signal processing steps before you fit MR spectra collected in-vivo. Some things that can be done include:

  • Converting spectroscopy files generated from Bruker scanners into a FITMAN compatible *.dat format
  • Removal of residual water signal from the in-vivo spectrum
  • Subtraction of a macromolecule spectrum from the full (metabolite + macromolecule) spectrum acquired during an interleaved acquisition.

FITMAN

FITMAN is a program used to post-process and fit MR spectra collected in-vivo. With FITMAN, you can:

  • read and convert spectroscopy files generated from GE, SIEMENS, and VARIAN scanners
  • perform post processing of MR spectra to remove eddy current artifacts and restore a Lorentzian lineshape
  • perform subtraction of macromolecule resonances
  • remove residual water signal
  • fit spectra (including fitting of water suppressed and unsuppressed data)
  • generate SPICeS and BARSTOOL compatible *.out files

SpICeS (Spectroscopy Interactive Component Selector)

SPICeS is a program used to visualize fitted spectral models. with SPICeS, you can:

  • visualize the raw spectra data (*.dat files) and fitted models (*.out files)
  • define groups of metabolites to visualize together
  • output the visualization with a variety of vector and raster image formats

BARSTOOL

BARSTOOL is a program used to quantify metabolites measured in-vivo. With this program, you can:

  • calculate metabolite ratios
  • calculate metabolite Cramér-Ráo lower bounds
  • calculate metabolite concentrations
  • perform brain extraction and gray matter/ white matter / CSF segmentation via a graphical interface to FSL BET and FAST commands
  • save results to a Microsoft Excel readable file

BARSTOOL-RV (Rodent Version)

BARSTOOL-RV is a version of the BARSTOOL program that works specifically for rodent spectroscopy data. With this program, you can:

  • calculate metabolite ratios
  • calculate metabolite Cramér-Ráo lower bounds
  • calculate metabolite concentrations
  • perform brain extraction and tissue/CSF segmentation on anatomical images via a graphical interface to PCNN3D and RATS
  • save results to a Microsoft Excel readable file

Credits

License

This software was developed for internal use by the Bartha Lab and Bartha Lab collaborators. It is not intended for commercial use.

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Project Link

https://github.com/dwong263/MAGIQ