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.

• Installation Instructions

Navigate to the folder containing the MAGIQ files and launch the program with the following commands:

cd <filepath to MAGIQ>
python main.py

You can launch the individual programs of the MAGIQ Software Suite using:

python pints.py
python apps.py
python fitman.py
python spices.py
python barstool.py

You can also run the "Rodent Version" of BARSTOOL using the command:

python barstoolrv.py

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

See the PINTS User Guide for usage instructions.

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.

See the APPS User Guide for usage instructions.

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

See the FITMAN User Guide for usage instructions.

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

See the SPICeS User Guide for usage instructions.

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

See the BARSTOOL User Guide for usage instructions.

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

See the BARSTOOL-RV User Guide for usage instructions.

Note that the "Bruker" aspects of this program has yet to be finalized. Use at your own peril!

PINTS: Dickson Wong ([email protected])

FITMAN: Robert Bartha ([email protected]), John Potwarka, and Dick Drost

SPICeS: Dickson Wong ([email protected])

BARSTOOL: Dickson Wong ([email protected]), Todd Stevens, John Adams ([email protected])

BARSTOOL-RV: Dickson Wong ([email protected]), Todd Stevens, John Adams ([email protected])

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