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.

Installation Instructions

Usage

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

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

See the PINTS User Guide for usage instructions.

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.

See the APPS User Guide for usage instructions.

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

See the FITMAN User Guide for usage instructions.

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

See the SPICeS User Guide for usage instructions.

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

See the BARSTOOL User Guide for usage instructions.

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

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!

Credits

PINTS: Dickson Wong (dwong263@uwo.ca)

FITMAN: Robert Bartha (rbartha@robarts.ca), John Potwarka, and Dick Drost

SPICeS: Dickson Wong (dwong263@uwo.ca)

BARSTOOL: Dickson Wong (dwong263@uwo.ca), Todd Stevens, John Adams (jadam33@uwo.ca)

BARSTOOL-RV: Dickson Wong (dwong263@uwo.ca), Todd Stevens, John Adams (jadam33@uwo.ca)

License

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

isolovey/MAGIQ