Changes between Version 82 and Version 83 of WikiStart

Oct 27, 2010, 6:55:57 PM (10 years ago)



  • WikiStart

    v82 v83  
    11= Welcome to the VeSPA Project =
    3 Vespa stands for Versatile Simulation Pulses and Analysis. The environment contains three magnetic resonance (MR) spectroscopy software applications called RFPulse, Simulation and Analysis. These are applications for MR RF pulse design, MR spectral simulation, and spectral processing and analysis of MR data.
     3VeSPA stands for Versatile Simulation Pulses and Analysis. The environment contains three magnetic resonance spectroscopy (MRS) software applications called RFPulse, Simulation and Analysis. These are applications for MR RF pulse design, MR spectral simulation, and spectral processing and analysis of MR data.
     5'''What is VeSPA''' (ShortVersion) ?
     7VeSPA is a project, the goal of which is to utilize current software engineering "best practices" to refactor 3 existing and widely used MRS software packages, written by the authors and colleagues, to create an integrated open source package for performing and analyzing MRS experiments. VeSPA, the resulting integrated package, provides a greatly enhanced, more complete, easier to use, easier to extend set of tools for MRS simulation and analysis. The original applications were written in closed source languages ([ GAVA/Gamma] and IDL_Vespa in [ IDL], and [ MatPulse] in [ Matlab]) that have licensing issues (primarily restricted use and substantial fees) that make their use for scientific collaboration problematic, as well as make them relatively difficult to extend and virtually impossible to integrate. Rewriting the applications in the open source language, [ Python], and utilizing the powerful [ NumPy], [ SciPy], and [ Matplotlib] libraries allows for a clean, robust and full featured integration of the packages in a way that provides a much more natural work flow for researchers as well as making the integrated package much more easily extended by those who need added functionality. As an example it has been straightforward for the authors to add functionality corresponding to recent developments in MRS, providing substantial added value to the integrated VeSPA package for a modest coding effort.
     9One of the goals of the earlier individual packages as well as the integrated package is to provide sophisticated tools to non experts who would otherwise have great difficulty in taking advantage of capabilities that have become available to researchers in MRS. The original MatPulse package written by Professor Gerald Matson encapsulated a large body of knowledge regarding RF pulse design allowed users with relatively little experience to explore and utilize that knowledge in a straightforward manner that resulted in rapid development of useful RF pulses. Similarly the gamma NMR simulation library written by Dr. Scott Smith allowed users with with limited knowledge of the underlying quantum mechanical details to write C++ programs that explored the effects of various pulse and pulse sequence designs using full quantum mechanical density matrix calculations. The GAVA/Gamma package was an attempt to further simplify NMR simulations by providing a graphical interface to a subset of the gamma library thus freeing users with no knowledge or interest in C++ programming to explore pulse and pulse sequence designs. The Simulation component of VeSPA goes even further by using the SWIG package to provide a python interface to gamma, referred to as pygamma. Simulation itself provides a graphical interface with powerful plotting and analysis functionality that is built on top of pygamma. But pygamma can be be used independently to produce powerful NMR simulations in python with the majority of the calculations performed in underlying fast C++ code. The Analysis component of VeSPA provides an updated, greatly extended, python version of the IDL_Vespa spectral fitting package originally written by the authors and colleagues. The updating and integration of these 3 packages provides greatly enhanced possibilities for exploring, developing, and analyzing MRS experiments; in the following we briefly describe some possible scenarios.         
     11'''How Can I Use VeSPA?'''
     13One of the simplest ways to use VeSPA is to take advantage of the updated and extended capabilities of the individual packages. RFPulse provides an improved interface for the design of standard MR pulses such as SLR and Adiabatic Pulses. Access to new functionality like generation of pulses via optimal control will provide previously unavailable capabilities. Simulation provides the ability to incorporate subtle effects on spectra such as field inhomogeneities and chemical shift offset effects by allowing users to incorporate their own pygamma code in simulations. Analysis will provide access to previously widely scattered and difficult to compare spectral analysis methods including some that were previously unavailable such as improved reference deconvolution methods.
     15A typical use of the integrated package will be to iteratively design a RF pulse and test it's effect on the spectra of metabolites of interest. Current details of the method for providing the pulses generated by RFpulse to the sequence design methods used by Simulation are under development but a tutorial linked to below shows how to read a text file containing a list of real and imaginary values representing a pulse, into pygamma code for a simulation. Once one is satisfied with the resulting pulse and pulse sequence design an experiment could be run and fit, using the Analysis package, against the Simulation results.
     17As part of the above scenario, results generated by the Simulation package are used by the Analysis package for spectral fitting. This is one of the two major methods currently in use for providing basis function for fitting MRS data. The other method is to apply the pulse sequence to be used in the experiment to phantoms containing the metabolites of interest (provided that the eventual application will be to a sample containing the set of metabolites such as a biological sample) and to use the resulting functions as "basis functions" for the fitting procedure. Both methods have strengths and weaknesses, and both can produce basis functions that can be used by the Analysis package but for a number of reasons the authors are advocates of the method of generating basis functions via spectral simulation. The VeSPA package is obviously specifically designed to make use of spectral simulations and tutorials below focus on how to generate "basis functions" using the Simulations package.   
    521== Overview ==
    7  * ShortVersion - What is Vespa?
    823 * TheDevelopers - Personal Profiles
    924 * [wiki:FAQ] - Frequently asked questions (about Simulation - for now)