Changes between Version 88 and Version 89 of WikiStart


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Nov 1, 2010, 3:45:32 PM (9 years ago)
Author:
kyoung
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    33VeSPA 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.
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    5 '''What is VeSPA''' ([https://scion.duhs.duke.edu/vespa/project/wiki/LongVersion Longer Version]) ?
     5'''What is VeSPA''' ([wiki:LongVersion Longer Version]) ?
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    77The Vespa package extends the maintenance and development of three previously developed magnetic resonance spectroscopy (MRS) software tools by migrating them into an integrated, open source, open development platform. Vespa stands for Versatile Simulation Pulses and Analysis.
     
    1919'''NIH grant number 1R01EB008387-01A1''' funded the maintenance and extension of these separate applications into a combined environment based entirely on the Python language.
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    22 '''What Can VeSPA Do for Me ?'''
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    24 One 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.
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    26 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.
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    28 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.
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    30 A 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.
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    32 As 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.   
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    3621== Overview ==
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    38  * [https://scion.duhs.duke.edu/vespa/project/wiki/LongVersion Detailed Description of VeSPA]
    39  * [https://scion.duhs.duke.edu/vespa/project/wiki/WhatCanVeSPA_Do How to Use VeSPA]
     23 * [wiki:LongVersion Detailed Description of VeSPA]
     24 * [wiki:WhatCanVeSPA_Do How to Use VeSPA]
    4025 * TheDevelopers - Personal Profiles
    4126 * [wiki:FAQ] - Frequently asked questions (about Simulation - for now)