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qmap

PURPOSE ^

Quantitative MRI Analysis Package

SYNOPSIS ^

This is a script file.

DESCRIPTION ^

 Quantitative MRI Analysis Package
 Version 0.1a (QMAP)   10-Jan-2012
 _________________________________________________________________________
     __    __  __          _____  
   / __ \ |  \/  |   /\   |  __ \ 
  | |  | || \  / |  /  \  | |__) |
  | |  | || |\/| | / /\ \ |  ___/  Quantitative MRI Analysis Package
  | |__| || |  | |/ ____ \| |      University of Wisconsin - Madison
   \___\_\|_|  |_/_/    \_\_|      (C) 2005-2012 | v0.01a | Jan-2011
 _________________________________________________________________________

 QMAP is a collection of quantitative MRI analysis software.
 This includes mathematical models of MRI sequences, as well as optimization
 routines to fit these models to experimental data. It also includes a number
 of support functions to handle data I/O and visualize results.

 The general format of a QMAP function is:
   [<parameter> <residuals>] = <parameter>_fit_<model>(<mri data>, <user parameters>, <fitting options>)

 <parameter> refers to some NMR spin system parameter(s) e.g. T1, T2,
 f (fraction of spins in a specific compartment), k (rate of exchange
 between compartments), etc.

 <model> refers to some model of the observed MRI behavior, such as the
 SPGR (fully incoherent) solution to the Bloch equations (Ernst formula)
 for determining T1, bSSFP (fully coherent) solution to the Bloch equations
 (Freeman-Hill formula) for determining T2, or solutions to the
 Bloch-McConnell equations to determine MT parameters.

 <mri data> refers to data collected in an experimental setting.

 <user parameters> refers to user-selectable parameters at the MRI console
 (such as TR/TE, flip angle, or MT pulse parameters). Proper choice of
 these parameters is generally necessary on a case-by-case basis to ensure
 accurate (unbiased) and precise (low noise) estimates. Future versions of
 QMAP will provide tools to optimize user parameters for a given experiment.

 <fitting options> refers to options that can be passed to the
 optimization routine. These may include an initial guess (to improve
 convergence), number of iterations, etc.

 Each function has its own specific syntax and options. Use matlab's 'doc'
 or 'help' functions for more information.

 Principal Investigator:
   Alexey A. Samsonov [samsonov@wisc.edu]
 Contributing Researchers:
   Samuel A. Hurley   [shurley@wisc.edu]
   Pouria Mossahebi   [mossahebi@wisc.edu]
 http://www.medphysics.wisc.edu/~samsonov/qmap/
 _________________________________________________________________________
 Copyright (c) 2005-2012, The Regents of the University of Wisconsin
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without 
 modification, are permitted provided that the following conditions are 
 met:
 
     * Redistributions of source code must retain the above copyright 
       notice, this list of conditions and the following disclaimer.
     * Redistributions in binary form must reproduce the above copyright 
       notice, this list of conditions and the following disclaimer in 
       the documentation and/or other materials provided with the distribution
       
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
 LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
 CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
 SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
 INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
 CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
 ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
 POSSIBILITY OF SUCH DAMAGE.
 _________________________________________________________________________
 Important Notice:

 This software is a research tool and is not intended for clinical use.
 This software is not certified as a commercial medical device (FDA or
 CE-1) for primary diagnostic imaging.
 _________________________________________________________________________

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 % Quantitative MRI Analysis Package
0002 % Version 0.1a (QMAP)   10-Jan-2012
0003 % _________________________________________________________________________
0004 %     __    __  __          _____
0005 %   / __ \ |  \/  |   /\   |  __ \
0006 %  | |  | || \  / |  /  \  | |__) |
0007 %  | |  | || |\/| | / /\ \ |  ___/  Quantitative MRI Analysis Package
0008 %  | |__| || |  | |/ ____ \| |      University of Wisconsin - Madison
0009 %   \___\_\|_|  |_/_/    \_\_|      (C) 2005-2012 | v0.01a | Jan-2011
0010 % _________________________________________________________________________
0011 %
0012 % QMAP is a collection of quantitative MRI analysis software.
0013 % This includes mathematical models of MRI sequences, as well as optimization
0014 % routines to fit these models to experimental data. It also includes a number
0015 % of support functions to handle data I/O and visualize results.
0016 %
0017 % The general format of a QMAP function is:
0018 %   [<parameter> <residuals>] = <parameter>_fit_<model>(<mri data>, <user parameters>, <fitting options>)
0019 %
0020 % <parameter> refers to some NMR spin system parameter(s) e.g. T1, T2,
0021 % f (fraction of spins in a specific compartment), k (rate of exchange
0022 % between compartments), etc.
0023 %
0024 % <model> refers to some model of the observed MRI behavior, such as the
0025 % SPGR (fully incoherent) solution to the Bloch equations (Ernst formula)
0026 % for determining T1, bSSFP (fully coherent) solution to the Bloch equations
0027 % (Freeman-Hill formula) for determining T2, or solutions to the
0028 % Bloch-McConnell equations to determine MT parameters.
0029 %
0030 % <mri data> refers to data collected in an experimental setting.
0031 %
0032 % <user parameters> refers to user-selectable parameters at the MRI console
0033 % (such as TR/TE, flip angle, or MT pulse parameters). Proper choice of
0034 % these parameters is generally necessary on a case-by-case basis to ensure
0035 % accurate (unbiased) and precise (low noise) estimates. Future versions of
0036 % QMAP will provide tools to optimize user parameters for a given experiment.
0037 %
0038 % <fitting options> refers to options that can be passed to the
0039 % optimization routine. These may include an initial guess (to improve
0040 % convergence), number of iterations, etc.
0041 %
0042 % Each function has its own specific syntax and options. Use matlab's 'doc'
0043 % or 'help' functions for more information.
0044 %
0045 % Principal Investigator:
0046 %   Alexey A. Samsonov [samsonov@wisc.edu]
0047 % Contributing Researchers:
0048 %   Samuel A. Hurley   [shurley@wisc.edu]
0049 %   Pouria Mossahebi   [mossahebi@wisc.edu]
0050 % http://www.medphysics.wisc.edu/~samsonov/qmap/
0051 % _________________________________________________________________________
0052 % Copyright (c) 2005-2012, The Regents of the University of Wisconsin
0053 % All rights reserved.
0054 %
0055 % Redistribution and use in source and binary forms, with or without
0056 % modification, are permitted provided that the following conditions are
0057 % met:
0058 %
0059 %     * Redistributions of source code must retain the above copyright
0060 %       notice, this list of conditions and the following disclaimer.
0061 %     * Redistributions in binary form must reproduce the above copyright
0062 %       notice, this list of conditions and the following disclaimer in
0063 %       the documentation and/or other materials provided with the distribution
0064 %
0065 % THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
0066 % AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
0067 % IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
0068 % ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
0069 % LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
0070 % CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
0071 % SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
0072 % INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
0073 % CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
0074 % ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
0075 % POSSIBILITY OF SUCH DAMAGE.
0076 % _________________________________________________________________________
0077 % Important Notice:
0078 %
0079 % This software is a research tool and is not intended for clinical use.
0080 % This software is not certified as a commercial medical device (FDA or
0081 % CE-1) for primary diagnostic imaging.
0082 % _________________________________________________________________________
0083 
0084 
0085 disp('    __    __  __          _____  ');
0086 disp('  / __ \ |  \/  |   /\   |  __ \ ');
0087 disp(' | |  | || \  / |  /  \  | |__) |');
0088 disp(' | |  | || |\/| | / /\ \ |  ___/  Quantitative MRI Analysis Package');
0089 disp(' | |__| || |  | |/ ____ \| |      University of Wisconsin - Madison');
0090 disp('  \___\_\|_|  |_/_/    \_\_|      (C) 2005-2012 | v0.01a | Jan-2012');
0091 disp('                                  ');
0092 disp('Type ''doc qmap'' for more information.');

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