ncigt-fil
The NC-IGT Fast Imaging Library

In MR imaging applications, the dominant constraint to image acquisition is time. As the field has matured, a number of methods have been developed to reduce the length of time needed to acquire an image by reducing the amount of data needed to reconstruct a clinically viable image. This reduction in acquired data requirements is achieve through encodings that are complementary to the fundamental Fourier encoding employed in MRI. This includes temporal-domain encodings, such as UNFOLD, and spatial-domain encodings, as in parallel MR imaging methods such as SENSE and GRAPPA.

This library of functions provides a number of reconstruction algorithms that accurately employ these advanced MR imaging methods. This includes

as well as a number of associated MR image reconstruction algorithms, including

As of version 0.96, the library is compatible with both GE and Siemens MR scanners. For GE MR scanners, file format support includes raw data output using the "P-file" format, and the "vrgf.dat" and "ref.dat" files to respectively correct for ramp-sampling and gradient-offset phase correction during EPI acquisitions.

This library was developed at the National Center for Image Guided Therapy by

igt-logo.png
Medical Imaging Physics Group
Dept. of Radiology
Brigham and Women's Hospital
75 Francis Street
Boston, MA 02115

Please direct inquires to: ncigt.nosp@m.-fil.nosp@m.@bwh..nosp@m.harv.nosp@m.ard.e.nosp@m.du

Acknowledgments

The development of this library was supported by the United States National Institute of Heath (NIH) under Grant U41 RR019703-01A.

Contributors: Bruno Madore (BWH), W. Scott Hoge (BWH), Greg Kirk (formerly BWH), Steven J. Haker (formerly BWH)

The FFT calculations are provided by the KISS FFT library.

KISS FFT is Copyright (c) 2003-2004 Mark Borgerding
All rights reserved.
Redistribution and use of KISS FFT in source and binary forms,
with or without modification, are permitted provided that the
following conditions are met:
      Redistributions of KISS FFT source code must retain the
      above copyright notice, this list of conditions and the
      following disclaimer.
      Redistributions of KISS FFT 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.
      Neither the author of KISS FFT nor the names of any KISS
      FFT contributors may be used to endorse or promote products
      derived from this software without specific prior written
      permission.
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.

Length 2N FFTs are handled by code derived from OOURA FFT:

    Copyright(C) 1996-2001 Takuya OOURA
    email: ooura -at- mmm -dot- t -dot- u-tokyo -dot- ac -dot- jp
    http://momonga.t.u-tokyo.ac.jp/~ooura/fft.html
    You may use, copy, modify this code for any purpose and 
    without fee. You may distribute this ORIGINAL package.

With version 0.9, the library now contains multiple functions to compute the Singular Value Decomposition (SVD) of a matrix.

The core SVD functions are an implementation of the bilateral diagonalization approach first described by Golub et. al. This algorithm is known to be extremely stable, and is drawn from the Colorado School of Mines Center for Wave Propogation Seismic Un*x C library.

Copyright (c) Colorado School of Mines, 2007.
--------------------------------------------------------------------
Credits: Ian Kay, Canadian Geological Survey, Ottawa, Ontario 1999.
This is a translation in C from code written in Fortran that
appeared in NETLIB, EISPACK, and SLATEC collections that was
itself a translation from an original Algol code that appeared
in:
  Golub, G. and C. Reinsch (1971) Handbook for automatic computation 
  II, Linear Algebra, p 134-151. SpringerVerlag, New York.
See also discussions of a similar code in Numerical Recipes in C.  
svd_sort: Nils Maercklin, GeoForschungsZentrum (GFZ) Potsdam, 
Germany, 2001.
--------------------------------------------------------------------
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.
      Neither the name of the Colorado School of Mines nor the
      names of its contributors may be used to endorse or
      promote products derived from this software without
      specific prior written permission.
Warranty Disclaimer:
THIS SOFTWARE IS PROVIDED BY THE COLORADO SCHOOL OF MINES 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 COLORADO SCHOOL OF MINES 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.

To support both the image-phase-alignment and virtual-body-coil functions, a second SVD implementation using a Lanczos iterative algorithm is now included. For the purpose of estimating the singular vectors associated the largest singular value of large matrices, this Lanczos approach is significantly faster than the more stable bi-diagonalization approach.

This code is derived from the netlib SVDPACK, via the SVDLIBC library (http://tedlab.mit.edu:16080/~dr/SVDLIBC/), and modified to be thread-safe. This code is

----------------------------------------------
(c) Copyright 2003, Douglas Rohde
adapted from SVDPACKC, which is
(c) Copyright 1993, University of Tennessee
 All Rights Reserved                          
----------------------------------------------

To support GROG functions, the library has begun to transition to Eigen3 for matrix decompositions since version 2.0. Version 2.0 uses eigen-3.1.4 (with the EIGEN_MPL2_ONLY flag), which is distributed under the MPL2 license:

// This Source Code Form is subject to the terms of the Mozilla
// Public License v. 2.0. If a copy of the MPL was not distributed
// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.