manual.bib

@string{ACMTMS = "ACM Trans. Math. Software "}
@string{AMS = "Ann. Math. Stat." }
@string{AOR = "Ann. Oper. Res."}
@string{AR = "Acad. Radiol."}
@string{CC = "Contr. Cybern"}
@string{EC = "Evol. Comput."}
@string{EJR = "Eur. J. Radiol."}
@string{GPEM = "Genet. Program. Evolvable. Mach."}
@string{IJCV = "Int. J. Comput. Vis."}
@string{IJROBP = "Int. J. Radiation Oncology Biol. Phys."}
@string{IVC = "Image Vis. Comput."}
@string{JCAT = "J. Comput. Assist. Tomo."}
@string{JOTA = "J. Optim. Theor. Appl."}
@string{JMIV = "J. Math. Imag. Vis." }
@string{JMS = "J. of Math. Sci."}
@string{JRNBS = "J. Res. Nat. Bur. Stand."}
@string{LAA = "Linear Algebra Appl."}
@string{MAC = "Mat. Apl. Comput."}
@string{MC = "Math. Comp." }
@string{Media = "Med. Image Anal."}
@string{MedPhys = "Med. Phys."}
@string{NC = "Nat. Comput."}
@string{PMB = "Phys. Med. Biol." }
@string{PR = "Pattern Recognit."}
@string{PRIA = "Pattern Recogn. Image Anal."}
@string{PRL = "Pattern Recogn. Lett."}
@string{SO = "Strahlenther. Onkol."}
@string{STSIP = "Sampling Theory in Signal and Image Processing"}
@string{TSC = "Theor. Comput. Sci."}



@ARTICLE{Brooks07,
  author =      {Brooks, R. and Arbel, T.},
  title =       {Improvements to the itk::{K}ernel{T}ransform and subclasses},
  journal =     {The Insight Journal},
  year =        {2007},
  volume =      {January - June},
  pages =       {},
  number =      {},
  url =         {http://hdl.handle.net/1926/494},
}

@article{Cru06:Generalized,
  author =   {Crum, W.~R. and Camara, O. and Hill, D.~L.~G.},
  title =    {Generalized overlap measures for evaluation and validation in medical image analysis},
  journal =  IEEE_J_MI,
  year =     2006,
  volume =   25,
  number =   11,
  pages =    {1451-1461}
}

@ARTICLE{Davis97,
  author =      {Davis, M.~H. and Khotanzad, A. and Flamig, D.~P. and Harms, S.~E.},
  title =       {A physics-based coordinate transformation for {3-D} image matching},
  journal =     IEEE_J_MI,
  year =        {1997},
  volume =      {26},
  pages =       {317-328},
  number =      {3},
}

@misc{elastix,
  author =      {Stefan Klein and Marius Staring},
  title =       {elastix},
  url =         {http://elastix.isi.uu.nl},
  howpublished = {http://elastix.isi.uu.nl},
  year =        {2004},
}

@article{Fis04:Unified,
  author =      {Fischer, B. and Modersitzki, J.},
  title =       {A unified approach to fast image registration and a new curvature based registration technique},
  journal =     LAA,
  year =        {2004},
  volume =      {380},
  pages =       {107 - 124},
  dummymonth =       {March}
}

@book{Hajnal01,
  dauthor =      {},
  title =       {Medical Image Registration},
  editor =      {Joseph V Hajnal and Derek L G Hill and David J Hawkes},
  publisher =   {CRC Press},
  year =        {2001},
  ISBN =        {0849300649},
}

@article{HillEA01,
  author =      {D.~L.~G.~Hill and P.~G.~Batchelor and M.~Holden and D. J. Hawkes},
  title =       {Medical Image Registration},
  journal =     PMB,
  year =        {2001},
  volume =      {46},
  pages =       {R1 - R45},
  number =      {3},
}

@InProceedings{Huizinga2014,
  author =      {Huizinga, Wyke and Klein, Stefan and Poot, Dirk H. J.},
  title =       {Fast Multidimensional {B}-spline Interpolation Using Template Metaprogramming},
  booktitle =   {6th International Workshop Biomedical Image Registration (WBIR)},
  volume =      {},
  series =      {},
  editors =     {Ourselin, S{\'e}bastien and Modat, Marc},
  dummyaddress =     {London, UK},
  year =        {2014},
  pages =       {11 - 20},
  dummymonth =       {July},
}

@manual{ITKSoftwareGuideSecondEdition,
  Title          = {The {ITK} {S}oftware {G}uide},
  dummyauthor         = {Luis {Ib\'a\~nez} and Will Schroeder and Lydia Ng and Josh Cates},
  author         = {L.~{Ib\'a\~nez} and W.~Schroeder and L.~Ng and J.~Cates},
  Organization   = {Kitware, Inc. ISBN 1-930934-15-7},
  dummyurl            = {http://www.itk.org/ItkSoftwareGuide.pdf},
  Edition        = {Second},
  year           = {2005}
}

@article{KleinEA07,
  author =       {S.~Klein and M.~Staring and J.~P.~W.~Pluim},
  title =        {Evaluation of Optimisation Methods for Nonrigid Medical Image Registration using Mutual Information and {B}-splines},
  journal =      IEEE_J_IP,
  year =         {2007},
  volume =       {16},
  number =       {12},
  pages =        {2879 - 2890},
  month =        {December},
}

@article{Kle08:Automatic,
  author =       {S.~Klein and U.~A.~van~der~Heide and I.~M.~Lips and M.~van~Vulpen and M.~Staring and J.~P.~W.~Pluim},
  title =        {Automatic segmentation of the prostate in {3D} {MR} images by atlas matching using localized mutual information},
  journal =      MedPhys,
  year =         {2008},
  volume =       {35},
  number =       {4},
  pages =        {1407 - 1417},
  month =        {April},
}

@article{Klein09,
  author  = {S.~Klein and J.~P.~W.~Pluim and M.~Staring and M.A.~Viergever},
  title   = {Adaptive Stochastic Gradient Descent Optimisation for Image Registration},
  journal = {International Journal of Computer Vision},
  volume  = {81},
  number  = {3},
  pages   = {227 - 239},
  month   = {March},
  year    = {2009},
}

@article{LesterEA99,
  author =       {H.~Lester and S.~R. Arridge},
  title =        {A survey of hierarchical non-linear medical image registration},
  journal =      PR,
  year =         {1999},
  volume =       {32},
  number =       {1},
  pages =        {129 - 149},
  dummymonth =   {??}
}

@article{MaesEA97,
  author =      {F. Maes and A. Collignon and D. Vandermeulen and G. Marchal and P. Suetens},
  title =       {Multimodality Image Registration by Maximization of Mutual Information},
  journal =     IEEE_J_MI,
  year =        {1997},
  volume =      {16},
  pages =       {187 - 198},
  number =      {2},
}

@article{MaintzEA98,
  author =      {Maintz, J. B. A. and Viergever, M. A.},
  title =       {A survey of medical image registration},
  journal =     Media,
  year =        {1998},
  volume =      {2},
  pages =       {1 - 36},
  number =      {1},
}

@article{MattesEA03,
  author =      {Mattes, D. and Haynor, D. R. and Vesselle, H. and Lewellen, T. K. and Eubank, W.},
  title =       {{PET}-{CT} image registration in the chest using free-form deformations},
  journal =     IEEE_J_MI,
  year =        {2003},
  volume =      {22},
  pages =       {120 - 128},
  number =      {1},
  dummymonth =       {January}
}

@article{Metz11,
  author = {C.T. Metz and S. Klein and M. Schaap and T. van Walsum and W.J. Niessen},
  journal = {Medical Image Analysis},
  year = {2011},
  volume = {15},
  number = {2},
  pages = {238-249},
  title = {Nonrigid registration of dynamic medical imaging data using {nD+t} {B}-splines and a
     groupwise optimization approach},
  abstract = {},
}


@book{Modersitzki04:Numerical,
  author =      {J.~Modersitzki},
  title =       {Numerical Methods for Image Registration},
  publisher =   {Oxford University Press},
  year =        {2004},
  ISBN =        {978-0198528418},
}

@InProceedings{Murphy08,
  author =      {K. Murphy and B. van Ginneken and J.P.W. Pluim and S. Klein and M. Staring},
  title =       {Semi-Automatic Reference Standard Construction for Quantitative Evaluation of Lung {CT} Registration},
  booktitle =   {Medical Image Computing and Computer-Assisted Intervention (MICCAI)},
  volume =      {5242},
  series =      {Lecture Notes in Computer Science},
  editors =     {Dimitris N. Metaxas and Leon Axel and Gabor Fichtinger and G{\'a}bor Sz{\'e}kely},
  dummyaddress =     {},
  year =        {2008},
  pages =       {1006 - 1013},
  dummymonth =       {October},
}

@book{NocedalEA99,
  author =      {J.~Nocedal and S.~J.~Wright},
  title =       {Numerical optimization},
  publisher =   {Springer-Verlag, New York},
  year =        {1999},
  ISBN =        {0-387-98793-2},
}

@InProceedings{Qiao2014,
  author =      {Y. Qiao and Lelieveldt, B.P.F. and M. Staring},
  title =       {Fast automatic estimation of the optimization step size for nonrigid image registration},
  booktitle =   {SPIE Medical Imaging: Image Processing},
  volume =      {},
  series =      {Proceedings of SPIE},
  editors =     {Nico Karssemeijer and Ehsan Samei},
  daddress =     {San Diego, CA, USA},
  year =        {2014},
  pages =       {},
  dummymonth =       {February},
}

@article{Qiao:2016,
  author  = {Yuchuan Qiao and Baldur van Lew and Boudewijn P.F Lelieveldt and Marius Staring},
  title   = {Fast Automatic Step Size Estimation for Gradient Descent Optimization of Image Registration},
  journal = IEEE_J_MI,
  volume  = {35},
  number  = {2},
  pages   = {391 - 403},
  month   = {February},
  year    = {2016},
}

@article{Roh04:Evaluation,
  author =       {T.~Rohlfing and R.~Brandt and R.~Menzel and C.~R.~{Maurer Jr.}},
  title =        {Evaluation of atlas selection strategies for atlas-based image
   segmentation with application to confocal microscopy images of bee brains},
  journal =      {NeuroImage},
  year =         {2004},
  dummymonth =   {April},
  volume =       {21},
  number =       {4},
  pages =        {1428-1442},
}

@article{Rohlfing2012,
  author = {Rohlfing, Torsten},
  title = {Image Similarity and Tissue Overlaps as Surrogates for Image Registration Accuracy: Widely Used but Unreliable},
  journal = IEEE_J_MI,
  year = 2012,
  volume = 31,
  number = 2,
  pages = {153--163},
  month = {Feb.},
}

@article{RueckertEA99,
  author =       {D.~Rueckert and L.~I.~Sonoda and C.~Hayes and D.~L.~G.~Hill and M.~O.~Leach and D.~J.~Hawkes},
  title =        {Nonrigid Registration Using Free-Form Deformations: Application to Breast {MR} Images},
  journal =      IEEE_J_MI,
  year =         {1999},
  volume =       {18},
  number =       {8},
  pages =        {712 - 721},
  dummymonth =        {August}
}

@ARTICLE{Shamonin2014,
  author      = {Denis P. Shamonin and Esther E. Bron and Boudewijn P.F. Lelieveldt and Marion Smits and Stefan Klein and Marius Staring},
  title       = {Fast Parallel Image Registration on {CPU} and {GPU} for Diagnostic Classification of {Alzheimer's} Disease},
  journal     = {Frontiers in Neuroinformatics},
  year        = {2014},
  volume      = {7},
  number      = {50},
  pages       = {1-15},
  dummymonth  = {January}
}

@article{Sotiras2013,
  author =       {A. Sotiras and C. Davatzikos and N. Paragios},
  title =        {Deformable Medical Image Registration: A Survey},
  journal =      IEEE_J_MI,
  volume =       {32},
  number =       {7},
  pages =        {1153 - 1190},
  year =         {2013},
}

@article{Spall98,
  author =       {J.~C.~Spall},
  title =        {Implementation of the Simultaneous Perturbation Method for Stochastic Optimization},
  journal =      IEEE_J_AES,
  volume =       {34},
  number =       {3},
  pages =        {817 - 823},
  year =         {1998},
}

@article{Staring07,
  author =       {M.~Staring and S.~Klein and J.~P.~W.~Pluim},
  title =        {A Rigidity Penalty Term for Nonrigid Registration},
  journal =      {Medical Physics},
  volume =       {34},
  number =       {11},
  pages =        {4098 - 4108},
  year =         {2007},
}

@article{Staring07a,
  author =       {Staring, M. and Klein, S. and Pluim, J. P. W.},
  title  =       {Nonrigid Registration with Tissue-Dependent Filtering of the Deformation Field},
  journal =      {Physics in Medicine and Biology},
  dummymonth  =  {December},
  year       =   {2007},
  volume   =     {52},
  number       = {23},
  pages        = {6879 - 6892}
}

@article{Staring09,
  author =       {M.~Staring AND U.~A. van~der~Heide AND S.~Klein AND M.~A. Viergever AND J.~P.~W.~Pluim},
  title =        {Registration of Cervical {MRI} Using Multifeature Mutual Information},
  journal =      {IEEE Transactions on Medical Imaging},
  volume =       {28},
  number =       {9},
  pages =        {1412-1421},
  dmonth =        {},
  year =         {2009}
}

@article{StaringKlein2010a,
  author =   {Staring, M. and Klein, S.},
  title =    {itk::Transforms supporting spatial derivatives},
  journal =  {The Insight Journal},
  year =     {2010},
  volume =   {},
  number =   {},
  pages =    {},
  url =      {http://hdl.handle.net/10380/3215},
}

@article{StaringKlein2010b,
  author =   {Staring, M. and Klein, S.},
  title =    {An image sampling framework for the ITK},
  journal =  {The Insight Journal},
  year =     {2010},
  volume =   {},
  number =   {},
  pages =    {},
  url =      {http://hdl.handle.net/10380/3190},
}

@article{Stu99:NMI,
  author =       {C.~Studholme and D.~L.~G.~Hill and D.~J.~Hawkes},
  title =        {An overlap invariant entropy measure of {3D} medical image alignment},
  journal =      PR,
  year =         {1999},
  dummymonth =        {},
  volume =       {32},
  number =       {},
  pages =        {71-86},
}

@article{ThevenazEA00a,
  author =      {P. Th\'evenaz and M. Unser},
  title =       {Optimization of Mutual Information for Multiresolution Image Registration},
  journal =     IEEE_J_IP,
  year =        {2000},
  volume =      {9},
  pages =       {2083 - 2099},
  number =      {12},
  dummymonth =       {December},
}

@article{The08:Halton,
  author =      {P.~Th\'evenaz and M.~Unser},
  title =       {Halton sampling for image registration based on mutual information},
  journal =     STSIP,
  year =        {2008},
  volume =      {7},
  pages =       {141-171},
  number =      {2},
  dummymonth =       {},
}

@article{Unser99,
  author =      {M. Unser},
  title =       {Splines: A perfect fit for signal and image processing},
  journal =     IEEE_M_SP,
  year =        {1999},
  volume =      {16},
  pages =       {22 - 38},
  number =      {6},
  dummymonth =       {November},
}

@article{ViolaEA97,
  author =      {Paul Viola and William M. {Wells III}},
  title =       {Alignment by Maximization of Mutual Information},
  journal =     IJCV,
  year =        {1997},
  volume =      {24},
  pages =       {137 - 154},
  number =      {2},
}

@article{Zit03:Image,
  author       = {Zitov{\' a}, B. and Flusser, J.},
  title        = {Image registration methods: a survey},
  journal      = IVC,
  year         = 2003,
  volume       = {21},
  number       = {11},
  pages        = {977-1000}
}