@article{Desikan2006968,
title = "An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest",
journal = "NeuroImage",
volume = "31",
number = "3",
pages = "968 - 980",
year = "2006",
note = "",
issn = "1053-8119",
doi = "DOI: 10.1016/j.neuroimage.2006.01.021",
url = "http://www.sciencedirect.com/science/article/B6WNP-4JFHF4P-1/2/0ec667d4c17eafb0a7c52fa3fd5aef1c",
author = "Rahul S. Desikan and Florent Ségonne and Bruce Fischl and Brian T. Quinn and Bradford C. Dickerson and Deborah Blacker and Randy L. Buckner and Anders M. Dale and R. Paul Maguire and Bradley T. Hyman and Marilyn S. Albert and Ronald J. Killiany"
} 

@article{Fischl01012004,
  author = {Fischl, Bruce and van der Kouwe, André and Destrieux, Christophe and Halgren, Eric and Ségonne, Florent and Salat, David H. and Busa, Evelina and Seidman, Larry J. and Goldstein, Jill and Kennedy, David and Caviness, Verne and Makris, Nikos and Rosen, Bruce and Dale, Anders M.}, 
  title = {{Automatically Parcellating the Human Cerebral Cortex}}, 
  volume = {14}, 
  number = {1}, 
  pages = {11-22}, 
  year = {2004}, 
  doi = {10.1093/cercor/bhg087}, 
  URL = {http://cercor.oxfordjournals.org/content/14/1/11.abstract}, 
  eprint = {http://cercor.oxfordjournals.org/content/14/1/11.full.pdf+html}, 
  journal = {Cerebral Cortex} 
}


@article{Fischl2004S69,
  title = "Sequence-independent segmentation of magnetic resonance images",
  journal = "NeuroImage",
  volume = "23",
  number = "Supplement 1",
  pages = "S69 - S84",
  year = "2004",
  note = "Mathematics in Brain Imaging",
  issn = "1053-8119",
  doi = "DOI: 10.1016/j.neuroimage.2004.07.016",
  url = "http://www.sciencedirect.com/science/article/B6WNP-4DCMGVT-2/2/7eee26326dc63f931b826eac33becc8b",
  author = "Bruce Fischl and David H. Salat and André J.W. van der Kouwe and Nikos Makris and Florent Ségonne and Brian T. Quinn and Anders M. Dale",
  keywords = "Morphometry",
  keywords = "MRI",
  keywords = "Alzheimer's disease"
}




@article{Fischl26092000,
author = {Fischl, Bruce and Dale, Anders M.}, 
title = {{Measuring the thickness of the human cerebral cortex from magnetic resonance images}}, 
volume = {97}, 
number = {20}, 
pages = {11050-11055}, 
year = {2000}, 
eprint = {http://www.pnas.org/content/97/20/11050.full.pdf+html}, 
journal = {Proceedings of the National Academy of Sciences of the United States of America}
}



@Article{FischlLiuDale,
  author =       {Fischl, B. and Liu, A. and Dale, A.~M.},
  title =        {Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex},
  journal =      {{IEEE} Medical Imaging},
  year =         {2001},
  volume =    {20},
  number =    {1},
  pages =     {70-80},
}


@Article{FischlSalat2002,
  author =       {Fischl, B. and Salat, D.~H. and Busa, E. and Albert, M. and Dieterich, M. and Haselgrove, C. and {van der Kouwe}, A. and Killiany, R. and Kennedy, D. and Klaveness, S. and Montillo, A. and Makris, N. and Rosen, B. and Dale, A.~M.},
  title =        {Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain},
  journal =      {Neuron},
  year =         {2002},
  volume =    {33},
  pages =     {341-355}
}



@article {HBM:HBM10,
author = {Fischl, Bruce and Sereno, Martin I. and Tootell, Roger B.H. and Dale, Anders M.},
title = {High-resolution intersubject averaging and a coordinate system for the cortical surface},
journal = {Human Brain Mapping},
volume = {8},
number = {4},
publisher = {John Wiley & Sons, Inc.},
issn = {1097-0193},
url = {http://dx.doi.org/10.1002/(SICI)1097-0193(1999)8:4<272::AID-HBM10>3.0.CO;2-4},
doi = {10.1002/(SICI)1097-0193(1999)8:4<272::AID-HBM10>3.0.CO;2-4},
pages = {272--284},
keywords = {intersubject averaging, coordinate systems, atlas},
year = {1999},
}




@article{Jovicich2006436,
  title = "Reliability in multi-site structural MRI studies: Effects of gradient non-linearity correction on phantom and human data",
  journal = "NeuroImage",
  volume = "30",
  number = "2",
  pages = "436 - 443",
  year = "2006",
  note = "",
  issn = "1053-8119",
  doi = "DOI: 10.1016/j.neuroimage.2005.09.046",
  url = "http://www.sciencedirect.com/science/article/B6WNP-4HM7S0B-2/2/4fa5ff26cad90ba3c9ed12b7e12ce3b6",
  author = "Jorge Jovicich and Silvester Czanner and Douglas Greve and Elizabeth Haley and Andre van der Kouwe and Randy Gollub and David Kennedy and Franz Schmitt and Gregory Brown and James MacFall and Bruce Fischl and Anders Dale",
  keywords = "Multi-site calibration",
  keywords = "Gradient non-linearity distortions",
  keywords = "Human structural MRI"
}


@Article{Kuperberg2003,
      AUTHOR = "Kuperberg, G. R. and Broome, M. and McGuire, P. K. and David, A. S. and Eddy, M. and Ozawa, F. and Goff, D. and West, W. C. and Williams, S.C.R. and van der Kouwe, Andre and Salat, David and Dale, Anders and Fischl, Bruce",
      TITLE = "Regionally localized thinning of the cerebral cortex in {S}chizophrenia",
      YEAR = "2003",
      JOURNAL = "Archives of General Psychiatry",
      VOLUME = "60",
      PAGES = "878-888"
} 

@article{Rosas12032002,
author = {Rosas, H. D. and Liu, A. K. and Hersch, S. and Glessner, M. and Ferrante, R. J. and Salat, D. H. and van der Kouwe, A. and Jenkins, B. G. and Dale, A. M. and Fischl, B.}, 
title = {{Regional and progressive thinning of the cortical ribbon in Huntington’s disease}}, 
volume = {58}, 
number = {5}, 
pages = {695-701}, 
year = {2002},
URL = {http://www.neurology.org/content/58/5/695.abstract}, 
eprint = {http://www.neurology.org/content/58/5/695.full.pdf+html}, 
journal = {Neurology} 
}




@Article{Salat2004,
      AUTHOR = "Salat, David and Buckner, R.L. and Snyder, A.Z. and Greve, Douglas N. and Desikan, R.S. and Busa, Evelina and Morris, J.C. and Dale, Anders and Fischl, Bruce",
      TITLE = "Thinning of the cerebral cortex in aging",
      YEAR = "2004",
      JOURNAL = "Cerebral Cortex",
      VOLUME = "14",
      PAGES = "721-730"
} 

@article{Segonne20041060,
title = "A hybrid approach to the skull stripping problem in MRI",
journal = "NeuroImage",
volume = "22",
number = "3",
pages = "1060 - 1075",
year = "2004",
note = "",
issn = "1053-8119",
doi = "DOI: 10.1016/j.neuroimage.2004.03.032",
url = "http://www.sciencedirect.com/science/article/B6WNP-4CF5CNY-1/2/33cc73136f06f019b2c11023e7a95341",
author = "F. Segonne and A. M. Dale and E. Busa and M. Glessner and D. Salat and H. K. Hahn and B. Fischl",
keywords = "Skull stripping",
keywords = "Brain segmentation",
keywords = "Watershed transformation",
keywords = "Template deformation",
keywords = "Atlas-based segmentation"
}


@Article{dale:99,
      AUTHOR = "Dale, Anders and Fischl, Bruce and Sereno, Martin I.",
      TITLE = "Cortical Surface-Based Analysis: I. Segmentation and Surface Reconstruction",
      YEAR = "1999",
      JOURNAL = "NeuroImage",
      VOLUME = "9",
      NUMBER = "2",
      PAGES = "179 - 194",
      ANNOTE = "DOI: 10.1006/nimg.1998.0395"
}

@Article{fischl:99,
      AUTHOR = "Fischl, Bruce and Sereno, Martin I. and Dale, Anders",
      TITLE = "Cortical Surface-Based Analysis: II: Inflation, Flattening, and a Surface-Based Coordinate System",
      YEAR = "1999",
      JOURNAL = "NeuroImage",
      VOLUME = "9",
      NUMBER = "2",
      PAGES = "195 - 207",
      ANNOTE = "DOI: 10.1006/nimg.1998.0396"
}



@Article{han:06,
      AUTHOR = "Han, Xiao and Jovicich, Jorge and Salat, David and van der Kouwe, Andre and Quinn, Brian and Czanner, Silvester and Busa, Evelina and Pacheco, Jenni and Albert, Marilyn and Killiany, Ronald and Maguire, Paul and Rosas, Diana and Makris, Nikos and Dale, Anders and Dickerson, Bradford and Fischl, Bruce",
      TITLE = "Reliability of {MRI}-derived measurements of human cerebral cortical thickness: {T}he effects of field strength, scanner upgrade and manufacturer",
      YEAR = "2006",
      JOURNAL = "NeuroImage",
      VOLUME = "32",
      NUMBER = "1",
      PAGES = "180-194",
      KEYWORDS = {Longitudinal Analysis}
}

@article{sledzijdenbos1998,
  author = "{Sled}, J.G. and {Zijdenbos}, A.P. and  {Evans}, A.C.",
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  title = "A nonparametric method for automatic correction of intensity nonuniformity in MRI data",
  journal = "IEEE Trans Med Imaging",
  volume = "17",
  pages = "87-97"
}


@article{spf2007,
  author ="Segonne, F. and  Pacheco, J. and  Fischl, B.",
  year = "2007",
  title = "Geometrically accurate topology-correction of cortical surfaces using nonseparating loops",
  journal = "IEEE Trans Med Imaging",
  volume = "26",
  pages = "518-529"
} 

@ARTICLE{reuter:robreg10,
   AUTHOR="Martin Reuter and Herminia Diana Rosas and Bruce Fischl",
   TITLE="Highly Accurate Inverse Consistent Registration: A Robust Approach",
   JOURNAL="NeuroImage",
   VOLUME="53",
   NUMBER="4",
   PAGES="1181--1196",
   DOI="10.1016/j.neuroimage.2010.07.020",
   URL="http://dx.doi.org/10.1016/j.neuroimage.2010.07.020",
   YEAR="2010",
}

@ARTICLE{reuter:bias11,
   AUTHOR="Martin Reuter and Bruce Fischl",
   TITLE="Avoiding Asymmetry-Induced Bias in Longitudinal Image Processing",
   JOURNAL="NeuroImage",
   VOLUME="57",
   NUMBER= "1",
   PAGES="19--21",
   DOI="10.1016/j.neuroimage.2011.02.076",
   URL="http://dx.doi.org/10.1016/j.neuroimage.2011.02.076",
   YEAR="2011",
}

@ARTICLE{reuter:long12,
   AUTHOR="Martin Reuter and Nicholas J. Schmansky and Herminia Diana Rosas and Bruce Fischl",
   TITLE="Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis",
   JOURNAL="NeuroImage",
   VOLUME="61",
   NUMBER="4",
   PAGES="1402--1418",
   DOI="10.1016/j.neuroimage.2012.02.084",
   URL="http://dx.doi.org/10.1016/j.neuroimage.2012.02.084",
   YEAR="2012",
}


@Article{pmid19059349,
   Author="Woolrich, M. W.  and Jbabdi, S.  and Patenaude, B.  and Chappell, M.  and Makni, S.  and Behrens, T.  and Beckmann, C.  and Jenkinson, M.  and Smith, S. M. ",
   Title="{{B}ayesian analysis of neuroimaging data in {F}{S}{L}}",
   Journal="Neuroimage",
   Year="2009",
   Volume="45",
   Number="1 Suppl",
   Pages="S173--186",
   Month="Mar",
   Note={[DOI:\href{https://dx.doi.org/10.1016/j.neuroimage.2008.10.055}{10.1016/j.neuroimage.2008.10.055}] [PubMed:\href{https://www.ncbi.nlm.nih.gov/pubmed/19059349}{19059349}] }
}

@Article{pmid15501092,
   Author="Smith, S. M.  and Jenkinson, M.  and Woolrich, M. W.  and Beckmann, C. F.  and Behrens, T. E.  and Johansen-Berg, H.  and Bannister, P. R.  and De Luca, M.  and Drobnjak, I.  and Flitney, D. E.  and Niazy, R. K.  and Saunders, J.  and Vickers, J.  and Zhang, Y.  and De Stefano, N.  and Brady, J. M.  and Matthews, P. M. ",
   Title="{{A}dvances in functional and structural {M}{R} image analysis and implementation as {F}{S}{L}}",
   Journal="Neuroimage",
   Year="2004",
   Volume="23 Suppl 1",
   Pages="S208--219",
   Note={[DOI:\href{https://dx.doi.org/10.1016/j.neuroimage.2004.07.051}{10.1016/j.neuroimage.2004.07.051}] [PubMed:\href{https://www.ncbi.nlm.nih.gov/pubmed/15501092}{15501092}] }
}

@Article{pmid21979382,
   Author="Jenkinson, M.  and Beckmann, C. F.  and Behrens, T. E.  and Woolrich, M. W.  and Smith, S. M. ",
   Title="{{F}{S}{L}}",
   Journal="Neuroimage",
   Year="2012",
   Volume="62",
   Number="2",
   Pages="782--790",
   Month="Aug",
   Note={[DOI:\href{https://dx.doi.org/10.1016/j.neuroimage.2011.09.015}{10.1016/j.neuroimage.2011.09.015}] [PubMed:\href{https://www.ncbi.nlm.nih.gov/pubmed/21979382}{21979382}] }
}

@misc{Notter2013,
  author = {Michael Notter},
  title = {gif_your_nifti},
  year = {2018},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/miykael/gif_your_nifti}},
  commit = {66cc30f988c0aff96d3263385b83e209e48aa4cc}
}


