references.bib

<bibtex>

@article{Iglesias2011,
	title = "Robust brain extraction across datasets and comparison with publicly available methods",
	journal = "IEEE Transactions on Medical Imaging",
	volume = "30",
	number = "9",
	pages = "1617--1634",
	year = "2011",
	doi = "doi:10.1109/TMI.2011.2138152",
	url = "http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=5742706",
	author = "J.E. Iglesias and C.Y. Liu and P.M. Thompson and T. Zu"
}

@article{Stein2012,
	title = "Identification of common variants associated with human hippocampal and intracranial volumes",
	journal = "Nature Genetics",
	volume = "44",
	number = "5",
	pages = "552--561",
	year = "2012",
	note = "",
	doi = "doi:10.1038/ng.2250",
	url = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3635491/",
	author = "Jason L. Stein and Sarah E. Medland and Alejandro Arias Vasquez and Derrek P. Hibar and Rudy E. Senstad and Anderson M. Winkler and Roberto Toro and Katja Appel and others"
}

@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 S{\'e}gonne 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,
	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",
	author = "Fischl, Bruce and van der Kouwe, Andr{\'e} and Destrieux, Christophe and Halgren, Eric and S{\'e}gonne, 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."
}

@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 S{\'e}gonne 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},
	month = {Jan}
}


@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.",
	year = "1998",
	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{lee2014,
	title="Altered network connectivity in frontotemporal dementia with {C9orf72} hexanucleotide repeat expansion",
	author="Lee, Suzee E and Khazenzon, Anna M and Trujillo, Andrew J and Guo, Christine C and Yokoyama, Jennifer S and Sharon, J Sha and Takada, Leonel T and Karydas, Anna M and Block, Nikolas R and Coppola, Giovanni and others",
	journal="Brain",
	pages="awu248",
	year="2014",
	publisher="Oxford Univ Press"
}

@article{seeley2008,
	title="Frontal paralimbic network atrophy in very mild behavioral variant frontotemporal dementia",
	author="Seeley, William W and Crawford, Richard and Rascovsky, Katya and Kramer, Joel H and Weiner, Michael and Miller, Bruce L and Gorno-Tempini, Maria Luisa",
	journal="Archives of neurology",
	volume="65",
	number="2",
	pages="249--255",
	year="2008",
	publisher="American Medical Association"
}

@article{nipype2011,
	An = "PMC3159964",
	Author = "Gorgolewski, Krzysztof and Burns, Christopher D and Madison, Cindee and Clark, Dav and Halchenko, Yaroslav O and Waskom, Michael L and Ghosh, Satrajit S",
	Date-Added = "2015-09-09 19:00:22 +0000",
	Date-Modified = "2015-09-09 19:00:22 +0000",
	Db = "PMC",
	Doi = "10.3389/fninf.2011.00013",
	Isbn = "1662-5196",
	J1 = "Front Neuroinform",
	Journal = "Frontiers in Neuroinformatics",
	Pages = "13",
	Publisher = "Frontiers Research Foundation",
	Title = "Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in {P}ython",
	Ty = "JOUR",
	U1 = "21897815"$[$"pmid"$]$"",
	Url = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159964/",
	Volume = "5",
	Year = "2011",
	Year1 = "2011/08/22",
	Year2 = "2011/06/23/received",
	Year3 = "2011/07/23/accepted",
	Bdsk-Url-1 = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159964/",
	Bdsk-Url-2 = "http://dx.doi.org/10.3389/fninf.2011.00013"
}

@article{jenkinson2012fsl,
	title={Fsl},
	author={Jenkinson, Mark and Beckmann, Christian F and Behrens, Timothy EJ and Woolrich, Mark W and Smith, Stephen M},
	journal={Neuroimage},
	volume={62},
	number={2},
	pages={782--790},
	year={2012},
	publisher={Elsevier}
}                  

@article{powerspurious2012,
	title = {Spurious but systematic correlations in functional connectivity {MRI} networks arise from subject motion},
	volume = {59},
	issn = {1095-9572},
	doi = {10.1016/j.neuroimage.2011.10.018},
	language = {eng},
	number = {3},
	journal = {NeuroImage},
	author = {Power, Jonathan D and Barnes, Kelly A and Snyder, Abraham Z and Schlaggar, Bradley L and Petersen, Steven E},
	month = feb,
	year = {2012},
	pmid = {22019881},
	pmcid = {PMC3254728},
	keywords = {Algorithms, Artifacts, Brain, Cohort Studies, Head Movements, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Motion, Oxygen, Software},
	pages = {2142--2154}
}


@Book{GnuMakeBook,
	author = 	 {John Graham-Cumming},
	title = 	 {The GNU Make Book},
	publisher = 	 {No Starch Press},
	year = 	 {2015},
}

@ARTICLE{py06nimg,
	author = {Paul A. Yushkevich and Joseph Piven and Cody Hazlett, Heather and
	Gimpel Smith, Rachel and Sean Ho and James C. Gee and Guido Gerig},
	title = {User-Guided {3D} Active Contour Segmentation of
	Anatomical Structures: Significantly Improved Efficiency and Reliability},
	journal = {Neuroimage},
	year = {2006},
	volume = {31},
	number = {3},
	pages = {1116--1128},
}

@article{ants,
	Abstract = {Publicly available scientific resources help establish evaluation standards, provide a platform for teaching and improve reproducibility. Version 4 of the Insight ToolKit (ITK(4)) seeks to establish new standards in publicly available image registration methodology. ITK(4) makes several advances in comparison to previous versions of ITK. ITK(4) supports both multivariate images and objective functions; it also unifies high-dimensional (deformation field) and low-dimensional (affine) transformations with metrics that are reusable across transform types and with composite transforms that allow arbitrary series of geometric mappings to be chained together seamlessly. Metrics and optimizers take advantage of multi-core resources, when available. Furthermore, ITK(4) reduces the parameter optimization burden via principled heuristics that automatically set scaling across disparate parameter types (rotations vs. translations). A related approach also constrains steps sizes for gradient-based optimizers. The result is that tuning for different metrics and/or image pairs is rarely necessary allowing the researcher to more easily focus on design/comparison of registration strategies. In total, the ITK(4) contribution is intended as a structure to support reproducible research practices, will provide a more extensive foundation against which to evaluate new work in image registration and also enable application level programmers a broad suite of tools on which to build. Finally, we contextualize this work with a reference registration evaluation study with application to pediatric brain labeling.},
	An = {PMC4009425},
	Author = {Avants, Brian B and Tustison, Nicholas J and Stauffer, Michael and Song, Gang and Wu, Baohua and Gee, James C},
	Date-Added = {2015-09-18 21:28:59 +0000},
	Date-Modified = {2015-09-18 21:28:59 +0000},
	Db = {PMC},
	Doi = {10.3389/fninf.2014.00044},
	Isbn = {1662-5196},
	J1 = {Front Neuroinform},
	Journal = {Frontiers in Neuroinformatics},
	Pages = {44},
	Publisher = {Frontiers Media S.A.},
	Title = {The Insight ToolKit image registration framework},
	Ty = {JOUR},
	U1 = {24817849{$[$}pmid{$]$}},
	Url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009425/},
	Volume = {8},
	Year = {2014},
	Year1 = {2014/04/28},
	Year2 = {2013/11/01/received},
	Year3 = {2014/03/30/accepted},
	Bdsk-Url-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009425/},
	Bdsk-Url-2 = {http://dx.doi.org/10.3389/fninf.2014.00044}
}

@article{ASLdementia,
	author = {Alsop, DC and Detre, JA and Golay, X and G\"unther, M and Hendrikse, J and Hernandez-Garcia, L and Lu, H and Macintosh, BJ and Parkes, LM and Smits, M and van Osch, MJ and Wang, DJ and Wong, EC and Zaharchuk, G},
	title = {Recommended implementation of arterial spin-labeled perfusion {MRI} for clinical applications: A consensus of the {ISMRM} perfusion study group and the European consortium for {ASL} in dementia},
	journal = {Magnetic Resonance in Medicine},
	year = {2015},
	volume = {73},
	number = {1},
	pages = {101--116},
}

</bibtex>