@article{van2013wu,
  title={The WU-Minn human connectome project: an overview},
  author={Van Essen, David C and Smith, Stephen M and Barch, Deanna M and Behrens, Timothy EJ and Yacoub, Essa and Ugurbil, Kamil and Wu-Minn HCP Consortium and others},
  journal={Neuroimage},
  volume={80},
  pages={62--79},
  year={2013},
  publisher={Elsevier}
}

@article{turk2019functional,
  title={Functional connectome of the fetal brain},
  author={Turk, Elise and van den Heuvel, Marion I. and Benders, Manon J. and de Heus, Roel and Franx, Arie and Manning, Janessa H. and Hect, Jasmine L. and Hernandez-Andrade, Edgar and Hassan, Sonia S. and Romero, Roberto and others},
  journal={Journal of Neuroscience},
  volume={39},
  number={49},
  pages={9716--9724},
  year={2019},
  publisher={Soc Neuroscience}
}

@article{howell2019unc,
  title={The {UNC/UMN} baby connectome project {(BCP)}: an overview of the study design and protocol development},
  author={Howell, Brittany R. and Styner, Martin A. and Gao, Wei and Yap, Pew-Thian and Wang, Li and Baluyot, Kristine and Yacoub, Essa and Chen, Geng and Potts, Taylor and Salzwedel, Andrew and others},
  journal={NeuroImage},
  volume={185},
  pages={891--905},
  year={2019},
  publisher={Elsevier}
}

@article{khalili2019automatic,
  title={Automatic brain tissue segmentation in fetal {MRI} using convolutional neural networks},
  author={Khalili, Nadieh and Lessmann, N. and Turk, Elise and Claessens, N. and de Heus, R. and Kolk, T. and Viergever, M.A. and Benders, M.J.N.L. and I{\v{s}}gum, I.},
  journal={Magnetic Resonance Imaging},
  volume={64},
  pages={77--89},
  year={2019},
  publisher={Elsevier}
}

@article{gaspar2019optimizing,
  title={Optimizing maternal fat suppression with constrained image-based shimming in fetal {MR}},
  author={Gaspar, Andreia S. and Nunes, Rita G. and Ferrazzi, Giulio and Hughes, Emer J. and Hutter, Jana and Malik, Shaihan J and McCabe, Laura and Baruteau, Kelly P. and Rutherford, Mary A. and Hajnal, Joseph V. and others},
  journal={Magnetic Resonance in Medicine},
  volume={81},
  number={1},
  pages={477--485},
  year={2019},
  publisher={Wiley Online Library}
}
@article{makropoulos2018review,
  title={A review on automatic fetal and neonatal brain {MRI} segmentation},
  author={Makropoulos, Antonios and Counsell, Serena J. and Rueckert, Daniel},
  journal={NeuroImage},
  volume={170},
  pages={231--248},
  year={2018},
  publisher={Elsevier}
}

@article{Makropoulos2018TheReconstruction,
    title = {{The developing human connectome project: A minimal processing pipeline for neonatal cortical surface reconstruction}},
    year = {2018},
    journal = {NeuroImage},
    author = {Makropoulos, Antonios and Robinson, Emma C. and Schuh, Andreas and Wright, Robert and Fitzgibbon, Sean and Bozek, Jelena and Counsell, Serena J. and Steinweg, Johannes and Vecchiato, Katy and Passerat-Palmbach, Jonathan and Lenz, Gregor and Mortari, Filippo and Tenev, Tencho and Duff, Eugene P. and Bastiani, Matteo and Cordero-Grande, Lucilio and Hughes, Emer and Tusor, Nora and Tournier, Jacques-Donald and Hutter, Jana and Price, Anthony N. and Teixeira, Rui Pedro A.G. and Murgasova, Maria and Victor, Suresh and Kelly, Christopher and Rutherford, Mary A. and Smith, Stephen M. and Edwards, A. David and Hajnal, Joseph V. and Jenkinson, Mark and Rueckert, Daniel},
    month = {6},
    pages = {88--112},
    volume = {173},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/29409960 https://linkinghub.elsevier.com/retrieve/pii/S1053811918300545},
    doi = {10.1016/j.neuroimage.2018.01.054},
    issn = {10538119},
    pmid = {29409960},
    keywords = {Cortical surface reconstruction, Developing human connectome project, Neonatal MRI, Pipeline, Segmentation, dHCP}
}

@article{Makropoulos2014AutomaticBrain,
    title = {{Automatic Whole Brain MRI Segmentation of the Developing Neonatal Brain}},
    year = {2014},
    journal = {IEEE Transactions on Medical Imaging},
    author = {Makropoulos, Antonios and Gousias, Ioannis S. and Ledig, Christian and Aljabar, Paul and Serag, Ahmed and Hajnal, Joseph V. and Edwards, A. David and Counsell, Serena J. and Rueckert, Daniel},
    number = {9},
    month = {9},
    pages = {1818--1831},
    volume = {33},
    url = {http://ieeexplore.ieee.org/document/6810848/},
    doi = {10.1109/TMI.2014.2322280},
    issn = {0278-0062}
}


@article{serag2013spatio,
  title={Spatio-temporal modeling and analysis of brain development},
  author={Serag, Ahmed},
  year={2013},
  publisher={Imperial College London}
}


@article{beare2016neonatal,
  title={Neonatal brain tissue classification with morphological adaptation and unified segmentation},
  author={Beare, Richard J. and Chen, Jian and Kelly, Claire E. and Alexopoulos, Dimitrios and Smyser, Christopher D. and Rogers, Cynthia E. and Loh, Wai Y. and Matthews, Lillian G. and Cheong, Jeanie L.Y. and Spittle, Alicia J. and others},
  journal={Frontiers in neuroinformatics},
  volume={10},
  pages={12},
  year={2016},
  publisher={Frontiers}
}

@article{prastawa2005automatic,
  title={Automatic segmentation of {MR} images of the developing newborn brain},
  author={Prastawa, Marcel and Gilmore, John H. and Lin, Weili and Gerig, Guido},
  journal={Medical Image Analysis},
  volume={9},
  number={5},
  pages={457--466},
  year={2005},
  publisher={Elsevier}
}

@article{anbeek2008probabilistic,
  title={Probabilistic brain tissue segmentation in neonatal magnetic resonance imaging},
  author={Anbeek, Petronella and Vincken, Koen L. and Groenendaal, Floris and Koeman, Annemieke and Van Osch, Matthias J.P. and Van der Grond, Jeroen},
  journal={Pediatric Research},
  volume={63},
  number={2},
  pages={158},
  year={2008},
  publisher={Nature Publishing Group}
}

@article{anbeek2013automatic,
  title={Automatic segmentation of eight tissue classes in neonatal brain {MRI}},
  author={Anbeek, Petronella and I{\v{s}}gum, Ivana and van Kooij, Britt J.M. and Mol, Christian P. and Kersbergen, Karina J. and Groenendaal, Floris and Viergever, Max A. and de Vries, Linda S. and Benders, Manon J.N.L.},
  journal={PloS one},
  volume={8},
  number={12},
  pages={e81895},
  year={2013},
  publisher={Public Library of Science}
}

@article{srhoj2012automatic,
  title={Automatic segmentation of neonatal brain {MRI} using atlas based segmentation and machine learning approach},
  author={Srhoj-Egekher, Vedran and Benders, M.J.N.L. and Kersbergen, Karina J. and Viergever, Max A. and Isgum, I.},
  journal={MICCAI Grand Challenge: Neonatal Brain Segmentation},
  volume={2012},
  year={2012}
}

@article{moeskops2015automatic,
  title={Automatic segmentation of {MR} brain images of preterm infants using supervised classification},
  author={Moeskops, Pim and Benders, Manon J.N.L. and Chi{\c{t}}ǎ, Sabina M. and Kersbergen, Karina J. and Groenendaal, Floris and de Vries, Linda S. and Viergever, Max A. and I{\v{s}}gum, Ivana},
  journal={NeuroImage},
  volume={118},
  pages={628--641},
  year={2015},
  publisher={Elsevier}
}

@article{moeskops2016automatic,
  title={Automatic segmentation of {MR} brain images with a convolutional neural network},
  author={Moeskops, Pim and Viergever, Max A. and Mendrik, Adri{\"e}nne M and de Vries, Linda S. and Benders, Manon J.N.L. and I{\v{s}}gum, Ivana},
  journal={IEEE Transactions on Medical Imaging},
  volume={35},
  number={5},
  pages={1252--1261},
  year={2016},
  publisher={IEEE}
}

@inproceedings{chictua2013automatic,
  title={Automatic segmentation of the preterm neonatal brain with {MRI} using supervised classification},
  author={Chi{\c{t}}{\u{a}}, Sabina M. and Benders, Manon and Moeskops, Pim and Kersbergen, Karina J. and Viergever, Max A. and I{\v{s}}gum, Ivana},
  booktitle={Medical Imaging 2013: Image Processing},
  volume={8669},
  pages={86693X},
  year={2013},
  organization={International Society for Optics and Photonics}
}

@article{wang2015links,
  title={LINKS: Learning-based multi-source IntegratioN frameworK for Segmentation of infant brain images},
  author={Wang, Li and Gao, Yaozong and Shi, Feng and Li, Gang and Gilmore, John H. and Lin, Weili and Shen, Dinggang},
  journal={NeuroImage},
  volume={108},
  pages={160--172},
  year={2015},
  publisher={Elsevier}
}

@inproceedings{sanroma2016building,
  title={Building an ensemble of complementary segmentation methods by exploiting probabilistic estimates},
  author={Sanroma, Gerard and Benkarim, Oualid M. and Piella, Gemma and Ballester, Miguel {\'A}ngel Gonz{\'a}lez},
  booktitle={International Workshop on Machine Learning in Medical Imaging},
  pages={27--35},
  year={2016},
  organization={Springer}
}

@inproceedings{habas2008atlas,
  title={Atlas-based segmentation of the germinal matrix from in utero clinical {MRI} of the fetal brain},
  author={Habas, Piotr A. and Kim, Kio and Rousseau, Francois and Glenn, Orit A. and Barkovich, A. James and Studholme, Colin},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={351--358},
  year={2008},
  organization={Springer}
}
@inproceedings{habas2009statistical,
  title={Statistical model of laminar structure for atlas-based segmentation of the fetal brain from in utero {MR} images},
  author={Habas, Piotr A. and Kim, Kio and Chandramohan, Dharshan and Rousseau, Francois and Glenn, Orit A. and Studholme, Colin},
  booktitle={Medical Imaging 2009: Image Processing},
  volume={7259},
  pages={725917},
  year={2009},
  organization={International Society for Optics and Photonics}
}

@article{habas2010atlas,
  title={Atlas-based segmentation of developing tissues in the human brain with quantitative validation in young fetuses},
  author={Habas, Piotr A. and Kim, Kio and Rousseau, Francois and Glenn, Orit A. and Barkovich, A. James and Studholme, Colin},
  journal={Human brain mapping},
  volume={31},
  number={9},
  pages={1348--1358},
  year={2010},
  publisher={Wiley Online Library}
}

@inproceedings{ison2012fully,
  title={Fully automated brain extraction and orientation in raw fetal {MRI}},
  author={Ison, Mark and Donner, R. and Dittrich, E. and Kasprian, Gregor and Prayer, Daniela and Langs, Georg},
  booktitle={Workshop on Paediatric and Perinatal Imaging, MICCAI},
  pages={17--24},
  year={2012}
}

@article{wright2014automatic,
  title={Automatic quantification of normal cortical folding patterns from fetal brain {MRI}},
  author={Wright, Robert and Kyriakopoulou, Vanessa and Ledig, Christian and Rutherford, Mary A. and Hajnal, Joseph V. and Rueckert, Daniel and Aljabar, Paul},
  journal={NeuroImage},
  volume={91},
  pages={21--32},
  year={2014},
  publisher={Elsevier}
}

@inproceedings{dittrich2011learning,
  title={Learning a spatio-temporal latent atlas for fetal brain segmentation},
  author={Dittrich, Eva and Riklin-Raviv, Tammy and Kasprian, Gregor and Brugger, Peter C. and Prayer, Daniela and Langs, Georg},
  booktitle={Proceedings of the MICCAI 2011 Workshop on Image Analysis of Human Brain Development (IAHBD 2011)},
  year={2011}
}

@article{gholipour2012multi,
  title={Multi-atlas multi-shape segmentation of fetal brain {MRI} for volumetric and morphometric analysis of ventriculomegaly},
  author={Gholipour, Ali and Akhondi-Asl, Alireza and Estroff, Judy A. and Warfield, Simon K.},
  journal={NeuroImage},
  volume={60},
  number={3},
  pages={1819--1831},
  year={2012},
  publisher={Elsevier}
}


@inproceedings{kainz2014fast,
  title={Fast fully automatic brain detection in fetal {MRI} using dense rotation invariant image descriptors},
  author={Kainz, Bernhard and Keraudren, Kevin and Kyriakopoulou, Vanessa and Rutherford, Mary and Hajnal, Joseph V. and Rueckert, Daniel},
  booktitle={2014 IEEE 11th International Symposium on Biomedical Imaging (ISBI)},
  pages={1230--1233},
  year={2014},
  organization={IEEE}
}

@article{keraudren2014automated,
  title={Automated fetal brain segmentation from {2D MRI} slices for motion correction},
  author={Keraudren, Kevin and Kuklisova-Murgasova, Maria and Kyriakopoulou, Vanessa and Malamateniou, Christina and Rutherford, Mary A. and Kainz, Bernhard and Hajnal, Joseph V. and Rueckert, Daniel},
  journal={NeuroImage},
  volume={101},
  pages={633--643},
  year={2014},
  publisher={Elsevier}
}

@article{rajchl2016deepcut,
  title={Deepcut: Object segmentation from bounding box annotations using convolutional neural networks},
  author={Rajchl, Martin and Lee, Matthew C.H. and Oktay, Ozan and Kamnitsas, Konstantinos and Passerat-Palmbach, Jonathan and Bai, Wenjia and Damodaram, Mellisa and Rutherford, Mary A. and Hajnal, Joseph V. and Kainz, Bernhard and others},
  journal={IEEE Transactions on Medical Imaging},
  volume={36},
  number={2},
  pages={674--683},
  year={2016},
  publisher={IEEE}
}

@article{ball2013development,
  title={Development of cortical microstructure in the preterm human brain},
  author={Ball, Gareth and Srinivasan, Latha and Aljabar, Paul and Counsell, Serena J. and Durighel, Giuliana and Hajnal, Joseph V. and Rutherford, Mary A. and Edwards, A. David},
  journal={Proceedings of the National Academy of Sciences},
  volume={110},
  number={23},
  pages={9541--9546},
  year={2013},
  publisher={National Acad Sciences}
}

@article{jiang2007mri,
  title={{MRI} of moving subjects using multislice snapshot images with volume reconstruction (SVR): application to fetal, neonatal, and adult brain studies},
  author={Jiang, Shuzhou and Xue, Hui and Glover, Alan and Rutherford, Mary and Rueckert, Daniel and Hajnal, Joseph V.},
  journal={IEEE Transactions on Medical Imaging},
  volume={26},
  number={7},
  pages={967--980},
  year={2007},
  publisher={IEEE}
}

@article{bastiani2019automated,
  title={Automated processing pipeline for neonatal diffusion {MRI in the developing Human Connectome Project}},
  author={Bastiani, Matteo and Andersson, Jesper L.R. and Cordero-Grande, Lucilio and Murgasova, Maria and Hutter, Jana and Price, Anthony N. and Makropoulos, Antonios and Fitzgibbon, Sean P. and Hughes, Emer and Rueckert, Daniel and others},
  journal={NeuroImage},
  volume={185},
  pages={750--763},
  year={2019},
  publisher={Elsevier}
}

@article{kyriakopoulou2013cortical,
  title={Cortical overgrowth in fetuses with isolated ventriculomegaly},
  author={Kyriakopoulou, Vanessa and Vatansever, Deniz and Elkommos, Samia and Dawson, Sarah and McGuinness, Amy and Allsop, Joanna and Moln{\'a}r, Zolt{\'a}n and Hajnal, Joseph and Rutherford, Mary},
  journal={Cerebral Cortex},
  volume={24},
  number={8},
  pages={2141--2150},
  year={2013},
  publisher={Oxford University Press}
}

@article{fitzgibbon2019developing,
  title={The developing Human Connectome Project (dHCP) automated resting-state functional processing framework for newborn infants},
  author={Fitzgibbon, Sean P. and Harrison, Samuel J. and Jenkinson, Mark and Baxter, Luke and Robinson, Emma C. and Bastiani, Matteo and Bozek, Jelena and Karolis, Vyacheslav and Grande, Lucilio Cordero and Price, Anthony N. and others},
  journal={BioRxiv},
  pages={766030},
  year={2019},
  publisher={Cold Spring Harbor Laboratory}
}

@article{doria2010emergence,
  title={Emergence of resting state networks in the preterm human brain},
  author={Doria, Valentina and Beckmann, Christian F. and Arichi, Tomoki and Merchant, Nazakat and Groppo, Michela and Turkheimer, Federico E. and Counsell, Serena J. and Murgasova, Maria and Aljabar, Paul and Nunes, Rita G. and others},
  journal={Proceedings of the National Academy of Sciences},
  volume={107},
  number={46},
  pages={20015--20020},
  year={2010},
  publisher={National Acad Sciences}
}

@article{van1997tension,
  title={A tension-based theory of morphogenesis and compact wiring in the central nervous system},
  author={Van Essen, David C.},
  journal={Nature},
  volume={385},
  number={6614},
  pages={313},
  year={1997},
  publisher={Nature Publishing Group}
}

@article{Habas2010ASegmentation,
    title = {{A spatiotemporal atlas of MR intensity, tissue probability and shape of the fetal brain with application to segmentation}},
    year = {2010},
    journal = {NeuroImage},
    author = {Habas, Piotr A. and Kim, Kio and Corbett-Detig, James M. and Rousseau, Francois and Glenn, Orit A. and Barkovich, A. James and Studholme, Colin},
    number = {2},
    month = {11},
    pages = {460--470},
    volume = {53},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/20600970 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC2930902 http://linkinghub.elsevier.com/retrieve/pii/S1053811910009122},
    doi = {10.1016/j.neuroimage.2010.06.054},
    issn = {10538119},
    pmid = {20600970}
}

@article{lecun2015deep,
  title={Deep learning},
  author={LeCun, Yann and Bengio, Yoshua and Hinton, Geoffrey},
  journal={Nature},
  volume={521},
  number={7553},
  pages={436--444},
  year={2015},
  publisher={Nature Publishing Group}
}

@article{Ronneberger2015U-Net:Segmentation,
    title = {{U-Net: Convolutional Networks for Biomedical Image Segmentation}},
    year = {2015},
    author = {Ronneberger, Olaf and Fischer, Philipp and Brox, Thomas},
    month = {5},
    url = {https://arxiv.org/abs/1505.04597},
    arxivId = {1505.04597}
}

@article{Kamnitsas2017EfficientSegmentation,
    title = {{Efficient multi-scale 3D CNN with fully connected CRF for accurate brain lesion segmentation}},
    year = {2017},
    journal = {Medical Image Analysis},
    author = {Kamnitsas, Konstantinos and Ledig, Christian and Newcombe, Virginia F.J. and Simpson, Joanna P. and Kane, Andrew D. and Menon, David K. and Rueckert, Daniel and Glocker, Ben},
    month = {2},
    pages = {61--78},
    volume = {36},
    publisher = {Elsevier},
    url = {https://www.sciencedirect.com/science/article/pii/S1361841516301839},
    doi = {10.1016/J.MEDIA.2016.10.004},
    issn = {1361-8415}
}

@article{Price2018ISMRM,
    title = {{Multiband zoom TSE Imaging: increasing efficiency with multiband tip-back pulses}},
    year = {2018},
    journal = {Proceedings of the International Society of Magnetic Resonance in Medicine},
    author = {Price, Anthony N. and Cordero-Grande, Lucilio and Malik, Shaihan J. and Hajnal, Joseph V.},
}

@article{Price2019ISMRM,
    title = {{The developing Human Connectome Project (dHCP): fetal acquisition protocol}},
    year = {2019},
    journal = {Proceedings of the International Society of Magnetic Resonance in Medicine},
    author = {Price, Anthony N. and Cordero-Grande, Lucilio and Hughes, Emer and Hiscocks, Suzanne and Green, Elaine and McCabe, Laura and Hutter, Jana and Ferrazzi, Giulio and Roberts, Thomas and Christiaens, Daan and Duff, Eugene and Karolis, Vyacheslav and Malik, Shaihan J. and Rutherford, Mary A. and Edwards, A. David and Hajnal, Joseph V.},
}


@article{Cordero2019ISMRM,
    title = {{“Automating fetal brain reconstruction using distance regression learning}},
    year = {2019},
    journal = {Proceedings of the International Society of Magnetic Resonance in Medicine},
    author = {Cordero-Grande, Lucilio AND Price, Anthony N. and Hughes, Emer and Wright, Robert and Rutherford, Mary A. and Hajnal, Joseph V.},
}

@article{gousias2012magnetic,
  title={Magnetic resonance imaging of the newborn brain: manual segmentation of labelled atlases in term-born and preterm infants},
  author={Gousias, Ioannis S. and Edwards, A. David and Rutherford, Mary A. and Counsell, Serena J. and Hajnal, Jo V. and Rueckert, Daniel and Hammers, Alexander},
  journal={Neuroimage},
  volume={62},
  number={3},
  pages={1499--1509},
  year={2012},
  publisher={Elsevier}
}