@book{Lamport:Book:1989,
 author = {Lamport, Leslie},
 title = {Latex: A Document Preparation System},
 year = {1986},
 isbn = {0-201-15790-X},
 publisher = {Addison-Wesley Longman Publishing Co., Inc.},
 address = {Boston, MA, USA},
}


@article{litjens2017survey,
  title={A survey on deep learning in medical image analysis},
  author={Litjens, Geert and Kooi, Thijs and Bejnordi, Babak Ehteshami and Setio, Arnaud Arindra Adiyoso and Ciompi, Francesco and Ghafoorian, Mohsen and Van Der Laak, Jeroen Awm and Van Ginneken, Bram and S{\'a}nchez, Clara I},
  journal={Medical image analysis},
  volume={42},
  pages={60--88},
  year={2017},
  publisher={Elsevier}
}

@article{zhang2001segmentation,
  title={Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm},
  author={Zhang, Yongyue and Brady, Michael and Smith, Stephen},
  journal={IEEE transactions on medical imaging},
  volume={20},
  number={1},
  pages={45--57},
  year={2001},
  publisher={Ieee}
}

@incollection{sudre2017generalised,
  title={Generalised dice overlap as a deep learning loss function for highly unbalanced segmentations},
  author={Sudre, Carole H and Li, Wenqi and Vercauteren, Tom and Ourselin, Sebastien and Cardoso, M Jorge},
  booktitle={Deep learning in medical image analysis and multimodal learning for clinical decision support},
  pages={240--248},
  year={2017},
  publisher={Springer}
}


@article{lemonade,
  title={LeMoNADe: Learned Motif and Neuronal Assembly Detection in calcium imaging videos},
  author={Kirschbaum, Elke and Hau{\ss}mann, Manuel and Wolf, Steffen and Sonntag, Hannah and Schneider, Justus and Elzoheiry, Shehabeldin and Kann, Oliver and Durstewitz, Daniel and Hamprecht, Fred A},
  journal={arXiv preprint arXiv:1806.09963},
  year={2018}
}

@article{puonti2016fast,
  title={Fast and sequence-adaptive whole-brain segmentation using parametric Bayesian modeling},
  author={Puonti, Oula and Iglesias, Juan Eugenio and Van Leemput, Koen},
  journal={NeuroImage},
  volume={143},
  pages={235--249},
  year={2016},
  publisher={Elsevier}
}

@misc{Authors06,
 author = {Authors},
 title = {The frobnicatable foo filter},
 note = {Face and Gesture  submission ID 324. Supplied as additional material {\tt fg324.pdf}},
 year = 2011
}

@misc{Authors06b,
 author = {Authors},
 title = {Frobnication tutorial},
 note = {Supplied as additional material {\tt tr.pdf}},
 year = 2006
}

@article{Alpher02,
author = {A. Alpher},
title = {Frobnication},
journal = {Journal of Foo},
volume = 12, 
number = 1, 
pages = {234--778}, 
year = 2002
}

@article{Alpher03,
author = {A. Alpher and  J.~P.~N. Fotheringham-Smythe},
title = {Frobnication revisited},
journal = {Journal of Foo},
volume = 13, 
number = 1, 
pages = {234--778}, 
year = 2003
}

@article{Alpher04,
author = {A. Alpher and J.~P.~N. Fotheringham-Smythe and G. Gamow},
title = {Can a machine frobnicate?},
journal = {Journal of Foo},
volume = 14, 
number = 1, 
pages = {234--778}, 
year = 2004
}


@article{seg_rev,
  title={Deep learning for brain MRI segmentation: state of the art and future directions},
  author={Akkus, Zeynettin and Galimzianova, Alfiia and Hoogi, Assaf and Rubin, Daniel L and Erickson, Bradley J},
  journal={Journal of digital imaging},
  volume={30},
  number={4},
  pages={449--459},
  year={2017},
  publisher={Springer}
}

@article{dolz20183d,
  title={3D fully convolutional networks for subcortical segmentation in MRI: A large-scale study},
  author={Dolz, Jose and Desrosiers, Christian and Ayed, Ismail Ben},
  journal={NeuroImage},
  volume={170},
  pages={456--470},
  year={2018},
  publisher={Elsevier}
}

@inproceedings{amod,
  title={Pulse sequence resilient fast brain segmentation},
  author={Jog, Amod and Fischl, Bruce},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={654--662},
  year={2018},
  organization={Springer}
}

@inproceedings{dalca1,
  title={Anatomical priors in convolutional networks for unsupervised biomedical segmentation},
  author={Dalca, Adrian V and Guttag, John and Sabuncu, Mert R},
  booktitle={Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
  pages={9290--9299},
  year={2018}
}

@article{dalca2,
  title={Unsupervised deep learning for Bayesian brain MRI segmentation},
  author={Dalca, Adrian V and Yu, Evan and Golland, Polina and Fischl, Bruce and Sabuncu, Mert R and Iglesias, Juan Eugenio},
  journal={arXiv preprint arXiv:1904.11319},
  year={2019}
}

@article{joyce,
  title={Deep multi-class segmentation without ground-truth labels},
  author={Joyce, Thomas and Chartsias, Agisilaos and Tsaftaris, Sotirios A},
  year={2018},
  journal={MIDL},
}

@inproceedings{zhao,
  title={Data augmentation using learned transformations for one-shot medical image segmentation},
  author={Zhao, Amy and Balakrishnan, Guha and Durand, Fredo and Guttag, John V and Dalca, Adrian V},
  booktitle={Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
  pages={8543--8553},
  year={2019}
}

@article{vae,
  title={Auto-encoding variational bayes},
  author={Kingma, Diederik P and Welling, Max},
  journal={arXiv preprint arXiv:1312.6114},
  year={2013}
}

@article{gumbel,
  title={Categorical reparameterization with gumbel-softmax},
  author={Jang, Eric and Gu, Shixiang and Poole, Ben},
  journal={arXiv preprint arXiv:1611.01144},
  year={2016}
}

@inproceedings{unet,
  title={U-net: Convolutional networks for biomedical image segmentation},
  author={Ronneberger, Olaf and Fischer, Philipp and Brox, Thomas},
  booktitle={International Conference on Medical image computing and computer-assisted intervention},
  pages={234--241},
  year={2015},
  organization={Springer}
}

@article{adam,
  title={Adam: A method for stochastic optimization},
  author={Kingma, Diederik P and Ba, Jimmy},
  journal={arXiv preprint arXiv:1412.6980},
  year={2014}
}

@article{oasis,
  title={Open Access Series of Imaging Studies ({OASIS}): cross-sectional {MRI} data in young, middle aged, nondemented, and demented older adults},
  author={Marcus and others},
  journal={Journal of Cognitive Neuroscience},
  year={2007}
}

@article{fischl2002whole,
  title={Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain},
  author={Fischl, Bruce and Salat, David H and Busa, Evelina and Albert, Marilyn and Dieterich, Megan and Haselgrove, Christian and Van Der Kouwe, Andre and Killiany, Ron and Kennedy, David and Klaveness, Shuna and others},
  journal={Neuron},
  volume={33},
  number={3},
  pages={341--355},
  year={2002},
  publisher={Elsevier}
}

@article{fischl2012freesurfer,
  title={FreeSurfer},
  author={Fischl, Bruce},
  journal={Neuroimage},
  volume={62},
  number={2},
  pages={774--781},
  year={2012},
  publisher={Elsevier}
}

@article{maddison2016concrete,
  title={The concrete distribution: A continuous relaxation of discrete random variables},
  author={Maddison, Chris J and Mnih, Andriy and Teh, Yee Whye},
  journal={arXiv preprint arXiv:1611.00712},
  year={2016}
}

@inproceedings{chaitanya2019semi,
  title={Semi-supervised and task-driven data augmentation},
  author={Chaitanya, Krishna and Karani, Neerav and Baumgartner, Christian F and Becker, Anton and Donati, Olivio and Konukoglu, Ender},
  booktitle={International Conference on Information Processing in Medical Imaging},
  pages={29--41},
  year={2019},
  organization={Springer}
}


@article{kamnitsas2017efficient,
  title={Efficient multi-scale 3D CNN with fully connected CRF for accurate brain lesion segmentation},
  author={Kamnitsas, Konstantinos and Ledig, Christian and Newcombe, Virginia FJ and Simpson, Joanna P and Kane, Andrew D and Menon, David K and Rueckert, Daniel and Glocker, Ben},
  journal={Medical image analysis},
  volume={36},
  pages={61--78},
  year={2017},
  publisher={Elsevier}
}

@article{lee2019few,
  title={Few Labeled Atlases are Necessary for Deep-Learning-Based Segmentation},
  author={Lee, Hyeon Woo and Sabuncu, Mert R and Dalca, Adrian V},
  journal={arXiv preprint arXiv:1908.04466},
  year={2019}
}

@inproceedings{dalca2018unsupervised,
  title={Unsupervised learning for fast probabilistic diffeomorphic registration},
  author={Dalca, Adrian V and Balakrishnan, Guha and Guttag, John and Sabuncu, Mert R},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={729--738},
  year={2018},
  organization={Springer}
}


@article{makhzani2015adversarial,
  title={Adversarial autoencoders},
  author={Makhzani, Alireza and Shlens, Jonathon and Jaitly, Navdeep and Goodfellow, Ian and Frey, Brendan},
  journal={arXiv preprint arXiv:1511.05644},
  year={2015}
}

@article{dempster1977maximum,
  title={Maximum likelihood from incomplete data via the EM algorithm},
  author={Dempster, Arthur P and Laird, Nan M and Rubin, Donald B},
  journal={Journal of the Royal Statistical Society: Series B (Methodological)},
  volume={39},
  number={1},
  pages={1--22},
  year={1977},
  publisher={Wiley Online Library}
}
@article{van1999automated,
  title={Automated model-based tissue classification of MR images of the brain},
  author={Van Leemput, Koen and Maes, Frederik and Vandermeulen, Dirk and Suetens, Paul},
  journal={IEEE transactions on medical imaging},
  volume={18},
  number={10},
  pages={897--908},
  year={1999},
  publisher={IEEE}
}

@article{sabuncu2010generative,
  title={A generative model for image segmentation based on label fusion},
  author={Sabuncu, Mert R and Yeo, BT Thomas and Van Leemput, Koen and Fischl, Bruce and Golland, Polina},
  journal={IEEE transactions on medical imaging},
  volume={29},
  number={10},
  pages={1714--1729},
  year={2010},
  publisher={IEEE}
}
