@article{kuklisova2012reconstruction,
  title={Reconstruction of fetal brain {MRI} with intensity matching and complete outlier removal},
  author={Kuklisova-Murgasova, Maria and Quaghebeur, Gerardine and Rutherford, Mary A and Hajnal, Joseph V and Schnabel, Julia A},
  journal={Medical image analysis},
  volume={16},
  number={8},
  pages={1550--1564},
  year={2012},
  publisher={Elsevier}
}

@article{kuklisova2011atlas,
  title={A dynamic {4D} probabilistic atlas of the developing brain},
  author={Kuklisova-Murgasova, Maria and Aljabar, Paul and Srinivasan, Latha and Counsell, Serena J and Doria, Valentina and Serag, Ahmed and Gousias, Ioannis S and Boardman, James P and Rutherford, Mary A and Edwards, A David and others},
  journal={NeuroImage},
  volume={54},
  number={4},
  pages={2750--2763},
  year={2011},
  publisher={Elsevier}
}

@article{da2025differential,
  title={Differential patterns of cortical expansion in fetal and preterm brain development},
  author={da Silva, Mariana and Liang, Kaili and Garcia, Kara E and Cardoso, M Jorge and Robinson, Emma C},
  journal={bioRxiv},
  year={2025}
}

@inproceedings{zalevskyi2024improving,
  title={Improving cross-domain brain tissue segmentation in fetal MRI with synthetic data},
  author={Zalevskyi, Vladyslav and Sanchez, Thomas and Roulet, Margaux and Aviles Verdera, Jordina and Hutter, Jana and Kebiri, Hamza and Bach Cuadra, Meritxell},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={437--447},
  year={2024},
  organization={Springer}
}


@inproceedings{cordero2019automating,
  title={Automating motion compensation in 3T fetal brain imaging: localize, align and reconstruct},
  author={Cordero-Grande, L and Price, AN and Hughes, EJ and Wright, R and Rutherford, MA and Hajnal, JV},
  booktitle={ISMRM},
  volume={2019},
  pages={1000},
  year={2019}
}

@article{guo2025motifs,
  title={Motifs of brain cortical folding from birth to adulthood: structural asymmetry and folding-functional links},
  author={Guo, Yourong and Suliman, Mohamed A and Williams, Logan ZJ and Besenczi, Renato and Liang, Kaili and Dahan, Simon and Kyriakopoulou, Vanessa and McAlonan, Grainne M and Hammers, Alexander and O’Muircheartaigh, Jonathan and others},
  journal={bioRxiv},
  pages={2025--03},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}

@inproceedings{schuh2017deformable,
  title={A deformable model for the reconstruction of the neonatal cortex},
  author={Schuh, Andreas and Makropoulos, Antonios and Wright, Robert and Robinson, Emma C and Tusor, Nora and Steinweg, Johannes and Hughes, Emer and Grande, Lucilio Cordero and Price, Anthony and Hutter, Jana and others},
  booktitle={2017 IEEE 14th international symposium on biomedical imaging (ISBI 2017)},
  pages={800--803},
  year={2017},
  organization={IEEE}
}

@article{suliman2025unsupervised,
  title={Unsupervised multimodal surface registration with geometric deep learning},
  author={Suliman, Mohamed A and Williams, Logan ZJ and Fawaz, Abdulah and Robinson, Emma C},
  journal={Medical Image Analysis},
  pages={103821},
  year={2025},
  publisher={Elsevier}
}

@article{scott2011growth,
  title={Growth trajectories of the human fetal brain tissues estimated from 3D reconstructed in utero MRI},
  author={Scott, Julia A and Habas, Piotr A and Kim, Kio and Rajagopalan, Vidya and Hamzelou, Kia S and Corbett-Detig, James M and Barkovich, A James and Glenn, Orit A and Studholme, Colin},
  journal={International Journal of Developmental Neuroscience},
  volume={29},
  number={5},
  pages={529--536},
  year={2011},
  publisher={Elsevier}
}

@article{gholipour2017normative,
  title={A normative spatiotemporal MRI atlas of the fetal brain for automatic segmentation and analysis of early brain growth},
  author={Gholipour, Ali and Rollins, Caitlin K and Velasco-Annis, Clemente and Ouaalam, Abdelhakim and Akhondi-Asl, Alireza and Afacan, Onur and Ortinau, Cynthia M and Clancy, Sean and Limperopoulos, Catherine and Yang, Edward and others},
  journal={Scientific reports},
  volume={7},
  number={1},
  pages={476},
  year={2017},
  publisher={Nature Publishing Group UK London}
}

@inproceedings{besenczi2024high,
  title={High performance groupwise cortical surface registration with multimodal surface matching},
  author={Besenczi, Renato and Guo, Yourong and Robinson, Emma C},
  booktitle={International Workshop on Biomedical Image Registration},
  pages={321--332},
  year={2024},
  organization={Springer}
}

@article{williams2023structural,
  title={Structural and functional asymmetry of the neonatal cerebral cortex},
  author={Williams, Logan ZJ and Fitzgibbon, Sean P and Bozek, Jelena and Winkler, Anderson M and Dimitrova, Ralica and Poppe, Tanya and Schuh, Andreas and Makropoulos, Antonios and Cupitt, John and O’Muircheartaigh, Jonathan and others},
  journal={Nature human behaviour},
  volume={7},
  number={6},
  pages={942--955},
  year={2023},
  publisher={Nature Publishing Group UK London}
}

@article{serag2012multi,
  title={A multi-channel 4D probabilistic atlas of the developing brain: application to fetuses and neonates},
  author={Serag, Ahmed and Kyriakopoulou, Vanessa and Rutherford, Mary A and Edwards, A David and Hajnal, Joseph V and Aljabar, Paul and Counsell, Serena J and Boardman, James and Rueckert, Daniel},
  journal={Annals of the BMVA},
  volume={2012},
  number={3},
  pages={1--14},
  year={2012}
}

@article{uus2025scanner,
  title={Scanner-based real-time three-dimensional brain+ body slice-to-volume reconstruction for t2-weighted 0.55-t low-field fetal magnetic resonance imaging},
  author={Uus, Alena and Neves Silva, Sara and Aviles Verdera, Jordina and Payette, Kelly and Hall, Megan and Colford, Kathleen and Luis, Aysha and Sousa, Helena and Ning, Zihan and Roberts, Thomas and others},
  journal={Pediatric Radiology},
  volume={55},
  number={3},
  pages={556--569},
  year={2025},
  publisher={Springer}
}

@inproceedings{wright2018lstm,
  title={LSTM spatial co-transformer networks for registration of 3D fetal US and MR brain images},
  author={Wright, Robert and Khanal, Bishesh and Gomez, Alberto and Skelton, Emily and Matthew, Jacqueline and Hajnal, Jo V and Rueckert, Daniel and Schnabel, Julia A},
  booktitle={International Workshop on Preterm, Perinatal and Paediatric Image Analysis},
  pages={149--159},
  year={2018},
  organization={Springer}
}

%%%% learning-based approaches
@inproceedings{wickramasinghe2020voxel2mesh,
  title={Voxel2Mesh: 3D mesh model generation from volumetric data},
  author={Wickramasinghe, Udaranga and Remelli, Edoardo and Knott, Graham and Fua, Pascal},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={299--308},
  year={2020},
  organization={Springer}
}
@inproceedings{cruz2021deepcsr,
  title={DeepCSR: A 3D deep learning approach for cortical surface reconstruction},
  author={Cruz, Rodrigo Santa and Lebrat, Leo and Bourgeat, Pierrick and Fookes, Clinton and Fripp, Jurgen and Salvado, Olivier},
  booktitle={Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision},
  pages={806--815},
  year={2021}
}
@inproceedings{gopinath2023cortical,
  title={Cortical analysis of heterogeneous clinical brain MRI scans for large-scale neuroimaging studies},
  author={Gopinath, Karthik and Greve, Douglas N and Das, Sudeshna and Arnold, Steve and Magdamo, Colin and Iglesias, Juan Eugenio},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={35--45},
  year={2023},
  organization={Springer}
}
@article{henschel2020fastsurfer,
  title={Fastsurfer-a fast and accurate deep learning based neuroimaging pipeline},
  author={Henschel, Leonie and Conjeti, Sailesh and Estrada, Santiago and Diers, Kersten and Fischl, Bruce and Reuter, Martin},
  journal={NeuroImage},
  volume={219},
  pages={117012},
  year={2020},
  publisher={Elsevier}
}
@article{wang2023ibeat,
  title={{iBEAT V2.0}: a multisite-applicable, deep learning-based pipeline for infant cerebral cortical surface reconstruction},
  author={Wang, Li and Wu, Zhengwang and Chen, Liangjun and Sun, Yue and Lin, Weili and Li, Gang},
  journal={Nature protocols},
  volume={18},
  number={5},
  pages={1488--1509},
  year={2023},
  publisher={Nature Publishing Group UK London}
}
@inproceedings{bongratz2022vox2cortex,
  title={Vox2Cortex: Fast explicit reconstruction of cortical surfaces from 3D MRI scans with geometric deep neural networks},
  author={Bongratz, Fabian and Rickmann, Anne-Marie and P{\"o}lsterl, Sebastian and Wachinger, Christian},
  booktitle={Proceedings of the IEEE/CVF conference on computer vision and pattern recognition},
  pages={20773--20783},
  year={2022}
}
@article{ma2022cortexode,
  title={{CortexODE}: Learning cortical surface reconstruction by neural {ODEs}},
  author={Ma, Qiang and Li, Liu and Robinson, Emma C and Kainz, Bernhard and Rueckert, Daniel and Alansary, Amir},
  journal={IEEE Transactions on Medical Imaging},
  volume={42},
  number={2},
  pages={430--443},
  year={2022},
  publisher={IEEE}
}
@inproceedings{ma2023conditional,
  title={Conditional temporal attention networks for neonatal cortical surface reconstruction},
  author={Ma, Qiang and Li, Liu and Kyriakopoulou, Vanessa and Hajnal, Joseph V and Robinson, Emma C and Kainz, Bernhard and Rueckert, Daniel},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={312--322},
  year={2023},
  organization={Springer}
}
@inproceedings{ma2024weakly,
  title={Weakly supervised learning of cortical surface reconstruction from segmentations},
  author={Ma, Qiang and Li, Liu and Robinson, Emma C and Kainz, Bernhard and Rueckert, Daniel},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={766--777},
  year={2024},
  organization={Springer}
}
@article{ma2025developing,
  title={The Developing Human Connectome Project: A fast deep learning-based pipeline for neonatal cortical surface reconstruction},
  author={Ma, Qiang and Liang, Kaili and Li, Liu and Masui, Saga and Guo, Yourong and Nosarti, Chiara and Robinson, Emma C and Kainz, Bernhard and Rueckert, Daniel},
  journal={Medical Image Analysis},
  volume={100},
  pages={103394},
  year={2025},
  publisher={Elsevier}
}
@inproceedings{price2019developing,
  title={The developing Human Connectome Project (dHCP): fetal acquisition protocol},
  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 Deprez, Maria and Roberts, Thomas and others},
  booktitle={Proceedings of the annual meeting of the International Society of Magnetic Resonance in Medicine (ISMRM)},
  volume={244},
  year={2019},
  organization={International Society for Magnetic Resonance in Medicine (ISMRM)}
}
@article{robinson2014msm,
  title={MSM: a new flexible framework for multimodal surface matching},
  author={Robinson, Emma C and Jbabdi, Saad and Glasser, Matthew F and Andersson, Jesper and Burgess, Gregory C and Harms, Michael P and Smith, Stephen M and Van Essen, David C and Jenkinson, Mark},
  journal={Neuroimage},
  volume={100},
  pages={414--426},
  year={2014},
  publisher={Elsevier}
}
@article{robinson2018multimodal,
  title={Multimodal surface matching with higher-order smoothness constraints},
  author={Robinson, Emma C and Garcia, Kara and Glasser, Matthew F and Chen, Zhengdao and Coalson, Timothy S and Makropoulos, Antonios and Bozek, Jelena and Wright, Robert and Schuh, Andreas and Webster, Matthew and others},
  journal={Neuroimage},
  volume={167},
  pages={453--465},
  year={2018},
  publisher={Elsevier}
}

@article{edwards2022developing,
  title={The Developing Human Connectome Project Neonatal Data Release},
  author={Edwards, A David and Rueckert, Daniel and Smith, Stephen M and Seada, Samy Abo and Alansary, Amir and Almalbis, Jennifer and Allsop, Joanna and Andersson, Jesper and Arichi, Tomoki and Arulkumaran, Sophie and others},
  journal={Frontiers in Neuroscience},
  volume={16},
  year={2022},
  publisher={Frontiers Media SA}
}

@article{dai2013ibeat,
  title={iBEAT: a toolbox for infant brain magnetic resonance image processing},
  author={Dai, Yakang and Shi, Feng and Wang, Li and Wu, Guorong and Shen, Dinggang},
  journal={Neuroinformatics},
  volume={11},
  number={2},
  pages={211--225},
  year={2013},
  publisher={Springer}
}

@article{bozek2018construction,
  title={Construction of a neonatal cortical surface atlas using multimodal surface matching in the developing human connectome project},
  author={Bozek, Jelena and Makropoulos, Antonios and Schuh, Andreas and Fitzgibbon, Sean and Wright, Robert and Glasser, Matthew F and Coalson, Timothy S and O'Muircheartaigh, Jonathan and Hutter, Jana and Price, Anthony N and others},
  journal={NeuroImage},
  volume={179},
  pages={11--29},
  year={2018},
  publisher={Elsevier}
}

@article{makropoulos2018developing,
  title={The developing human connectome project: A minimal processing pipeline for neonatal cortical surface reconstruction},
  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 others},
  journal={Neuroimage},
  volume={173},
  pages={88--112},
  year={2018},
  publisher={Elsevier}
}

@article{makropoulos2014automatic,
  title={Automatic whole brain MRI segmentation of the developing neonatal brain},
  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},
  journal={IEEE transactions on medical imaging},
  volume={33},
  number={9},
  pages={1818--1831},
  year={2014},
  publisher={IEEE}
}

@article{makropoulos2016regional,
  title={Regional growth and atlasing of the developing human brain},
  author={Makropoulos, Antonios and Aljabar, Paul and Wright, Robert and H{"u}ning, Britta and Merchant, Nazakat and Arichi, Tomoki and Tusor, Nora and Hajnal, Joseph V and Edwards, A David and Counsell, Serena J and others},
  journal={Neuroimage},
  volume={125},
  pages={456--478},
  year={2016},
  publisher={Elsevier}
}

@article{uus2023retrospective,
  title={Retrospective motion correction in foetal MRI for clinical applications: existing methods, applications and integration into clinical practice},
  author={Uus, Alena U and Egloff Collado, Alexia and Roberts, Thomas A and Hajnal, Joseph V and Rutherford, Mary A and Deprez, Maria},
  journal={The British journal of radiology},
  volume={96},
  number={1147},
  pages={20220071},
  year={2023},
  publisher={The British Institute of Radiology.}
}

@article{zollei2020infant,
  title={Infant FreeSurfer: An automated segmentation and surface extraction pipeline for T1-weighted neuroimaging data of infants 0--2 years},
  author={Z{\"o}llei, Lilla and Iglesias, Juan Eugenio and Ou, Yangming and Grant, P Ellen and Fischl, Bruce},
  journal={Neuroimage},
  volume={218},
  pages={116946},
  year={2020},
  publisher={Elsevier}
}

@article{cardoso2022monai,
  title={Monai: An open-source framework for deep learning in healthcare},
  author={Cardoso, M Jorge and Li, Wenqi and Brown, Richard and Ma, Nic and Kerfoot, Eric and Wang, Yiheng and Murrey, Benjamin and Myronenko, Andriy and Zhao, Can and Yang, Dong and others},
  journal={arXiv preprint arXiv:2211.02701},
  year={2022}
}

@article{garcia2025longitudinal,
  title={Longitudinal magnetic resonance imaging reveals differences in cortical expansion in fetuses with congenital heart defects},
  author={Garcia, Kara E and Taylor, Kaylin and Bhaskara, Meghana and Velasco-Annis, Clemente and Vieth, John and Garrett, Joshua and Patel, Jessica and Pointer, Benjamin and Cao, Sha and Newburger, Jane W and others},
  journal={Cerebral Cortex},
  volume={35},
  number={8},
  pages={bhaf220},
  year={2025},
  publisher={Oxford University Press}
}

@article{gardner2018gpytorch,
  title={Gpytorch: Blackbox matrix-matrix gaussian process inference with gpu acceleration},
  author={Gardner, Jacob and Pleiss, Geoff and Weinberger, Kilian Q and Bindel, David and Wilson, Andrew G},
  journal={Advances in neural information processing systems},
  volume={31},
  year={2018}
}

@article{karolis2023developing,
  title={Developing Human Connectome Project spatio-temporal surface atlas of the fetal brain},
  author={Karolis, Vycheslav and Williams, Logan and Kyriakopoulou, Vanessa and Bozek, Jelena and Uus, Alena and Makropoulos, Antonios and Schuh, Andreas and Cordero Grande, Lucilio and Hughes, Emer and Price, Anthony and others},
  year={2023}
}

@article{kyriakopoulou2014cortical,
  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={2014},
  publisher={Oxford University Press}
}

@article{story2021brain,
  title={Brain volumetry in fetuses that deliver very preterm: an MRI pilot study},
  author={Story, Lisa and Davidson, Alice and Patkee, Prachi and Fleiss, Bobbi and Kyriakopoulou, Vanessa and Colford, Kathleen and Sankaran, Srividhya and Seed, Paul and Jones, Alice and Hutter, Jana and others},
  journal={NeuroImage: Clinical},
  volume={30},
  pages={102650},
  year={2021},
  publisher={Elsevier}
}

@article{dubois2021mri,
  title={MRI of the neonatal brain: a review of methodological challenges and neuroscientific advances},
  author={Dubois, Jessica and Alison, Marianne and Counsell, Serena J and Hertz-Pannier, Lucie and H{\"u}ppi, Petra S and Benders, Manon JNL},
  journal={Journal of Magnetic Resonance Imaging},
  volume={53},
  number={5},
  pages={1318--1343},
  year={2021},
  publisher={Wiley Online Library}
}

@article{yang2025harmonization,
  title={Harmonization in Magnetic Resonance Imaging: A Survey of Acquisition, Image-level, and Feature-level Methods},
  author={Yang, Qinqin and Shomal-Zadeh, Firoozeh and Gholipour, Ali},
  journal={arXiv preprint arXiv:2507.16962},
  year={2025}
}

@article{xu2025site,
  title={Site effects in multisite fetal brain MRI: morphological insights into early brain development},
  author={Xu, Xinyi and Sun, Cong and Yu, Hong and Yan, Guohui and Zhu, Qingqing and Kong, Xianglei and Pan, Yibin and Xu, Haoan and Zheng, Tianshu and Zhou, Chi and others},
  journal={European Radiology},
  volume={35},
  number={4},
  pages={1830--1842},
  year={2025},
  publisher={Springer}
}

@article{rutherford2008mr,
  title={MR imaging methods for assessing fetal brain development},
  author={Rutherford, Mary and Jiang, Shuzhou and Allsop, Joanna and Perkins, Lucinda and Srinivasan, Latha and Hayat, Tayyib and Kumar, Sailesh and Hajnal, Jo},
  journal={Developmental neurobiology},
  volume={68},
  number={6},
  pages={700--711},
  year={2008},
  publisher={Wiley Online Library}
}

@article{uus2023bounti, title={BOUNTI: Brain vOlumetry and aUtomated parcellatioN for 3D feTal MRI}, url={http://dx.doi.org/10.7554/eLife.88818.1}, DOI={10.7554/elife.88818.1}, publisher={eLife Sciences Publications, Ltd}, author={Uus, Alena U. and Kyriakopoulou, Vanessa and Makropoulos, Antonios and Fukami-Gartner, Abi and Cromb, Daniel and Davidson, Alice and Cordero-Grande, Lucilio and Price, Anthony N. and Grigorescu, Irina and Williams, Logan Z. J. and Robinson, Emma C. and Lloyd, David and Pushparajah, Kuberan and Story, Lisa and Hutter, Jana and Counsell, Serena J. and Edwards, A. David and Rutherford, Mary A. and Hajnal, Joseph V. and Deprez, Maria}, year={2023}, month=aug }

@article{uus2021multi,
  title={Multi-channel 4D parametrized atlas of macro-and microstructural neonatal brain development},
  author={Uus, Alena and Grigorescu, Irina and Pietsch, Maximilian and Batalle, Dafnis and Christiaens, Daan and Hughes, Emer and Hutter, Jana and Cordero Grande, Lucilio and Price, Anthony N and Tournier, Jacques-Donald and others},
  journal={Frontiers in Neuroscience},
  volume={15},
  pages={661704},
  year={2021},
  publisher={Frontiers Media SA}
}


@article{fischl1999cortical,
  title={Cortical surface-based analysis: II: inflation, flattening, and a surface-based coordinate system},
  author={Fischl, Bruce and Sereno, Martin I and Dale, Anders M},
  journal={Neuroimage},
  volume={9},
  number={2},
  pages={195--207},
  year={1999},
  publisher={Elsevier}
}

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


%%%%%%%%%%%%%%%%%%% sulcnet
@inproceedings{suliman2022deep,
  title={A deep-discrete learning framework for spherical surface registration},
  author={Suliman, Mohamed A and Williams, Logan ZJ and Fawaz, Abdulah and Robinson, Emma C},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={119--129},
  year={2022},
  organization={Springer}
}
@inproceedings{monti2017geometric,
  title={Geometric deep learning on graphs and manifolds using mixture model cnns},
  author={Monti, Federico and Boscaini, Davide and Masci, Jonathan and Rodola, Emanuele and Svoboda, Jan and Bronstein, Michael M},
  booktitle={Proceedings of the IEEE conference on computer vision and pattern recognition},
  pages={5115--5124},
  year={2017}
}
@inproceedings{zhao2019spherical,
  title={Spherical U-Net on cortical surfaces: methods and applications},
  author={Zhao, Fenqiang and Xia, Shunren and Wu, Zhengwang and Duan, Dingna and Wang, Li and Lin, Weili and Gilmore, John H and Shen, Dinggang and Li, Gang},
  booktitle={International Conference on Information Processing in Medical Imaging},
  pages={855--866},
  year={2019},
  organization={Springer}
}

