@article{ho2020denoising,
  title={Denoising Diffusion Probabilistic Models},
  author={Jonathan Ho and Ajay Jain and Pieter Abbeel},
  year={2020},
  journal={arXiv preprint arxiv:2006.11239}
}

@ARTICLE{Spherical_unet,
  author={Zhao, Fenqiang and Wu, Zhengwang and Wang, Li and Lin, Weili and Gilmore, John H. and Xia, Shunren and Shen, Dinggang and Li, Gang},
  journal={IEEE Transactions on Medical Imaging}, 
  title={Spherical Deformable U-Net: Application to Cortical Surface Parcellation and Development Prediction}, 
  year={2021},
  volume={40},
  number={4},
  pages={1217-1228},
  keywords={Convolution;Task analysis;Shape;Computer architecture;Distortion;Biomedical imaging;Surface treatment;Convolutional neural network;deformable networks;U-Net;parcellation;cortical surface;triangular mesh},
  doi={10.1109/TMI.2021.3050072}}

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issn = {1053-8119},
author = {Anders M. Dale and Bruce Fischl and Martin I. Sereno},
keywords = {segmentation, cortical surface reconstruction.},
}

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  year={2008},
  volume={27},
  number={5},
  pages={664-673}}

@article{MUELLER2005869,
title = {The Alzheimer's Disease Neuroimaging Initiative},
journal = {Neuroimaging Clinics of North America},
volume = {15},
number = {4},
pages = {869-877},
year = {2005},
note = {Alzheimer's Disease: 100 Years of Progress},
issn = {1052-5149},
author = {Susanne G. Mueller and Michael W. Weiner and Leon J. Thal and Ronald C. Petersen and Clifford Jack and William Jagust and John Q. Trojanowski and Arthur W. Toga and Laurel Beckett}
}

@article {10.7554/eLife.85082,
title = {Evidence for embracing normative modeling},
author = {Rutherford, Saige and Barkema, Pieter and Tso, Ivy F and Sripada, Chandra and Beckmann, Christian F and Ruhe, Henricus G and Marquand, Andre F},
volume = 12,
year = 2023,
month = {mar},
pub_date = {2023-03-13},
pages = {e85082},
citation = {eLife 2023;12:e85082},
doi = {10.7554/eLife.85082},
journal = {eLife},
issn = {2050-084X},
publisher = {eLife Sciences Publications, Ltd},
}

@inproceedings{ICAM,
author = {Bass, C and Silva, MD and Sudre, CH and Tudosiu, P-D and Smith, SM and Robinson, EC},
year = {2020},
month = {01},
pages = {},
title = {ICAM: Interpretable Classification via Disentangled Representations and Feature Attribution Mapping}
}

@article{RAVI2022102257,
title = {Degenerative adversarial neuroimage nets for brain scan simulations: Application in ageing and dementia},
journal = {Medical Image Analysis},
volume = {75},
pages = {102257},
year = {2022},
issn = {1361-8415},
doi = {https://doi.org/10.1016/j.media.2021.102257},
author = {Daniele Ravi and Stefano B. Blumberg and Silvia Ingala and Frederik Barkhof and Daniel C. Alexander and Neil P. Oxtoby},
}

@InProceedings{10.1007/978-3-031-43904-9_6,
author="Zhang, Jianwei
and Shi, Yonggang",
title="Personalized Patch-Based Normality Assessment of Brain Atrophy in Alzheimer's Disease",
booktitle="Medical Image Computing and Computer Assisted Intervention -- MICCAI 2023",
year="2023",
publisher="Springer Nature Switzerland",
address="Cham",
pages="55--62",
}

@article{HUTTON2009371,
title = {A comparison between voxel-based cortical thickness and voxel-based morphometry in normal aging},
journal = {NeuroImage},
volume = {48},
number = {2},
pages = {371-380},
year = {2009},
issn = {1053-8119},
author = {Chloe Hutton and Bogdan Draganski and John Ashburner and Nikolaus Weiskopf},
keywords = {Morphometry, VBM, Cortical thickness, Aging},
}

@article{LERCH2005163,
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issn = {1053-8119},
author = {Jason P. Lerch and Alan C. Evans},
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@INPROCEEDINGS{9008303,
  author={Hwang, Seong Jae and Tao, Zirui and Singh, Vikas and Kim, Won Hwa},
  booktitle={2019 IEEE/CVF International Conference on Computer Vision (ICCV)}, 
  title={Conditional Recurrent Flow: Conditional Generation of Longitudinal Samples With Applications to Neuroimaging}, 
  year={2019},
  volume={},
  number={},
  pages={10691-10700},
  keywords={Adaptation models;Brain modeling;Computational modeling;Cognition;Couplings;Biological neural networks;Diseases},
  doi={10.1109/ICCV.2019.01079}}

@InProceedings{10.1007/978-3-030-87234-2_67,
author="Zhang, Jiong
and Shi, Yonggang",
title="Personalized Matching and Analysis of Cortical Folding Patterns via Patch-Based Intrinsic Brain Mapping",
booktitle="Medical Image Computing and Computer Assisted Intervention -- MICCAI 2021",
year="2021",
publisher="Springer International Publishing",
address="Cham",
pages="710--720"
}

@inproceedings{rombach2022highresolution,
      title={High-Resolution Image Synthesis with Latent Diffusion Models}, 
      author={Robin Rombach and Andreas Blattmann and Dominik Lorenz and Patrick Esser and Björn Ommer},
      year={2022},
       booktitle = {arXiv: 2112.10752},
}


@inproceedings{nichol2021improved,
  title={Improved denoising diffusion probabilistic models},
  author={Nichol, Alexander Quinn and Dhariwal, Prafulla},
  booktitle={International conference on machine learning},
  pages={8162--8171},
  year={2021},
  organization={PMLR}
}


@inproceedings{salimans2022progressive,
      title={Progressive Distillation for Fast Sampling of Diffusion Models}, 
      author={Tim Salimans and Jonathan Ho},
      year={2022},
       booktitle = {arXiv: 2202.00512},
}

@article{BAI2022353,
title = {A novel Alzheimer’s disease detection approach using GAN-based brain slice image enhancement},
journal = {Neurocomputing},
volume = {492},
pages = {353-369},
year = {2022},
issn = {0925-2312},
author = {Tian Bai and Mingyu Du and Lin Zhang and Lei Ren and Li Ruan and Yuan Yang and Guanghao Qian and Zihao Meng and Li Zhao and M. Jamal Deen},
}

@article{HCP,
title = {The Human Connectome Project: A data acquisition perspective},
journal = {NeuroImage},
volume = {62},
number = {4},
pages = {2222-2231},
year = {2012},
note = {Connectivity},
issn = {1053-8119},
doi = {https://doi.org/10.1016/j.neuroimage.2012.02.018},
url = {https://www.sciencedirect.com/science/article/pii/S1053811912001954},
author = {D.C. {Van Essen} and K. Ugurbil and E. Auerbach and D. Barch and T.E.J. Behrens and R. Bucholz and A. Chang and L. Chen and M. Corbetta and S.W. Curtiss and S. {Della Penna} and D. Feinberg and M.F. Glasser and N. Harel and A.C. Heath and L. Larson-Prior and D. Marcus and G. Michalareas and S. Moeller and R. Oostenveld and S.E. Petersen and F. Prior and B.L. Schlaggar and S.M. Smith and A.Z. Snyder and J. Xu and E. Yacoub},
keywords = {Connectivity, fMRI, Diffusion imaging, MEG/EEG, Twins, Behavior},
abstract = {The Human Connectome Project (HCP) is an ambitious 5-year effort to characterize brain connectivity and function and their variability in healthy adults. This review summarizes the data acquisition plans being implemented by a consortium of HCP investigators who will study a population of 1200 subjects (twins and their non-twin siblings) using multiple imaging modalities along with extensive behavioral and genetic data. The imaging modalities will include diffusion imaging (dMRI), resting-state fMRI (R-fMRI), task-evoked fMRI (T-fMRI), T1- and T2-weighted MRI for structural and myelin mapping, plus combined magnetoencephalography and electroencephalography (MEG/EEG). Given the importance of obtaining the best possible data quality, we discuss the efforts underway during the first two years of the grant (Phase I) to refine and optimize many aspects of HCP data acquisition, including a new 7T scanner, a customized 3T scanner, and improved MR pulse sequences.}
}

@article{kingma2013auto,
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  year={2013}
}

@misc{xie2024corticalsurfacediffusiongenerative,
      title={Cortical Surface Diffusion Generative Models}, 
      author={Zhenshan Xie and Simon Dahan and Logan Z. J. Williams and M. Jorge Cardoso and Emma C. Robinson},
      year={2024},
      eprint={2402.04753},
      archivePrefix={arXiv},
      primaryClass={eess.IV},
      url={https://arxiv.org/abs/2402.04753}, 
}

@article{kingma2014adam,
  title={Adam: A method for stochastic optimization},
  author={Kingma, Diederik P},
  journal={arXiv preprint arXiv:1412.6980},
  year={2014}
}

@article{loshchilov2016sgdr,
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  journal={arXiv preprint arXiv:1608.03983},
  year={2016}
}

@article{heusel2017gans,
  title={Gans trained by a two time-scale update rule converge to a local nash equilibrium},
  author={Heusel, Martin and Ramsauer, Hubert and Unterthiner, Thomas and Nessler, Bernhard and Hochreiter, Sepp},
  journal={Advances in neural information processing systems},
  volume={30},
  year={2017}
}

@online{plotly, author = {Plotly Technologies Inc.}, title = {Collaborative data science}, publisher = {Plotly Technologies Inc.}, address = {Montreal, QC}, year = {2015}}

@article{yeo2009spherical,
  title={Spherical demons: fast diffeomorphic landmark-free surface registration},
  author={Yeo, BT Thomas and Sabuncu, Mert R and Vercauteren, Tom and Ayache, Nicholas and Fischl, Bruce and Golland, Polina},
  journal={IEEE transactions on medical imaging},
  volume={29},
  number={3},
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  publisher={IEEE}
}

@article{fischl2004automatically,
  title={Automatically parcellating the human 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 others},
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  number={1},
  pages={11--22},
  year={2004},
  publisher={Oxford University Press}
}

@InProceedings{pmlr-v139-nichol21a,
    title       = {Improved Denoising Diffusion Probabilistic Models},
    author      = {Nichol, Alexander Quinn and Dhariwal, Prafulla},
    booktitle   = {Proceedings of the 38th International Conference on Machine Learning},
    pages       = {8162--8171},
    year        = {2021},
    editor      = {Meila, Marina and Zhang, Tong},
    volume      = {139},
    series      = {Proceedings of Machine Learning Research},
    month       = {18--24 Jul},
    publisher   = {PMLR},
    pdf         = {http://proceedings.mlr.press/v139/nichol21a/nichol21a.pdf},
    url         = {https://proceedings.mlr.press/v139/nichol21a.html},
}

@article{Song2021DenoisingDI,
    title   = {Denoising Diffusion Implicit Models},
    author  = {Jiaming Song and Chenlin Meng and Stefano Ermon},
    journal = {ArXiv},
    year    = {2021},
    volume  = {abs/2010.02502}
}