@misc{.ed,
  title = {Topup - {{FslWiki}}},
  urldate = {2022-07-20}
}

@misc{.ee,
  title = {Eddy - {{FslWiki}}},
  urldate = {2022-07-20}
}

@misc{.fm,
  title = {Synthesized B0 for Diffusion Distortion Correction ({{Synb0-DisCo}}) - {{ClinicalKey}}},
  urldate = {2024-07-02}
}

@misc{.ft,
  title = {Sdcflows 0+unknown Documentation},
  urldate = {2025-02-05}
}

@misc{.fu,
  title = {Magnetism},
  journal = {Questions and Answers \hspace{0pt}in MRI},
  urldate = {2025-02-25},
  langid = {english}
}

@article{Abreu.Duarte.2021,
  title = {Quantitative {{Assessment}} of the {{Impact}} of {{Geometric Distortions}} and {{Their Correction}} on {{fMRI Data Analyses}}},
  author = {Abreu, Rodolfo and Duarte, Jo{\~a}o Valente},
  year = 2021,
  month = mar,
  journal = {Front. Neurosci.},
  volume = {15},
  publisher = {Frontiers},
  issn = {1662-453X},
  urldate = {2024-12-20},
  langid = {english}
}

@article{Aggarwal.etal.2020,
  title = {{{MoDL-MUSSELS}}: {{Model-Based Deep Learning}} for {{Multishot Sensitivity-Encoded Diffusion MRI}}},
  shorttitle = {{{MoDL-MUSSELS}}},
  author = {Aggarwal, Hemant K. and Mani, Merry P. and Jacob, Mathews},
  year = 2020,
  month = apr,
  journal = {IEEE Transactions on Medical Imaging},
  volume = {39},
  number = {4},
  pages = {1268--1277},
  issn = {1558-254X},
  urldate = {2024-10-25}
}

@article{Andersson.etal.2001,
  title = {Modeling {{Geometric Deformations}} in {{EPI Time Series}}},
  author = {Andersson, Jesper L.R. and Hutton, Chloe and Ashburner, John and Turner, Robert and Friston, Karl},
  year = 2001,
  month = may,
  journal = {NeuroImage},
  volume = {13},
  number = {5},
  pages = {903--919},
  issn = {10538119},
  urldate = {2024-11-01},
  copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
  langid = {english}
}

@article{Andersson.etal.2003,
  title = {How to Correct Susceptibility Distortions in Spin-Echo Echo-Planar Images: Application to Diffusion Tensor Imaging},
  shorttitle = {How to Correct Susceptibility Distortions in Spin-Echo Echo-Planar Images},
  author = {Andersson, Jesper L. R. and Skare, Stefan and Ashburner, John},
  year = 2003,
  month = oct,
  journal = {NeuroImage},
  volume = {20},
  number = {2},
  pages = {870--888},
  issn = {1053-8119},
  urldate = {2022-07-20},
  langid = {english}
}

@inproceedings{Andersson.etal.2012,
  title = {A Comprehensive {{Gaussian Process}} Framework for Correcting Distortions and Movements in Diffusion Images},
  booktitle = {Proc. {{Intl}}. {{Soc}}. {{Mag}}. {{Reson}}. {{Med}}.},
  author = {Andersson, Jesper L R and Xu, Junquian and Yacoub, Essa and Auerbach, Edward and Moeller, Steen and Ugurbil, Kamil},
  year = 2012,
  pages = {1},
  langid = {english}
}

@article{Andersson.etal.2016,
  title = {Incorporating Outlier Detection and Replacement into a Non-Parametric Framework for Movement and Distortion Correction of Diffusion {{MR}} Images},
  author = {Andersson, Jesper L. R and Graham, Mark S. and Zsoldos, Enik{\H o} and Sotiropoulos, Stamatios N.},
  year = 2016,
  month = nov,
  journal = {NeuroImage},
  volume = {141},
  pages = {556--572},
  issn = {1053-8119},
  urldate = {2024-10-31}
}

@article{Andersson.etal.2017,
  title = {Towards a Comprehensive Framework for Movement and Distortion Correction of Diffusion {{MR}} Images: {{Within}} Volume Movement},
  shorttitle = {Towards a Comprehensive Framework for Movement and Distortion Correction of Diffusion {{MR}} Images},
  author = {Andersson, Jesper L. R. and Graham, Mark S. and Drobnjak, Ivana and Zhang, Hui and Filippini, Nicola and Bastiani, Matteo},
  year = 2017,
  month = may,
  journal = {NeuroImage},
  volume = {152},
  pages = {450--466},
  issn = {1053-8119},
  urldate = {2022-07-20},
  langid = {english}
}

@article{Andersson.etal.2018,
  title = {Susceptibility-Induced Distortion That Varies Due to Motion: {{Correction}} in Diffusion {{MR}} without Acquiring Additional Data},
  shorttitle = {Susceptibility-Induced Distortion That Varies Due to Motion},
  author = {Andersson, Jesper L. R. and Graham, Mark S. and Drobnjak, Ivana and Zhang, Hui and Campbell, Jon},
  year = 2018,
  month = may,
  journal = {NeuroImage},
  volume = {171},
  pages = {277--295},
  issn = {1053-8119},
  urldate = {2022-07-20},
  langid = {english}
}

@article{Andersson.Skare.2002,
  title = {A {{Model-Based Method}} for {{Retrospective Correction}} of {{Geometric Distortions}} in {{Diffusion-Weighted EPI}}},
  author = {Andersson, Jesper L.R. and Skare, Stefan},
  year = 2002,
  month = may,
  journal = {NeuroImage},
  volume = {16},
  number = {1},
  pages = {177--199},
  issn = {10538119},
  urldate = {2024-11-01},
  copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
  langid = {english}
}

@article{Andersson.Sotiropoulos.2015,
  title = {Non-Parametric Representation and Prediction of Single- and Multi-Shell Diffusion-Weighted {{MRI}} Data Using {{Gaussian}} Processes},
  author = {Andersson, Jesper L. R. and Sotiropoulos, Stamatios N.},
  year = 2015,
  month = nov,
  journal = {NeuroImage},
  volume = {122},
  pages = {166--176},
  issn = {1053-8119},
  urldate = {2022-08-11},
  langid = {english}
}

@article{Andersson.Sotiropoulos.2016,
  title = {An Integrated Approach to Correction for Off-Resonance Effects and Subject Movement in Diffusion {{MR}} Imaging},
  author = {Andersson, Jesper L. R. and Sotiropoulos, Stamatios N.},
  year = 2016,
  month = jan,
  journal = {NeuroImage},
  volume = {125},
  pages = {1063--1078},
  issn = {1053-8119},
  urldate = {2022-07-20},
  langid = {english}
}

@incollection{Arsigny.etal.2006a,
  title = {A {{Log-Euclidean Framework}} for {{Statistics}} on {{Diffeomorphisms}}},
  booktitle = {Medical {{Image Computing}} and {{Computer-Assisted Intervention}} -- {{MICCAI}} 2006},
  author = {Arsigny, Vincent and Commowick, Olivier and Pennec, Xavier and Ayache, Nicholas},
  editor = {Hutchison, David and Kanade, Takeo and Kittler, Josef and Kleinberg, Jon M. and Mattern, Friedemann and Mitchell, John C. and Naor, Moni and Nierstrasz, Oscar and Pandu Rangan, C. and Steffen, Bernhard and Sudan, Madhu and Terzopoulos, Demetri and Tygar, Dough and Vardi, Moshe Y. and Weikum, Gerhard and Larsen, Rasmus and Nielsen, Mads and Sporring, Jon},
  year = 2006,
  volume = {4190},
  pages = {924--931},
  publisher = {Springer Berlin Heidelberg},
  address = {Berlin, Heidelberg},
  urldate = {2025-11-19},
  isbn = {978-3-540-44707-8 978-3-540-44708-5},
  langid = {english}
}

@article{Ashburner.2007,
  title = {A Fast Diffeomorphic Image Registration Algorithm},
  author = {Ashburner, John},
  year = 2007,
  month = oct,
  journal = {NeuroImage},
  volume = {38},
  number = {1},
  pages = {95--113},
  issn = {10538119},
  urldate = {2024-11-01},
  copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
  langid = {english}
}

@article{Avants.etal.2008,
  title = {Symmetric Diffeomorphic Image Registration with Cross-Correlation: {{Evaluating}} Automated Labeling of Elderly and Neurodegenerative Brain},
  shorttitle = {Symmetric Diffeomorphic Image Registration with Cross-Correlation},
  author = {Avants, B. B. and Epstein, C. L. and Grossman, M. and Gee, J. C.},
  year = 2008,
  month = feb,
  journal = {Medical Image Analysis},
  series = {Special {{Issue}} on {{The Third International Workshop}} on {{Biomedical Image Registration}} -- {{WBIR}} 2006},
  volume = {12},
  number = {1},
  pages = {26--41},
  issn = {1361-8415},
  urldate = {2023-11-18}
}

@article{Babayan.etal.2019,
  title = {A Mind-Brain-Body Dataset of {{MRI}}, {{EEG}}, Cognition, Emotion, and Peripheral Physiology in Young and Old Adults},
  author = {Babayan, Anahit and Erbey, Miray and Kumral, Deniz and Reinelt, Janis D. and Reiter, Andrea M. F. and R{\"o}bbig, Josefin and Schaare, H. Lina and Uhlig, Marie and Anwander, Alfred and Bazin, Pierre-Louis and Horstmann, Annette and Lampe, Leonie and Nikulin, Vadim V. and {Okon-Singer}, Hadas and Preusser, Sven and Pampel, Andr{\'e} and Rohr, Christiane S. and Sacher, Julia and {Th{\"o}ne-Otto}, Angelika and Trapp, Sabrina and Nierhaus, Till and Altmann, Denise and Arelin, Katrin and Bl{\"o}chl, Maria and Bongartz, Edith and Breig, Patric and Cesnaite, Elena and Chen, Sufang and Cozatl, Roberto and Czerwonatis, Saskia and Dambrauskaite, Gabriele and Dreyer, Maria and Enders, Jessica and Engelhardt, Melina and Fischer, Marie Michele and Forschack, Norman and Golchert, Johannes and Golz, Laura and Guran, C. Alexandrina and Hedrich, Susanna and Hentschel, Nicole and Hoffmann, Daria I. and Huntenburg, Julia M. and Jost, Rebecca and Kosatschek, Anna and Kunzendorf, Stella and Lammers, Hannah and Lauckner, Mark E. and Mahjoory, Keyvan and Kanaan, Ahmad S. and Mendes, Natacha and Menger, Ramona and Morino, Enzo and N{\"a}the, Karina and Neubauer, Jennifer and Noyan, Handan and Oligschl{\"a}ger, Sabine and {Panczyszyn-Trzewik}, Patricia and Poehlchen, Dorothee and Putzke, Nadine and Roski, Sabrina and Schaller, Marie-Catherine and Schieferbein, Anja and Schlaak, Benito and Schmidt, Robert and Gorgolewski, Krzysztof J. and Schmidt, Hanna Maria and Schrimpf, Anne and Stasch, Sylvia and Voss, Maria and Wiedemann, Annett and Margulies, Daniel S. and Gaebler, Michael and Villringer, Arno},
  year = 2019,
  month = feb,
  journal = {Sci Data},
  volume = {6},
  number = {1},
  pages = {180308},
  publisher = {Nature Publishing Group},
  issn = {2052-4463},
  urldate = {2025-02-28},
  copyright = {2019 The Author(s)},
  langid = {english}
}

@article{Balakrishnan.etal.2019,
  title = {{{VoxelMorph}}: {{A Learning Framework}} for {{Deformable Medical Image Registration}}},
  shorttitle = {{{VoxelMorph}}},
  author = {Balakrishnan, Guha and Zhao, Amy and Sabuncu, Mert R. and Guttag, John and Dalca, Adrian V.},
  year = 2019,
  month = aug,
  journal = {IEEE Transactions on Medical Imaging},
  volume = {38},
  number = {8},
  pages = {1788--1800},
  issn = {1558-254X},
  urldate = {2024-10-18}
}

@article{Begnoche.etal.2022,
  title = {{{EPI}} Susceptibility Correction Introduces Significant Differences Far from Local Areas of High Distortion},
  author = {Begnoche, John P. and Schilling, Kurt G. and Boyd, Brian D. and Cai, Leon Y. and Taylor, Warren D. and Landman, Bennett A.},
  year = 2022,
  month = oct,
  journal = {Magnetic Resonance Imaging},
  volume = {92},
  pages = {1--9},
  issn = {0730-725X},
  urldate = {2024-10-25}
}

@misc{Bore.etal.2025,
  title = {Scilpy},
  author = {Bor{\'e}, Arnaud and Rheault, Francois and Caron, Alex Valcourt},
  year = 2025,
  month = nov,
  urldate = {2025-12-02},
  howpublished = {Sherbrooke Connectivity Imaging Lab}
}

@article{Byra.etal.2023,
  title = {Exploring the Performance of Implicit Neural Representations for Brain Image Registration},
  author = {Byra, Michal and Poon, Charissa and Rachmadi, Muhammad Febrian and Schlachter, Matthias and Skibbe, Henrik},
  year = 2023,
  month = oct,
  journal = {Sci Rep},
  volume = {13},
  number = {1},
  pages = {17334},
  publisher = {Nature Publishing Group},
  issn = {2045-2322},
  urldate = {2024-10-27},
  copyright = {2023 The Author(s)},
  langid = {english}
}

@article{Cai.etal.2021,
  title = {{{MASiVar}}: {{Multisite}}, Multiscanner, and Multisubject Acquisitions for Studying Variability in Diffusion Weighted {{MRI}}},
  shorttitle = {{{MASiVar}}},
  author = {Cai, Leon Y. and Yang, Qi and Kanakaraj, Praitayini and Nath, Vishwesh and Newton, Allen T. and Edmonson, Heidi A. and Luci, Jeffrey and Conrad, Benjamin N. and Price, Gavin R. and Hansen, Colin B. and Kerley, Cailey I. and Ramadass, Karthik and Yeh, Fang-Cheng and Kang, Hakmook and Garyfallidis, Eleftherios and Descoteaux, Maxime and Rheault, Francois and Schilling, Kurt G. and Landman, Bennett A.},
  year = 2021,
  journal = {Magnetic Resonance in Medicine},
  volume = {86},
  number = {6},
  pages = {3304--3320},
  issn = {1522-2594},
  urldate = {2022-06-02},
  langid = {english}
}

@article{Calhoun.etal.2017,
  title = {The Impact of {{T1}} versus {{EPI}} Spatial Normalization Templates for {{fMRI}} Data Analyses},
  author = {Calhoun, Vince D. and Wager, Tor D. and Krishnan, Anjali and Rosch, Keri S. and Seymour, Karen E. and Nebel, Mary Beth and Mostofsky, Stewart H. and Nyalakanai, Prashanth and Kiehl, Kent},
  year = 2017,
  journal = {Human Brain Mapping},
  volume = {38},
  number = {11},
  pages = {5331--5342},
  issn = {1097-0193},
  urldate = {2025-02-15},
  copyright = {\copyright{} 2017 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.},
  langid = {english}
}

@article{Chang.Fitzpatrick.1992,
  title = {A Technique for Accurate Magnetic Resonance Imaging in the Presence of Field Inhomogeneities},
  author = {Chang, H. and Fitzpatrick, J.M.},
  year = 1992,
  month = sep,
  journal = {IEEE Transactions on Medical Imaging},
  volume = {11},
  number = {3},
  pages = {319--329},
  issn = {1558-254X},
  urldate = {2024-10-18}
}

@misc{Chen.etal.2021,
  title = {Learning {{Continuous Image Representation}} with {{Local Implicit Image Function}}},
  author = {Chen, Yinbo and Liu, Sifei and Wang, Xiaolong},
  year = 2021,
  month = apr,
  number = {arXiv:2012.09161},
  eprint = {2012.09161},
  primaryclass = {cs},
  publisher = {arXiv},
  urldate = {2022-10-03},
  archiveprefix = {arXiv}
}

@misc{Chopra.etal.2024,
  title = {The {{Transdiagnostic Connectome Project}}: A Richly Phenotyped Open Dataset for Advancing the Study of Brain-Behavior Relationships in Psychiatry},
  shorttitle = {The {{Transdiagnostic Connectome Project}}},
  author = {Chopra, Sidhant and Cocuzza, Carrisa V. and Lawhead, Connor and Ricard, Jocelyn A. and Labache, Lo{\"i}c and Patrick, Lauren M. and Kumar, Poornima and Rubenstein, Arielle and Moses, Julia and Chen, Lia and Blankenbaker, Crystal and Gillis, Bryce and Germine, Laura T. and {Harpaz-Rote}, Ilan and Yeo, BT Thomas and Baker, Justin T. and Holmes, Avram J.},
  year = 2024,
  month = jun,
  pages = {2024.06.18.24309054},
  publisher = {medRxiv},
  urldate = {2025-01-14},
  archiveprefix = {medRxiv},
  copyright = {\copyright{} 2024, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NoDerivs 4.0 International), CC BY-ND 4.0, as described at http://creativecommons.org/licenses/by-nd/4.0/},
  langid = {english}
}

@article{Cieslak.etal.2021,
  title = {{{QSIPrep}}: An Integrative Platform for Preprocessing and Reconstructing Diffusion {{MRI}} Data},
  shorttitle = {{{QSIPrep}}},
  author = {Cieslak, Matthew and Cook, Philip A. and He, Xiaosong and Yeh, Fang-Cheng and Dhollander, Thijs and Adebimpe, Azeez and Aguirre, Geoffrey K. and Bassett, Danielle S. and Betzel, Richard F. and Bourque, Josiane and Cabral, Laura M. and Davatzikos, Christos and Detre, John A. and Earl, Eric and Elliott, Mark A. and Fadnavis, Shreyas and Fair, Damien A. and Foran, Will and Fotiadis, Panagiotis and Garyfallidis, Eleftherios and Giesbrecht, Barry and Gur, Ruben C. and Gur, Raquel E. and Kelz, Max B. and Keshavan, Anisha and Larsen, Bart S. and Luna, Beatriz and Mackey, Allyson P. and Milham, Michael P. and Oathes, Desmond J. and Perrone, Anders and Pines, Adam R. and Roalf, David R. and {Richie-Halford}, Adam and Rokem, Ariel and Sydnor, Valerie J. and Tapera, Tinashe M. and Tooley, Ursula A. and Vettel, Jean M. and Yeatman, Jason D. and Grafton, Scott T. and Satterthwaite, Theodore D.},
  year = 2021,
  month = jul,
  journal = {Nat Methods},
  volume = {18},
  number = {7},
  pages = {775--778},
  publisher = {Nature Publishing Group},
  issn = {1548-7105},
  urldate = {2025-12-01},
  copyright = {2021 The Author(s), under exclusive licence to Springer Nature America, Inc.},
  langid = {english}
}

@article{Clarke.etal.2020,
  title = {Multi-Site Harmonization of 7 Tesla {{MRI}} Neuroimaging Protocols},
  author = {Clarke, William T. and Mougin, Olivier and Driver, Ian D. and Rua, Catarina and Morgan, Andrew T. and Asghar, Michael and Clare, Stuart and Francis, Susan and Wise, Richard G. and Rodgers, Christopher T. and Carpenter, Adrian and Muir, Keith and Bowtell, Richard},
  year = 2020,
  month = feb,
  journal = {NeuroImage},
  volume = {206},
  pages = {116335},
  issn = {1053-8119},
  urldate = {2025-02-05}
}

@article{Cusack.etal.2003b,
  title = {An {{Evaluation}} of the {{Use}} of {{Magnetic Field Maps}} to {{Undistort Echo-Planar Images}}},
  author = {Cusack, Rhodri and Brett, Matthew and Osswald, Katja},
  year = 2003,
  month = jan,
  journal = {NeuroImage},
  volume = {18},
  number = {1},
  pages = {127--142},
  issn = {1053-8119},
  urldate = {2025-02-25}
}

@article{Dohmatob.etal.2018,
  title = {Inter-Subject {{Registration}} of {{Functional Images}}: {{Do We Need Anatomical Images}}?},
  shorttitle = {Inter-Subject {{Registration}} of {{Functional Images}}},
  author = {Dohmatob, Elvis and Varoquaux, Gael and Thirion, Bertrand},
  year = 2018,
  month = feb,
  journal = {Front. Neurosci.},
  volume = {12},
  publisher = {Frontiers},
  issn = {1662-453X},
  urldate = {2025-02-15},
  langid = {english}
}

@article{Drobnjak.etal.2006,
  title = {Development of a Functional Magnetic Resonance Imaging Simulator for Modeling Realistic Rigid-Body Motion Artifacts},
  author = {Drobnjak, Ivana and Gavaghan, David and S{\"u}li, Endre and {Pitt-Francis}, Joe and Jenkinson, Mark},
  year = 2006,
  journal = {Magnetic Resonance in Medicine},
  volume = {56},
  number = {2},
  pages = {364--380},
  issn = {1522-2594},
  urldate = {2024-11-02},
  copyright = {Copyright \copyright{} 2006 Wiley-Liss, Inc.},
  langid = {english}
}

@article{Du.etal.2002,
  title = {Correction of Concomitant Magnetic Field-Induced Image Artifacts in Nonaxial Echo-Planar Imaging},
  author = {Du, Yiping P. and Joe Zhou, Xiaohong and Bernstein, Matt A.},
  year = 2002,
  journal = {Magnetic Resonance in Medicine},
  volume = {48},
  number = {3},
  pages = {509--515},
  issn = {1522-2594},
  urldate = {2024-11-01},
  copyright = {Copyright \copyright{} 2002 Wiley-Liss, Inc.},
  langid = {english}
}

@article{Duong.etal.2020a,
  title = {Susceptibility Artifact Correction for Sub-Millimeter {{fMRI}} Using Inverse Phase Encoding Registration and {{T1}} Weighted Regularization},
  author = {Duong, S. T. M. and Phung, S. L. and Bouzerdoum, A. and Boyd Taylor, H. G. and Puckett, A. M. and Schira, M. M.},
  year = 2020,
  month = apr,
  journal = {Journal of Neuroscience Methods},
  volume = {336},
  pages = {108625},
  issn = {0165-0270},
  urldate = {2024-10-25}
}

@article{Duong.etal.2020b,
  title = {An Unsupervised Deep Learning Technique for Susceptibility Artifact Correction in Reversed Phase-Encoding {{EPI}} Images},
  author = {Duong, Soan T. M. and Phung, Son L. and Bouzerdoum, Abdesselam and Schira, Mark M.},
  year = 2020,
  month = sep,
  journal = {Magnetic Resonance Imaging},
  volume = {71},
  pages = {1--10},
  issn = {0730-725X},
  urldate = {2024-10-25}
}

@inproceedings{Esteban.etal.2014,
  title = {Simulation-Based Evaluation of Susceptibility Distortion Correction Methods in Diffusion {{MRI}} for Connectivity Analysis},
  booktitle = {2014 {{IEEE}} 11th {{International Symposium}} on {{Biomedical Imaging}} ({{ISBI}})},
  author = {Esteban, Oscar and Daducci, Alessandro and Caruyer, Emmanuel and O'Brien, Kieran and {Ledesma-Carbayo}, Mar{\'i}a J. and {Bach-Cuadra}, Meritxell and Santos, Andr{\'e}s},
  year = 2014,
  month = apr,
  pages = {738--741},
  issn = {1945-8452},
  urldate = {2024-12-20}
}

@article{Esteban.etal.2019a,
  title = {{{fMRIPrep}}: A Robust Preprocessing Pipeline for Functional {{MRI}}},
  shorttitle = {{{fMRIPrep}}},
  author = {Esteban, Oscar and Markiewicz, Christopher J. and Blair, Ross W. and Moodie, Craig A. and Isik, A. Ilkay and Erramuzpe, Asier and Kent, James D. and Goncalves, Mathias and DuPre, Elizabeth and Snyder, Madeleine and Oya, Hiroyuki and Ghosh, Satrajit S. and Wright, Jessey and Durnez, Joke and Poldrack, Russell A. and Gorgolewski, Krzysztof J.},
  year = 2019,
  month = jan,
  journal = {Nat Methods},
  volume = {16},
  number = {1},
  pages = {111--116},
  publisher = {Nature Publishing Group},
  issn = {1548-7105},
  urldate = {2025-02-28},
  copyright = {2018 The Author(s), under exclusive licence to Springer Nature America, Inc.},
  langid = {english}
}

@article{Farzaneh.etal.1990,
  title = {Analysis of {{T2}} Limitations and Off-Resonance Effects on Spatial Resolution and Artifacts in Echo-Planar Imaging},
  author = {Farzaneh, Farhad and Riederer, Stephen J. and Pelc, Norbert J.},
  year = 1990,
  journal = {Magnetic Resonance in Medicine},
  volume = {14},
  number = {1},
  pages = {123--139},
  issn = {1522-2594},
  urldate = {2024-10-25},
  copyright = {Copyright \copyright{} 1990 Wiley-Liss, Inc., A Wiley Company},
  langid = {english}
}

@inproceedings{Finn.etal.2017,
  title = {Model-{{Agnostic Meta-Learning}} for {{Fast Adaptation}} of {{Deep Networks}}},
  booktitle = {Proceedings of the 34th {{International Conference}} on {{Machine Learning}}},
  author = {Finn, Chelsea and Abbeel, Pieter and Levine, Sergey},
  year = 2017,
  month = jul,
  pages = {1126--1135},
  publisher = {PMLR},
  issn = {2640-3498},
  urldate = {2025-12-02},
  langid = {english}
}

@inproceedings{Fritz.etal.2014,
  title = {Comparison of {{EPI}} Distortion Correction Methods at {{3T}} and {{7T}}},
  booktitle = {{{OHBM Annual Meeting}}},
  author = {Fritz, Levin and {Joost Mulders} and {Hester Breman} and {Judith Peters} and {Matteo Bastiani} and {Alard Roebroeck} and {Jesper Andersson} and {John Ashburner} and {Nikolaus Weiskopf} and {Rainer Goebel}},
  year = 2014,
  address = {Hamburg, Germany}
}

@inproceedings{Galvis.etal.2016,
  title = {Effects of {{EPI}} Distortion Correction Pipelines on the Connectome in {{Parkinson}}'s {{Disease}}},
  booktitle = {Medical {{Imaging}} 2016: {{Image Processing}}},
  author = {Galvis, Justin and Mezher, Adam F. and Ragothaman, Anjanibhargavi and {Villalon-Reina}, Julio E. and Fletcher, P. Thomas and Thompson, Paul M. and Prasad, Gautam},
  year = 2016,
  month = mar,
  volume = {9784},
  pages = {895--901},
  publisher = {SPIE},
  urldate = {2025-11-26}
}

@article{Garyfallidis.etal.2014,
  title = {Dipy, a Library for the Analysis of Diffusion {{MRI}} Data},
  author = {Garyfallidis, Eleftherios and Brett, Matthew and Amirbekian, Bagrat and Rokem, Ariel and Van Der Walt, Stefan and Descoteaux, Maxime and {Nimmo-Smith}, Ian},
  year = 2014,
  journal = {Frontiers in Neuroinformatics},
  volume = {8},
  issn = {1662-5196},
  urldate = {2022-03-01}
}

@inproceedings{Gholipour.etal.2006,
  title = {Distortion {{Correction}} via {{Non-rigid Registration}} of {{Functional}} to {{Anatomical Magnetic Resonance Brain Images}}},
  booktitle = {2006 {{International Conference}} on {{Image Processing}}},
  author = {Gholipour, Ali and Kehtarnavaz, Nasser and Gopinath, Kaundinya and Briggs, Richard and Devous, Michael and Haley, Robert},
  year = 2006,
  month = oct,
  pages = {1181--1184},
  issn = {2381-8549},
  urldate = {2024-12-20}
}

@article{Glasser.etal.2013,
  title = {The Minimal Preprocessing Pipelines for the {{Human Connectome Project}}},
  author = {Glasser, Matthew F. and Sotiropoulos, Stamatios N. and Wilson, J. Anthony and Coalson, Timothy S. and Fischl, Bruce and Andersson, Jesper L. and Xu, Junqian and Jbabdi, Saad and Webster, Matthew and Polimeni, Jonathan R. and Van Essen, David C. and Jenkinson, Mark},
  year = 2013,
  month = oct,
  journal = {NeuroImage},
  volume = {80},
  pages = {105--124},
  langid = {english}
}

@article{Goldman.etal.2008,
  title = {Evaluation of the Six-Minute Walk in Multiple Sclerosis Subjects and Healthy Controls},
  author = {Goldman, Myla D and Marrie, Ruth Ann and Cohen, Jeffrey A},
  year = 2008,
  month = apr,
  journal = {Mult Scler},
  volume = {14},
  number = {3},
  pages = {383--390},
  publisher = {SAGE Publications Ltd STM},
  issn = {1352-4585},
  urldate = {2025-09-14},
  langid = {english}
}

@article{Goldman.etal.2023,
  title = {Progression Risk Stratification with Six-Minute Walk Gait Speed Trajectory in Multiple Sclerosis},
  author = {Goldman, Myla D. and Chen, Shanshan and Motl, Robert and Pearsall, Rylan and Oh, Unsong and Brenton, J. Nicholas},
  year = 2023,
  month = oct,
  journal = {Front. Neurol.},
  volume = {14},
  publisher = {Frontiers},
  issn = {1664-2295},
  urldate = {2025-09-14},
  langid = {english}
}

@article{Gonzalez-Castillo.etal.2013,
  title = {Effects of Image Contrast on Functional {{MRI}} Image Registration},
  author = {{Gonzalez-Castillo}, Javier and Duthie, Kristen N. and Saad, Ziad S. and Chu, Carlton and Bandettini, Peter A. and Luh, Wen-Ming},
  year = 2013,
  month = feb,
  journal = {NeuroImage},
  volume = {67},
  pages = {163--174},
  issn = {1053-8119},
  urldate = {2025-02-23}
}

@article{Graham.etal.2016,
  title = {Realistic Simulation of Artefacts in Diffusion {{MRI}} for Validating Post-Processing Correction Techniques},
  author = {Graham, Mark S. and Drobnjak, Ivana and Zhang, Hui},
  year = 2016,
  month = jan,
  journal = {NeuroImage},
  volume = {125},
  pages = {1079--1094},
  issn = {1053-8119},
  urldate = {2024-11-02}
}

@article{Graham.etal.2017,
  title = {Quantitative Assessment of the Susceptibility Artefact and Its Interaction with Motion in Diffusion {{MRI}}},
  author = {Graham, Mark S. and Drobnjak, Ivana and Jenkinson, Mark and Zhang, Hui},
  year = 2017,
  month = oct,
  journal = {PLOS ONE},
  volume = {12},
  number = {10},
  pages = {e0185647},
  publisher = {Public Library of Science},
  issn = {1932-6203},
  urldate = {2022-07-20},
  langid = {english}
}

@article{Greve.Fischl.2009,
  title = {Accurate and Robust Brain Image Alignment Using Boundary-Based Registration},
  author = {Greve, Douglas N. and Fischl, Bruce},
  year = 2009,
  month = oct,
  journal = {NeuroImage},
  volume = {48},
  number = {1},
  pages = {63--72},
  issn = {1053-8119},
  urldate = {2025-03-10}
}

@article{Gu.Eklund.2019,
  title = {Evaluation of {{Six Phase Encoding Based Susceptibility Distortion Correction Methods}} for {{Diffusion MRI}}},
  author = {Gu, Xuan and Eklund, Anders},
  year = 2019,
  month = dec,
  journal = {Front. Neuroinform.},
  volume = {13},
  publisher = {Frontiers},
  issn = {1662-5196},
  urldate = {2024-10-15},
  langid = {english}
}

@phdthesis{Guo.2019,
  type = {Thesis},
  title = {Multi-Modal Image Registration with Unsupervised Deep Learning},
  author = {Guo, Courtney K.},
  year = 2019,
  urldate = {2025-10-28},
  copyright = {MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission.},
  langid = {english},
  school = {Massachusetts Institute of Technology},
  annotation = {Accepted: 2019-12-05T18:05:47Z}
}

@inproceedings{Han.etal.2023,
  title = {Diffeomorphic {{Image Registration With Neural Velocity Field}}},
  booktitle = {Proceedings of the {{IEEE}}/{{CVF Winter Conference}} on {{Applications}} of {{Computer Vision}}},
  author = {Han, Kun and Sun, Shanlin and Yan, Xiangyi and You, Chenyu and Tang, Hao and Naushad, Junayed and Ma, Haoyu and Kong, Deying and Xie, Xiaohui},
  year = 2023,
  pages = {1869--1879},
  urldate = {2024-11-01},
  langid = {english}
}

@article{Haselgrove.Moore.1996,
  title = {Correction for Distortion of Echo-Planar Images Used to Calculate the Apparent Diffusion Coefficient},
  author = {Haselgrove, John C. and Moore, James R.},
  year = 1996,
  journal = {Magnetic Resonance in Medicine},
  volume = {36},
  number = {6},
  pages = {960--964},
  issn = {1522-2594},
  urldate = {2022-07-22},
  langid = {english}
}

@article{Haskell.etal.2023,
  title = {Off-Resonance Artifact Correction for {{MRI}}: {{A}} Review},
  shorttitle = {Off-Resonance Artifact Correction for {{MRI}}},
  author = {Haskell, Melissa W. and Nielsen, Jon-Fredrik and Noll, Douglas C.},
  year = 2023,
  journal = {NMR in Biomedicine},
  volume = {36},
  number = {5},
  pages = {e4867},
  issn = {1099-1492},
  urldate = {2024-10-17},
  copyright = {\copyright{} 2022 The Authors. NMR in Biomedicine published by John Wiley \& Sons Ltd.},
  langid = {english}
}

@article{Hedouin.etal.2017,
  title = {Block-{{Matching Distortion Correction}} of {{Echo-Planar Images With Opposite Phase Encoding Directions}}},
  author = {H{\'e}douin, Renaud and Commowick, Olivier and Bannier, Elise and Scherrer, Benoit and Taquet, Maxime and Warfield, Simon K. and Barillot, Christian},
  year = 2017,
  month = may,
  journal = {IEEE Transactions on Medical Imaging},
  volume = {36},
  number = {5},
  pages = {1106--1115},
  issn = {1558-254X}
}

@article{Holland.etal.2010,
  title = {Efficient Correction of Inhomogeneous Static Magnetic Field-Induced Distortion in {{Echo Planar Imaging}}},
  author = {Holland, Dominic and Kuperman, Joshua M. and Dale, Anders M.},
  year = 2010,
  month = mar,
  journal = {NeuroImage},
  volume = {50},
  number = {1},
  pages = {175--183},
  issn = {1053-8119},
  urldate = {2022-07-29},
  langid = {english}
}

@article{Hoopes.etal.2022,
  title = {{{SynthStrip}}: Skull-Stripping for Any Brain Image},
  shorttitle = {{{SynthStrip}}},
  author = {Hoopes, Andrew and Mora, Jocelyn S. and Dalca, Adrian V. and Fischl, Bruce and Hoffmann, Malte},
  year = 2022,
  month = oct,
  journal = {NeuroImage},
  volume = {260},
  pages = {119474},
  issn = {1053-8119},
  urldate = {2025-11-17}
}

@article{Hu.etal.2020,
  title = {Distortion Correction of Single-Shot {{EPI}} Enabled by Deep-Learning},
  author = {Hu, Zhangxuan and Wang, Yishi and Zhang, Zhe and Zhang, Jieying and Zhang, Huimao and Guo, Chunjie and Sun, Yuejiao and Guo, Hua},
  year = 2020,
  month = nov,
  journal = {NeuroImage},
  volume = {221},
  pages = {117170},
  issn = {10538119},
  urldate = {2024-10-25},
  langid = {english}
}

@inproceedings{Huang.etal.2026,
  title = {Physics-{{Informed Implicit Neural Representations}} for~{{Joint B0 Estimation}} and~{{Echo Planar Imaging}}},
  booktitle = {Medical {{Image Computing}} and {{Computer Assisted Intervention}} -- {{MICCAI}} 2025},
  author = {Huang, Wenqi and Wang, Nan and Liao, Congyu and Lin, Yimeng and Gao, Mengze and Rueckert, Daniel and Setsompop, Kawin},
  editor = {Gee, James C. and Alexander, Daniel C. and Hong, Jaesung and Iglesias, Juan Eugenio and Sudre, Carole H. and Venkataraman, Archana and Golland, Polina and Kim, Jong Hyo and Park, Jinah},
  year = 2026,
  pages = {481--490},
  publisher = {Springer Nature Switzerland},
  address = {Cham},
  isbn = {978-3-032-04947-6},
  langid = {english}
}

@phdthesis{Huntenburg.2014,
  title = {Evaluating Nonlinear Coregistration of {{BOLD EPI}} and T1w Images},
  author = {Huntenburg, Julia M},
  year = 2014,
  school = {Freie Universit\"at Berlin}
}

@article{Hutton.etal.2002,
  title = {Image {{Distortion Correction}} in {{fMRI}}: {{A Quantitative Evaluation}}},
  shorttitle = {Image {{Distortion Correction}} in {{fMRI}}},
  author = {Hutton, Chloe and Bork, Andreas and Josephs, Oliver and Deichmann, Ralf and Ashburner, John and Turner, Robert},
  year = 2002,
  month = may,
  journal = {NeuroImage},
  volume = {16},
  number = {1},
  pages = {217--240},
  issn = {1053-8119},
  urldate = {2025-02-05}
}

@article{Irfanoglu.etal.2012,
  title = {Effects of Image Distortions Originating from Susceptibility Variations and Concomitant Fields on Diffusion {{MRI}} Tractography Results},
  author = {Irfanoglu, M. Okan and Walker, Lindsay and Sarlls, Joelle and Marenco, Stefano and Pierpaoli, Carlo},
  year = 2012,
  month = may,
  journal = {NeuroImage},
  volume = {61},
  number = {1},
  pages = {275--288},
  issn = {1053-8119},
  urldate = {2022-07-21},
  langid = {english}
}

@article{Irfanoglu.etal.2015,
  title = {{{DR-BUDDI}} ({{Diffeomorphic Registration}} for {{Blip-Up}} Blip-{{Down Diffusion Imaging}}) Method for Correcting Echo Planar Imaging Distortions},
  author = {Irfanoglu, M. Okan and Modi, Pooja and Nayak, Amritha and Hutchinson, Elizabeth B. and Sarlls, Joelle and Pierpaoli, Carlo},
  year = 2015,
  month = feb,
  journal = {NeuroImage},
  volume = {106},
  pages = {284--299},
  issn = {1053-8119},
  urldate = {2022-07-22},
  langid = {english}
}

@article{Jamadar.etal.2019,
  title = {Simultaneous Task-Based {{BOLD-fMRI}} and [18-{{F}}] {{FDG}} Functional {{PET}} for Measurement of Neuronal Metabolism in the Human Visual Cortex},
  author = {Jamadar, Sharna D. and Ward, Phillip GD. and Li, Shenpeng and Sforazzini, Francesco and Baran, Jakub and Chen, Zhaolin and Egan, Gary F.},
  year = 2019,
  month = apr,
  journal = {NeuroImage},
  volume = {189},
  pages = {258--266},
  issn = {1053-8119},
  urldate = {2024-11-18}
}

@article{Jenkinson.2001,
  title = {Improved Unwarping of {{EPI}} Images Using Regularised {{B0}} Maps},
  author = {Jenkinson, Mark},
  year = 2001,
  month = jun,
  journal = {NeuroImage},
  series = {Originally Published as {{Volume}} 13, {{Number}} 6, {{Part}} 2},
  volume = {13},
  number = {6, Supplement},
  pages = {165},
  issn = {1053-8119},
  urldate = {2025-02-25}
}

@inproceedings{Jenkinson.2004,
  title = {Improving the Registration of {{B0-disorted EPI}} Images Using Calculated Cost Function Weights -- {{ScienceOpen}}},
  booktitle = {Tenth {{Int}}. {{Conf}}. on {{Functional Mapping}} of the {{Human Brain}}},
  author = {Jenkinson, Mark},
  year = 2004,
  urldate = {2025-02-13}
}

@inproceedings{jenkinson2002perturbation,
  title = {Perturbation Calculation of {{B0}} Field for Non-Conducting Materials},
  booktitle = {Proc. {{Int}}. {{Soc}}. of Magnetic Resonance in Medicine},
  author = {Jenkinson, Mark and Wilson, James L and Jezzard, Peter},
  year = 2002
}

@article{Jezzard.Balaban.1995,
  title = {Correction for Geometric Distortion in Echo Planar Images from {{B0}} Field Variations},
  author = {Jezzard, Peter and Balaban, Robert S.},
  year = 1995,
  journal = {Magnetic Resonance in Medicine},
  volume = {34},
  number = {1},
  pages = {65--73},
  issn = {1522-2594},
  urldate = {2022-08-04},
  langid = {english}
}

@article{Jezzard.etal.1998,
  title = {Characterization of and Correction for Eddy Current Artifacts in Echo Planar Diffusion Imaging},
  author = {Jezzard, Peter and Barnett, Alan S. and Pierpaoli, Carlo},
  year = 1998,
  journal = {Magnetic Resonance in Medicine},
  volume = {39},
  number = {5},
  pages = {801--812},
  issn = {1522-2594},
  urldate = {2024-10-29},
  copyright = {Copyright \copyright{} 1998 Wiley-Liss, Inc., A Wiley Company},
  langid = {english}
}

@misc{Jimeno.etal.2024,
  title = {{{GDCNet}}: {{Calibrationless}} Geometric Distortion Correction of Echo Planar Imaging Data Using Deep Learning},
  shorttitle = {{{GDCNet}}},
  author = {Jimeno, Marina Manso and Bachi, Keren and Gardner, George and Hurd, Yasmin L. and Vaughan Jr., John Thomas and Geethanath, Sairam},
  year = 2024,
  month = feb,
  number = {arXiv:2402.18777},
  eprint = {2402.18777},
  primaryclass = {cs, eess},
  publisher = {arXiv},
  urldate = {2024-10-15},
  archiveprefix = {arXiv}
}

@book{Johansen-Berg.Behrens.2014,
  title = {Diffusion {{MRI}}: From Quantitative Measurement to in-Vivo Neuroanatomy},
  shorttitle = {Diffusion {{MRI}}},
  author = {{Johansen-Berg}, Heidi and Behrens, Timothy E. J.},
  year = 2014,
  edition = {2nd ed},
  publisher = {Elsevier/Academic Press},
  address = {Amsterdam},
  isbn = {978-0-12-396460-1},
  langid = {english},
  lccn = {616.075 48}
}

@inproceedings{Joue.etal.2018,
  title = {Susceptibility Distortion Correction for {{fMRI}}},
  booktitle = {Proc. {{Intl}}. {{Soc}}. {{Mag}}. {{Reson}}. {{Med}}. 26},
  author = {Joue, Gina and Sommer, Tobias and Mohammadi, Siawoosh},
  year = 2018,
  langid = {english}
}

@article{Jovicich.etal.2006,
  title = {Reliability in Multi-Site Structural {{MRI}} Studies: {{Effects}} of Gradient Non-Linearity Correction on Phantom and Human Data},
  shorttitle = {Reliability in Multi-Site Structural {{MRI}} Studies},
  author = {Jovicich, Jorge and Czanner, Silvester and Greve, Douglas and Haley, Elizabeth and {van der Kouwe}, Andre and Gollub, Randy and Kennedy, David and Schmitt, Franz and Brown, Gregory and MacFall, James and Fischl, Bruce and Dale, Anders},
  year = 2006,
  month = apr,
  journal = {NeuroImage},
  volume = {30},
  number = {2},
  pages = {436--443},
  issn = {1053-8119},
  urldate = {2022-09-16},
  langid = {english}
}

@inproceedings{Kazerouni.etal.2024,
  title = {{{INCODE}}: {{Implicit Neural Conditioning With Prior Knowledge Embeddings}}},
  shorttitle = {{{INCODE}}},
  booktitle = {Proceedings of the {{IEEE}}/{{CVF Winter Conference}} on {{Applications}} of {{Computer Vision}}},
  author = {Kazerouni, Amirhossein and Azad, Reza and Hosseini, Alireza and Merhof, Dorit and Bagci, Ulas},
  year = 2024,
  pages = {1298--1307},
  urldate = {2024-01-17},
  langid = {english}
}

@article{Kumazawa.etal.2015,
  title = {Image-Based Estimation Method for Field Inhomogeneity in Brain Echo-Planar Images with Geometric Distortion Using k-Space Textures},
  author = {Kumazawa, Seiji and Yoshiura, Takashi and Honda, Hiroshi},
  year = 2015,
  journal = {Concepts in Magnetic Resonance Part B: Magnetic Resonance Engineering},
  volume = {45},
  number = {3},
  pages = {142--152},
  issn = {1552-504X},
  urldate = {2022-08-04},
  langid = {english}
}

@article{Kybic.etal.2000,
  title = {Unwarping of Unidirectionally Distorted {{EPI}} Images},
  author = {Kybic, J. and Thevenaz, P. and Nirkko, A. and Unser, M.},
  year = 2000,
  month = feb,
  journal = {IEEE Transactions on Medical Imaging},
  volume = {19},
  number = {2},
  pages = {80--93},
  issn = {1558-254X},
  urldate = {2025-12-01}
}

@misc{LaMontagne.etal.2019,
  title = {{{OASIS-3}}: {{Longitudinal Neuroimaging}}, {{Clinical}}, and {{Cognitive Dataset}} for {{Normal Aging}} and {{Alzheimer Disease}}},
  shorttitle = {{{OASIS-3}}},
  author = {LaMontagne, Pamela J. and Benzinger, Tammie LS and Morris, John C. and Keefe, Sarah and Hornbeck, Russ and Xiong, Chengjie and Grant, Elizabeth and Hassenstab, Jason and Moulder, Krista and Vlassenko, Andrei G. and Raichle, Marcus E. and Cruchaga, Carlos and Marcus, Daniel},
  year = 2019,
  month = dec,
  pages = {2019.12.13.19014902},
  publisher = {medRxiv},
  issn = {1901-4902},
  urldate = {2024-11-05},
  archiveprefix = {medRxiv},
  copyright = {\copyright{} 2019, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NoDerivs 4.0 International), CC BY-ND 4.0, as described at http://creativecommons.org/licenses/by-nd/4.0/},
  langid = {english}
}

@inproceedings{Legouhy.etal.2022,
  title = {Correction of~{{Susceptibility Distortion}} in~{{EPI}}: {{A Semi-supervised Approach}} with~{{Deep Learning}}},
  shorttitle = {Correction of~{{Susceptibility Distortion}} in~{{EPI}}},
  booktitle = {Computational {{Diffusion MRI}}},
  author = {Legouhy, Antoine and Graham, Mark and Guerreri, Michele and Stee, Whitney and Villemonteix, Thomas and Peigneux, Philippe and Zhang, Hui},
  editor = {{Cetin-Karayumak}, Suheyla and Christiaens, Daan and Figini, Matteo and Guevara, Pamela and Pieciak, Tomasz and Powell, Elizabeth and Rheault, Francois},
  year = 2022,
  pages = {38--49},
  publisher = {Springer Nature Switzerland},
  address = {Cham},
  isbn = {978-3-031-21206-2},
  langid = {english}
}

@article{Liao.etal.2018,
  title = {Referenceless Distortion Correction of Gradient-Echo Echo-Planar Imaging under Inhomogeneous Magnetic Fields Based on a Deep Convolutional Neural Network},
  author = {Liao, Pu and Zhang, Jun and Zeng, Kun and Yang, Yonggui and Cai, Shuhui and Guo, Gang and Cai, Congbo},
  year = 2018,
  month = sep,
  journal = {Computers in Biology and Medicine},
  volume = {100},
  pages = {230--238},
  issn = {00104825},
  urldate = {2024-10-25},
  langid = {english}
}

@article{Liu.etal.2021,
  title = {Improving Distortion Correction for Isotropic High-Resolution {{3D}} Diffusion {{MRI}} by Optimizing {{Jacobian}} Modulation},
  author = {Liu, Simin and Xiong, Yuhui and Dai, Erpeng and Zhang, Jieying and Guo, Hua},
  year = 2021,
  journal = {Magnetic Resonance in Medicine},
  volume = {86},
  number = {5},
  pages = {2780--2794},
  issn = {1522-2594},
  urldate = {2024-10-25},
  copyright = {\copyright{} 2021 International Society for Magnetic Resonance in Medicine},
  langid = {english}
}

@inproceedings{Loshchilov.Hutter.2018,
  title = {Decoupled {{Weight Decay Regularization}}},
  booktitle = {International {{Conference}} on {{Learning Representations}}},
  author = {Loshchilov, Ilya and Hutter, Frank},
  year = 2018,
  month = sep,
  urldate = {2025-12-10},
  langid = {english}
}

@article{Lv.etal.2018,
  title = {Resting-{{State Functional MRI}}: {{Everything That Nonexperts Have Always Wanted}} to {{Know}}},
  shorttitle = {Resting-{{State Functional MRI}}},
  author = {Lv, H. and Wang, Z. and Tong, E. and Williams, L. M. and Zaharchuk, G. and Zeineh, M. and {Goldstein-Piekarski}, A. N. and Ball, T. M. and Liao, C. and Wintermark, M.},
  year = 2018,
  month = aug,
  journal = {American Journal of Neuroradiology},
  volume = {39},
  number = {8},
  pages = {1390--1399},
  publisher = {American Journal of Neuroradiology},
  issn = {0195-6108, 1936-959X},
  urldate = {2025-03-26},
  chapter = {Functional},
  copyright = {\copyright{} 2018 by American Journal of Neuroradiology. Indicates open access to non-subscribers at www.ajnr.org},
  langid = {english},
  pmid = {29348136}
}

@article{Madhyastha.etal.2014,
  title = {Longitudinal Reliability of Tract-Based Spatial Statistics in Diffusion Tensor Imaging},
  author = {Madhyastha, Tara and M{\'e}rillat, Susan and Hirsiger, Sarah and Bezzola, Ladina and Liem, Franziskus and Grabowski, Thomas and J{\"a}ncke, Lutz},
  year = 2014,
  journal = {Human Brain Mapping},
  volume = {35},
  number = {9},
  pages = {4544--4555},
  issn = {1097-0193},
  urldate = {2025-12-01},
  copyright = {Copyright \copyright{} 2014 Wiley Periodicals, Inc.},
  langid = {english}
}

@article{Manjon.etal.2010,
  title = {Adaptive Non-Local Means Denoising of {{MR}} Images with Spatially Varying Noise Levels},
  author = {Manj{\'o}n, Jos{\'e} V. and Coup{\'e}, Pierrick and {Mart{\'i}-Bonmat{\'i}}, Luis and Collins, D. Louis and Robles, Montserrat},
  year = 2010,
  journal = {Journal of Magnetic Resonance Imaging},
  volume = {31},
  number = {1},
  pages = {192--203},
  issn = {1522-2586},
  urldate = {2023-09-13},
  copyright = {Copyright \copyright{} 2009 Wiley-Liss, Inc.},
  langid = {english}
}

@article{Marr.Hildreth.1980,
  title = {Theory of Edge Detection},
  author = {Marr, D. and Hildreth, E.},
  year = 1980,
  month = feb,
  journal = {Proc Biol Sci},
  volume = {207},
  number = {1167},
  pages = {187--217},
  issn = {0080-4649},
  urldate = {2025-12-02}
}

@inproceedings{Mattes.etal.2001,
  title = {Nonrigid Multimodality Image Registration},
  booktitle = {Medical {{Imaging}} 2001: {{Image Processing}}},
  author = {Mattes, David and Haynor, David R. and Vesselle, Hubert and Lewellyn, Thomas K. and Eubank, William},
  year = 2001,
  month = jul,
  volume = {4322},
  pages = {1609--1620},
  publisher = {SPIE},
  urldate = {2025-02-10}
}

@inproceedings{Mehta.etal.2021b,
  title = {Modulated {{Periodic Activations}} for {{Generalizable Local Functional Representations}}},
  booktitle = {Proceedings of the {{IEEE}}/{{CVF International Conference}} on {{Computer Vision}}},
  author = {Mehta, Ishit and Gharbi, Micha{\"e}l and Barnes, Connelly and Shechtman, Eli and Ramamoorthi, Ravi and Chandraker, Manmohan},
  year = 2021,
  pages = {14214--14223},
  urldate = {2025-02-06},
  langid = {english}
}

@article{Moler.VanLoan.2003,
  title = {Nineteen {{Dubious Ways}} to {{Compute}} the {{Exponential}} of a {{Matrix}}, {{Twenty-Five Years Later}}},
  author = {Moler, Cleve and Van Loan, Charles},
  year = 2003,
  month = jan,
  journal = {SIAM Rev.},
  volume = {45},
  number = {1},
  pages = {3--49},
  publisher = {{Society for Industrial and Applied Mathematics}},
  issn = {0036-1445},
  urldate = {2025-11-19}
}

@article{Ofverstedt.etal.2022,
  title = {Fast Computation of Mutual Information in the Frequency Domain with Applications to Global Multimodal Image Alignment},
  author = {{\"O}fverstedt, Johan and Lindblad, Joakim and Sladoje, Nata{\v s}a},
  year = 2022,
  month = jul,
  journal = {Pattern Recognition Letters},
  volume = {159},
  pages = {196--203},
  issn = {01678655},
  urldate = {2025-02-10},
  langid = {english}
}

@inproceedings{Pearsall.etal.2024,
  title = {Validation of a {{Risk Stratification Tool}} for {{MS Progression}}},
  booktitle = {Multiple {{Sclerosis Journal}}},
  author = {Pearsall, Rylan and Spears, Tyler and Fletcher, Tom and Chen, Shanshan and Oh, Unsong and Goldman, Myla},
  year = 2024,
  volume = {30},
  address = {West Palm Beach, Florida}
}

@article{Pierpaoli.2010,
  title = {Artifacts in {{Diffusion MRI}}},
  author = {Pierpaoli, Carlo},
  year = 2010,
  month = nov,
  urldate = {2022-07-29},
  langid = {english}
}

@article{Pluim.etal.2003,
  title = {Mutual-Information-Based Registration of Medical Images: A Survey},
  shorttitle = {Mutual-Information-Based Registration of Medical Images},
  author = {Pluim, J.P.W. and Maintz, J.B.A. and Viergever, M.A.},
  year = 2003,
  month = aug,
  journal = {IEEE Transactions on Medical Imaging},
  volume = {22},
  number = {8},
  pages = {986--1004},
  issn = {1558-254X},
  urldate = {2025-11-07}
}

@misc{Poulin.etal.2021,
  title = {{{TractoInferno}}: {{A}} Large-Scale, Open-Source, Multi-Site Database for Machine Learning {{dMRI}} Tractography},
  shorttitle = {{{TractoInferno}}},
  author = {Poulin, Philippe and Theaud, Guillaume and Rheault, Francois and {St-Onge}, Etienne and Bore, Arnaud and Renauld, Emmanuelle and de Beaumont, Louis and Guay, Samuel and Jodoin, Pierre-Marc and Descoteaux, Maxime},
  year = 2021,
  month = nov,
  primaryclass = {New Results},
  pages = {2021.11.29.470422},
  publisher = {bioRxiv},
  urldate = {2022-07-06},
  archiveprefix = {bioRxiv},
  chapter = {New Results},
  copyright = {\copyright{} 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), CC BY-NC 4.0, as described at http://creativecommons.org/licenses/by-nc/4.0/},
  langid = {english}
}

@article{Poulin.etal.2022,
  title = {{{TractoInferno}} - {{A}} Large-Scale, Open-Source, Multi-Site Database for Machine Learning {{dMRI}} Tractography},
  author = {Poulin, Philippe and Theaud, Guillaume and Rheault, Francois and {St-Onge}, Etienne and Bore, Arnaud and Renauld, Emmanuelle and {de Beaumont}, Louis and Guay, Samuel and Jodoin, Pierre-Marc and Descoteaux, Maxime},
  year = 2022,
  month = nov,
  journal = {Sci Data},
  volume = {9},
  number = {1},
  pages = {725},
  publisher = {Nature Publishing Group},
  issn = {2052-4463},
  urldate = {2025-03-14},
  copyright = {2022 The Author(s)},
  langid = {english}
}

@inproceedings{Poynton.etal.2008,
  title = {Fieldmap-{{Free Retrospective Registration}} and {{Distortion Correction}} for {{EPI-Based Functional Imaging}}},
  booktitle = {Medical {{Image Computing}} and {{Computer-Assisted Intervention}} -- {{MICCAI}} 2008},
  author = {Poynton, Clare and Jenkinson, Mark and Whalen, Stephen and Golby, Alexandra J. and Wells, William},
  editor = {Metaxas, Dimitris and Axel, Leon and Fichtinger, Gabor and Sz{\'e}kely, G{\'a}bor},
  year = 2008,
  pages = {271--279},
  publisher = {Springer},
  address = {Berlin, Heidelberg},
  isbn = {978-3-540-85990-1},
  langid = {english}
}

@article{Qiao.Shi.2022,
  title = {Unsupervised {{Deep Learning}} for {{FOD-Based Susceptibility Distortion Correction}} in {{Diffusion MRI}}},
  author = {Qiao, Yuchuan and Shi, Yonggang},
  year = 2022,
  month = may,
  journal = {IEEE Transactions on Medical Imaging},
  volume = {41},
  number = {5},
  pages = {1165--1175},
  issn = {1558-254X},
  urldate = {2024-10-25}
}

@inproceedings{Qiu.etal.2026,
  title = {Unsupervised {{Learning-Based Susceptibility Artifact Correction}} for {{Diffusion-Weighted MRI}} in {{Multiple Organs}}},
  booktitle = {Medical {{Image Computing}} and {{Computer Assisted Intervention}} -- {{MICCAI}} 2025},
  author = {Qiu, Shihan and Miron, Radu and Li, Yahang and Eichner, Cornelius and Feiweier, Thorsten and Janardhanan, Nirmal and Clifford, Bryan and Darwish, Omar and Mostapha, Mahmoud and Nadar, Mariappan S.},
  editor = {Gee, James C. and Alexander, Daniel C. and Hong, Jaesung and Iglesias, Juan Eugenio and Sudre, Carole H. and Venkataraman, Archana and Golland, Polina and Kim, Jong Hyo and Park, Jinah},
  year = 2026,
  pages = {635--644},
  publisher = {Springer Nature Switzerland},
  address = {Cham},
  isbn = {978-3-032-05169-1},
  langid = {english}
}

@article{Reber.etal.1998,
  title = {Correction of off Resonance-Related Distortion in Echo-Planar Imaging Using {{EPI-based}} Field Maps},
  author = {Reber, Paul J. and Wong, Eric C. and Buxton, Richard B. and Frank, Lawrence R.},
  year = 1998,
  journal = {Magnetic Resonance in Medicine},
  volume = {39},
  number = {2},
  pages = {328--330},
  issn = {1522-2594},
  urldate = {2022-08-04},
  langid = {english}
}

@article{Rohde.etal.2004,
  title = {Comprehensive Approach for Correction of Motion and Distortion in Diffusion-Weighted {{MRI}}},
  author = {Rohde, G.k. and Barnett, A.s. and Basser, P.j. and Marenco, S. and Pierpaoli, C.},
  year = 2004,
  journal = {Magnetic Resonance in Medicine},
  volume = {51},
  number = {1},
  pages = {103--114},
  issn = {1522-2594},
  urldate = {2022-07-21},
  langid = {english}
}

@article{Rohlfing.2012,
  title = {Image {{Similarity}} and {{Tissue Overlaps}} as {{Surrogates}} for {{Image Registration Accuracy}}: {{Widely Used}} but {{Unreliable}}},
  shorttitle = {Image {{Similarity}} and {{Tissue Overlaps}} as {{Surrogates}} for {{Image Registration Accuracy}}},
  author = {Rohlfing, Torsten},
  year = 2012,
  month = feb,
  journal = {IEEE Transactions on Medical Imaging},
  volume = {31},
  number = {2},
  pages = {153--163},
  issn = {1558-254X},
  urldate = {2024-10-25}
}

@inproceedings{Ronneberger.etal.2015,
  title = {U-{{Net}}: {{Convolutional Networks}} for {{Biomedical Image Segmentation}}},
  shorttitle = {U-{{Net}}},
  booktitle = {Medical {{Image Computing}} and {{Computer-Assisted Intervention}} -- {{MICCAI}} 2015},
  author = {Ronneberger, Olaf and Fischer, Philipp and Brox, Thomas},
  editor = {Navab, Nassir and Hornegger, Joachim and Wells, William M. and Frangi, Alejandro F.},
  year = 2015,
  series = {Lecture {{Notes}} in {{Computer Science}}},
  pages = {234--241},
  publisher = {Springer International Publishing},
  address = {Cham},
  isbn = {978-3-319-24574-4},
  langid = {english}
}

@misc{Roopchansingh.etal.2020,
  title = {{{EPI Distortion Correction}} Is {{Easy}} and {{Useful}}, and {{You Should Use It}}: {{A}} Case Study with Toddler Data},
  shorttitle = {{{EPI Distortion Correction}} Is {{Easy}} and {{Useful}}, and {{You Should Use It}}},
  author = {Roopchansingh, Vinai and French, Jerry J. and Nielson, Dylan M. and Reynolds, Richard C. and Glen, Daniel R. and Souza, Precilla D' and Taylor, Paul A. and Cox, Robert W. and Thurm, Audrey E.},
  year = 2020,
  month = sep,
  primaryclass = {Confirmatory Results},
  pages = {2020.09.28.306787},
  publisher = {bioRxiv},
  urldate = {2025-02-05},
  archiveprefix = {bioRxiv},
  chapter = {Confirmatory Results},
  copyright = {\copyright{} 2020, Posted by Cold Spring Harbor Laboratory. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license},
  langid = {english}
}

@misc{Royer.etal.2021,
  title = {An {{Open MRI Dataset}} for {{Multiscale Neuroscience}}},
  author = {Royer, Jessica and {Rodr{\'i}guez-Cruces}, Ra{\'u}l and Tavakol, Shahin and Larivi{\`e}re, Sara and Herholz, Peer and Li, Qiongling and de Wael, Reinder Vos and Paquola, Casey and Benkarim, Oualid and Park, Bo-yong and Lowe, Alexander J. and Margulies, Daniel and Smallwood, Jonathan and Bernasconi, Andrea and Bernasconi, Neda and Frauscher, Birgit and Bernhardt, Boris C.},
  year = 2021,
  month = aug,
  primaryclass = {New Results},
  pages = {2021.08.04.454795},
  publisher = {bioRxiv},
  urldate = {2025-11-17},
  archiveprefix = {bioRxiv},
  chapter = {New Results},
  copyright = {\copyright{} 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
  langid = {english}
}

@article{Royer.etal.2022,
  title = {An {{Open MRI Dataset For Multiscale Neuroscience}}},
  author = {Royer, Jessica and {Rodr{\'i}guez-Cruces}, Ra{\'u}l and Tavakol, Shahin and Larivi{\`e}re, Sara and Herholz, Peer and Li, Qiongling and {Vos de Wael}, Reinder and Paquola, Casey and Benkarim, Oualid and Park, Bo-yong and Lowe, Alexander J. and Margulies, Daniel and Smallwood, Jonathan and Bernasconi, Andrea and Bernasconi, Neda and Frauscher, Birgit and Bernhardt, Boris C.},
  year = 2022,
  month = sep,
  journal = {Sci Data},
  volume = {9},
  number = {1},
  pages = {569},
  publisher = {Nature Publishing Group},
  issn = {2052-4463},
  urldate = {2025-11-26},
  copyright = {2022 The Author(s)},
  langid = {english}
}

@article{Rueckert.etal.1999,
  title = {Nonrigid Registration Using Free-Form Deformations: Application to Breast {{MR}} Images},
  shorttitle = {Nonrigid Registration Using Free-Form Deformations},
  author = {Rueckert, D. and Sonoda, L.I. and Hayes, C. and Hill, D.L.G. and Leach, M.O. and Hawkes, D.J.},
  year = 1999,
  month = aug,
  journal = {IEEE Transactions on Medical Imaging},
  volume = {18},
  number = {8},
  pages = {712--721},
  issn = {1558-254X},
  urldate = {2024-11-01}
}

@article{Ruthotto.etal.2012,
  title = {Diffeomorphic Susceptibility Artifact Correction of Diffusion-Weighted Magnetic Resonance Images},
  author = {Ruthotto, L. and Kugel, H. and Olesch, J. and Fischer, B. and Modersitzki, J. and Burger, M. and Wolters, C. H.},
  year = 2012,
  month = sep,
  journal = {Phys. Med. Biol.},
  volume = {57},
  number = {18},
  pages = {5715--5731},
  publisher = {IOP Publishing},
  issn = {0031-9155},
  urldate = {2022-07-29},
  langid = {english}
}

@article{Schallmo.etal.2021,
  title = {Assessing Methods for Geometric Distortion Compensation in 7 {{T}} Gradient Echo Functional {{MRI}} Data},
  author = {Schallmo, Michael-Paul and Weldon, Kimberly B. and Burton, Philip C. and Sponheim, Scott R. and Olman, Cheryl A.},
  year = 2021,
  journal = {Human Brain Mapping},
  volume = {42},
  number = {13},
  pages = {4205--4223},
  issn = {1097-0193},
  urldate = {2024-12-20},
  copyright = {\copyright{} 2021 The Authors. Human Brain Mapping published by Wiley Periodicals LLC.},
  langid = {english}
}

@article{Schilling.etal.2019,
  title = {Synthesized B0 for Diffusion Distortion Correction ({{Synb0-DisCo}})},
  author = {Schilling, Kurt G. and Blaber, Justin and Huo, Yuankai and Newton, Allen and Hansen, Colin and Nath, Vishwesh and Shafer, Andrea T. and Williams, Owen and Resnick, Susan M. and Rogers, Baxter and Anderson, Adam W. and Landman, Bennett A.},
  year = 2019,
  month = dec,
  journal = {Magnetic Resonance Imaging},
  volume = {64},
  pages = {62--70},
  issn = {0730725X},
  urldate = {2024-10-25},
  langid = {english}
}

@article{Shen.etal.2024,
  title = {{{NeRP}}: {{Implicit Neural Representation Learning With Prior Embedding}} for {{Sparsely Sampled Image Reconstruction}}},
  shorttitle = {{{NeRP}}},
  author = {Shen, Liyue and Pauly, John and Xing, Lei},
  year = 2024,
  month = jan,
  journal = {IEEE Trans. Neural Netw. Learning Syst.},
  volume = {35},
  number = {1},
  pages = {770--782},
  issn = {2162-237X, 2162-2388},
  urldate = {2024-01-17},
  langid = {english}
}

@misc{Sitzmann.etal.2020,
  title = {Implicit {{Neural Representations}} with {{Periodic Activation Functions}}},
  author = {Sitzmann, Vincent and Martel, Julien N. P. and Bergman, Alexander W. and Lindell, David B. and Wetzstein, Gordon},
  year = 2020,
  month = jun,
  number = {arXiv:2006.09661},
  eprint = {2006.09661},
  primaryclass = {cs, eess},
  publisher = {arXiv},
  urldate = {2022-09-20},
  archiveprefix = {arXiv}
}

@inproceedings{Skare.Bammer.2010,
  title = {Jacobian Weighting of Distortion Corrected {{EPI}} Data},
  booktitle = {Proc. {{Intl}}. {{Soc}}. {{Mag}}. {{Reson}}. {{Med}}.},
  author = {Skare, S and Bammer, R},
  year = 2010,
  volume = {18},
  langid = {english}
}

@article{Smith.2002,
  title = {Fast Robust Automated Brain Extraction},
  author = {Smith, Stephen M.},
  year = 2002,
  journal = {Human Brain Mapping},
  volume = {17},
  number = {3},
  pages = {143--155},
  issn = {1097-0193},
  urldate = {2023-09-13},
  copyright = {Copyright \copyright{} 2002 Wiley-Liss, Inc.},
  langid = {english}
}

@article{Studholme.etal.2000,
  title = {Accurate Alignment of Functional {{EPI}} Data to Anatomical {{MRI}} Using a Physics-Based Distortion Model},
  author = {Studholme, C. and Constable, R.T. and Duncan, J.S.},
  year = 2000,
  month = nov,
  journal = {IEEE Transactions on Medical Imaging},
  volume = {19},
  number = {11},
  pages = {1115--1127},
  issn = {1558-254X},
  urldate = {2024-10-25}
}

@article{Sun.etal.2024,
  title = {Medical Image Registration via Neural Fields},
  author = {Sun, Shanlin and Han, Kun and You, Chenyu and Tang, Hao and Kong, Deying and Naushad, Junayed and Yan, Xiangyi and Ma, Haoyu and Khosravi, Pooya and Duncan, James S. and Xie, Xiaohui},
  year = 2024,
  month = oct,
  journal = {Medical Image Analysis},
  volume = {97},
  pages = {103249},
  issn = {1361-8415},
  urldate = {2025-11-10}
}

@inproceedings{Tancik.etal.2020b,
  title = {Fourier {{Features Let Networks Learn High Frequency Functions}} in {{Low Dimensional Domains}}},
  booktitle = {Advances in {{Neural Information Processing Systems}}},
  author = {Tancik, Matthew and Srinivasan, Pratul and Mildenhall, Ben and {Fridovich-Keil}, Sara and Raghavan, Nithin and Singhal, Utkarsh and Ramamoorthi, Ravi and Barron, Jonathan and Ng, Ren},
  year = 2020,
  volume = {33},
  pages = {7537--7547},
  publisher = {Curran Associates, Inc.},
  urldate = {2025-06-25}
}

@inproceedings{Tao.etal.2009,
  title = {A {{Variational Image-Based Approach}} to the {{Correction}} of {{Susceptibility Artifacts}} in the {{Alignment}} of {{Diffusion Weighted}} and {{Structural MRI}}},
  booktitle = {Information {{Processing}} in {{Medical Imaging}}},
  author = {Tao, Ran and Fletcher, P. Thomas and Gerber, Samuel and Whitaker, Ross T.},
  year = 2009,
  pages = {664--675},
  publisher = {Springer},
  address = {Berlin, Heidelberg},
  isbn = {978-3-642-02498-6},
  langid = {english}
}

@article{Tax.etal.2022,
  title = {What's New and What's next in Diffusion {{MRI}} Preprocessing},
  author = {Tax, Chantal M. W. and Bastiani, Matteo and Veraart, Jelle and Garyfallidis, Eleftherios and Okan Irfanoglu, M.},
  year = 2022,
  month = apr,
  journal = {NeuroImage},
  volume = {249},
  pages = {118830},
  issn = {1053-8119},
  urldate = {2022-07-21},
  langid = {english}
}

@article{Thevenaz.Unser.2000,
  title = {Optimization of Mutual Information for Multiresolution Image Registration},
  author = {Thevenaz, P. and Unser, M.},
  year = 2000,
  month = dec,
  journal = {IEEE Transactions on Image Processing},
  volume = {9},
  number = {12},
  pages = {2083--2099},
  issn = {1941-0042},
  urldate = {2025-02-10}
}

@inproceedings{Tian.etal.2025,
  title = {{{NePhi}}: {{Neural Deformation Fields}} for~{{Approximately Diffeomorphic Medical Image Registration}}},
  shorttitle = {{{NePhi}}},
  booktitle = {Computer {{Vision}} -- {{ECCV}} 2024},
  author = {Tian, Lin and Greer, Hastings and Jos{\'e} Est{\'e}par, Ra{\'u}l San and Sengupta, Roni and Niethammer, Marc},
  editor = {Leonardis, Ale{\v s} and Ricci, Elisa and Roth, Stefan and Russakovsky, Olga and Sattler, Torsten and Varol, G{\"u}l},
  year = 2025,
  pages = {213--237},
  publisher = {Springer Nature Switzerland},
  address = {Cham},
  isbn = {978-3-031-73223-2},
  langid = {english}
}

@article{Tournier.etal.2019,
  title = {{{MRtrix3}}: {{A}} Fast, Flexible and Open Software Framework for Medical Image Processing and Visualisation},
  shorttitle = {{{MRtrix3}}},
  author = {Tournier, J-Donald and Smith, Robert and Raffelt, David and Tabbara, Rami and Dhollander, Thijs and Pietsch, Maximilian and Christiaens, Daan and Jeurissen, Ben and Yeh, Chun-Hung and Connelly, Alan},
  year = 2019,
  month = nov,
  journal = {NeuroImage},
  volume = {202},
  pages = {116137},
  issn = {1053-8119},
  urldate = {2022-03-30},
  langid = {english}
}

@article{Treiber.etal.2016,
  title = {Characterization and {{Correction}} of {{Geometric Distortions}} in 814 {{Diffusion Weighted Images}}},
  author = {Treiber, Jeffrey Mark and White, Nathan S. and Steed, Tyler Christian and Bartsch, Hauke and Holland, Dominic and Farid, Nikdokht and McDonald, Carrie R. and Carter, Bob S. and Dale, Anders Martin and Chen, Clark C.},
  year = 2016,
  month = mar,
  journal = {PLOS ONE},
  volume = {11},
  number = {3},
  pages = {e0152472},
  publisher = {Public Library of Science},
  issn = {1932-6203},
  urldate = {2025-02-07},
  langid = {english}
}

@article{Tustison.etal.2010,
  title = {{{N4ITK}}: {{Improved N3 Bias Correction}}},
  shorttitle = {{{N4ITK}}},
  author = {Tustison, Nicholas J. and Avants, Brian B. and Cook, Philip A. and Zheng, Yuanjie and Egan, Alexander and Yushkevich, Paul A. and Gee, James C.},
  year = 2010,
  month = jun,
  journal = {IEEE Transactions on Medical Imaging},
  volume = {29},
  number = {6},
  pages = {1310--1320},
  issn = {1558-254X},
  urldate = {2024-11-05}
}

@article{VanEssen.etal.2013,
  ids = {VanEssen.etal.2013b},
  title = {The {{WU-Minn Human Connectome Project}}: {{An}} Overview},
  shorttitle = {The {{WU-Minn Human Connectome Project}}},
  author = {Van Essen, David C. and Smith, Stephen M. and Barch, Deanna M. and Behrens, Timothy E. J. and Yacoub, Essa and Ugurbil, Kamil},
  year = 2013,
  month = oct,
  journal = {NeuroImage},
  series = {Mapping the {{Connectome}}},
  volume = {80},
  pages = {62--79},
  issn = {1053-8119},
  urldate = {2022-06-21},
  langid = {english}
}

@article{vanHarten.etal.2024,
  title = {Robust {{Deformable Image Registration Using Cycle-Consistent Implicit Representations}}},
  author = {{van Harten}, Louis D. and Stoker, Jaap and I{\v s}gum, Ivana},
  year = 2024,
  month = feb,
  journal = {IEEE Transactions on Medical Imaging},
  volume = {43},
  number = {2},
  pages = {784--793},
  issn = {1558-254X},
  urldate = {2025-10-28}
}

@misc{Vasconcelos.etal.2023,
  title = {{{UncertaINR}}: {{Uncertainty Quantification}} of {{End-to-End Implicit Neural Representations}} for {{Computed Tomography}}},
  shorttitle = {{{UncertaINR}}},
  author = {Vasconcelos, Francisca and He, Bobby and Singh, Nalini and Teh, Yee Whye},
  year = 2023,
  month = may,
  number = {arXiv:2202.10847},
  eprint = {2202.10847},
  publisher = {arXiv},
  urldate = {2024-11-02},
  archiveprefix = {arXiv}
}

@article{Veraart.etal.2016,
  title = {Denoising of Diffusion {{MRI}} Using Random Matrix Theory},
  author = {Veraart, Jelle and Novikov, Dmitry S. and Christiaens, Daan and {Ades-aron}, Benjamin and Sijbers, Jan and Fieremans, Els},
  year = 2016,
  month = nov,
  journal = {NeuroImage},
  volume = {142},
  pages = {394--406},
  issn = {1053-8119},
  urldate = {2022-07-21},
  langid = {english}
}

@article{Viola.WellsIII.1997,
  title = {Alignment by {{Maximization}} of {{Mutual Information}}},
  author = {Viola, Paul and Wells III, William M.},
  year = 1997,
  month = sep,
  journal = {International Journal of Computer Vision},
  volume = {24},
  number = {2},
  pages = {137--154},
  issn = {1573-1405},
  urldate = {2025-11-07},
  langid = {english}
}

@article{Wan.etal.1997,
  title = {Reduction of Geometric and Intensity Distortions in Echo-Planar Imaging Using a Multireference Scan},
  author = {Wan, Xin and Gullberg, Grant T. and Parker, Dennis L. and Zeng, Gengsheng L.},
  year = 1997,
  journal = {Magnetic Resonance in Medicine},
  volume = {37},
  number = {6},
  pages = {932--942},
  issn = {1522-2594},
  urldate = {2025-12-01},
  copyright = {Copyright \copyright{} 1997 Wiley-Liss, Inc., A Wiley Company},
  langid = {english}
}

@article{Wang.etal.2004,
  title = {Image Quality Assessment: From Error Visibility to Structural Similarity},
  shorttitle = {Image Quality Assessment},
  author = {Wang, Zhou and Bovik, A.C. and Sheikh, H.R. and Simoncelli, E.P.},
  year = 2004,
  month = apr,
  journal = {IEEE TIP},
  volume = {13},
  number = {4},
  pages = {600--612},
  issn = {1941-0042}
}

@article{Wang.etal.2017,
  title = {Evaluation of {{Field Map}} and {{Nonlinear Registration Methods}} for {{Correction}} of {{Susceptibility Artifacts}} in {{Diffusion MRI}}},
  author = {Wang, Sijia and Peterson, Daniel J. and Gatenby, J. C. and Li, Wenbin and Grabowski, Thomas J. and Madhyastha, Tara M.},
  year = 2017,
  month = feb,
  journal = {Front. Neuroinform.},
  volume = {11},
  publisher = {Frontiers},
  issn = {1662-5196},
  urldate = {2024-10-25},
  langid = {english}
}

@inproceedings{Wolterink.etal.2022,
  title = {Implicit {{Neural Representations}} for {{Deformable Image Registration}}},
  booktitle = {Proceedings of {{The}} 5th {{International Conference}} on {{Medical Imaging}} with {{Deep Learning}}},
  author = {Wolterink, Jelmer M. and Zwienenberg, Jesse C. and Brune, Christoph},
  year = 2022,
  month = dec,
  pages = {1349--1359},
  publisher = {PMLR},
  issn = {2640-3498},
  urldate = {2024-01-11},
  langid = {english}
}

@inproceedings{Wu.etal.2008,
  title = {Comparison of {{EPI Distortion Correction Methods}} in {{Diffusion Tensor MRI Using}} a {{Novel Framework}}},
  booktitle = {Medical {{Image Computing}} and {{Computer-Assisted Intervention}} -- {{MICCAI}} 2008},
  author = {Wu, Minjie and Chang, Lin-Ching and Walker, Lindsay and Lemaitre, Herve and Barnett, Alan S. and Marenco, Stefano and Pierpaoli, Carlo},
  editor = {Metaxas, Dimitris and Axel, Leon and Fichtinger, Gabor and Sz{\'e}kely, G{\'a}bor},
  year = 2008,
  series = {Lecture {{Notes}} in {{Computer Science}}},
  pages = {321--329},
  publisher = {Springer},
  address = {Berlin, Heidelberg},
  isbn = {978-3-540-85990-1},
  langid = {english}
}

@article{Wu.Miller.2017,
  title = {Image Formation in Diffusion {{MRI}}: {{A}} Review of Recent Technical Developments},
  shorttitle = {Image Formation in Diffusion {{MRI}}},
  author = {Wu, Wenchuan and Miller, Karla L.},
  year = 2017,
  journal = {Journal of Magnetic Resonance Imaging},
  volume = {46},
  number = {3},
  pages = {646--662},
  issn = {1522-2586},
  urldate = {2022-07-27},
  langid = {english}
}

@inproceedings{Xie.etal.2021,
  title = {Unsupervised {{Cycle-Consistent Network}} for {{Removing Susceptibility Artifacts}} in {{Single-shot EPI}}},
  booktitle = {Proceedings of {{The}} 13th {{Asian Conference}} on {{Machine Learning}}},
  author = {Xie, Weida and Chen, Shi and Bao, Qingjia and Liu, Kewen and Li, Zhao and Li, Xiaojun and Bai, Chongxin and Li, Piqiang and Liu, Chaoyang and Martins, Otikovs},
  year = 2021,
  month = nov,
  pages = {1723--1738},
  publisher = {PMLR},
  issn = {2640-3498},
  urldate = {2024-10-25},
  langid = {english}
}

@article{Xiong.etal.2019,
  title = {Distortion Correction for High-Resolution Single-Shot {{EPI DTI}} Using a Modified Field-Mapping Method},
  author = {Xiong, Yuhui and Li, Guangqi and Dai, Erpeng and Wang, Yishi and Zhang, Zhe and Guo, Hua},
  year = 2019,
  journal = {NMR in Biomedicine},
  volume = {32},
  number = {9},
  pages = {e4124},
  issn = {1099-1492},
  urldate = {2024-10-25},
  copyright = {\copyright{} 2019 John Wiley \& Sons, Ltd.},
  langid = {english}
}

@article{Yan.etal.2015,
  title = {Developmental Cognitive Neurosciecne: {{Functional}} Connectomics Agenda for Human Brain Lifespan Development},
  shorttitle = {Developmental Cognitive Neurosciecne},
  author = {Yan, ZhiXiong and Liu, Xun and Tan, ShuPing and Tan, YunLong and Wei, GaoXia and Yang, Zhi and Zuo, XiNian},
  year = 2015,
  month = dec,
  journal = {CSB},
  volume = {61},
  number = {7},
  pages = {718--727},
  publisher = {Science China Press},
  issn = {0023-074X},
  urldate = {2025-12-01},
  langid = {american}
}

@misc{Ye.etal.2021,
  title = {Simultaneous {{Super-Resolution}} and {{Distortion Correction}} for {{Single-shot EPI DWI}} Using {{Deep Learning}}},
  author = {Ye, Xinyu and Wang, Peipei and Li, Sisi and Zhang, Jieying and Lian, Yuan and Zhang, Yajing and Lu, Jie and Guo, Hua},
  year = 2021,
  month = dec,
  primaryclass = {New Results},
  pages = {2021.12.03.470880},
  publisher = {bioRxiv},
  urldate = {2024-07-02},
  archiveprefix = {bioRxiv},
  chapter = {New Results},
  copyright = {\copyright{} 2021, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
  langid = {english}
}

@article{Yu.etal.2023,
  title = {Distortion Correction of Functional {{MRI}} without Reverse Phase Encoding Scans or Field Maps},
  author = {Yu, Tian and Cai, Leon Y. and Torrisi, Salvatore and Vu, An Thanh and Morgan, Victoria L. and Goodale, Sarah E. and Ramadass, Karthik and Meisler, Steven L. and Lv, Jinglei and Warren, Aaron E.L. and Englot, Dario J. and Cutting, Laurie and Chang, Catie and Gore, John C. and Landman, Bennett A. and Schilling, Kurt G.},
  year = 2023,
  month = nov,
  journal = {Magnetic Resonance Imaging},
  volume = {103},
  pages = {18--27},
  issn = {0730725X},
  urldate = {2024-10-29},
  langid = {english}
}

@article{Zahneisen.etal.2020,
  title = {Deep Flow-Net for {{EPI}} Distortion Estimation},
  author = {Zahneisen, Benjamin and Baeumler, Kathrin and Zaharchuk, Greg and Fleischmann, Dominik and Zeineh, Michael},
  year = 2020,
  month = aug,
  journal = {NeuroImage},
  volume = {217},
  pages = {116886},
  issn = {10538119},
  urldate = {2024-10-25},
  langid = {english}
}

@article{ZaidAlkilani.etal.2024,
  title = {{{FD-Net}}: {{An}} Unsupervised Deep Forward-Distortion Model for Susceptibility Artifact Correction in {{EPI}}},
  shorttitle = {{{FD-Net}}},
  author = {Zaid Alkilani, Abdallah and {\c C}ukur, Tolga and Saritas, Emine Ulku},
  year = 2024,
  journal = {Magnetic Resonance in Medicine},
  volume = {91},
  number = {1},
  pages = {280--296},
  issn = {1522-2594},
  urldate = {2024-07-02},
  copyright = {\copyright{} 2023 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals LLC on behalf of International Society for Magnetic Resonance in Medicine.},
  langid = {english}
}

@inproceedings{Zhang.etal.2018,
  title = {The {{Unreasonable Effectiveness}} of {{Deep Features}} as a {{Perceptual Metric}}},
  booktitle = {Proceedings of the {{IEEE Conference}} on {{Computer Vision}} and {{Pattern Recognition}}},
  author = {Zhang, Richard and Isola, Phillip and Efros, Alexei A. and Shechtman, Eli and Wang, Oliver},
  year = 2018,
  pages = {586--595},
  urldate = {2024-11-02}
}

@article{Zuo.etal.2014,
  title = {An Open Science Resource for Establishing Reliability and Reproducibility in Functional Connectomics},
  author = {Zuo, Xi-Nian and Anderson, Jeffrey S. and Bellec, Pierre and Birn, Rasmus M. and Biswal, Bharat B. and Blautzik, Janusch and Breitner, John C. S. and Buckner, Randy L. and Calhoun, Vince D. and Castellanos, F. Xavier and Chen, Antao and Chen, Bing and Chen, Jiangtao and Chen, Xu and Colcombe, Stanley J. and Courtney, William and Craddock, R. Cameron and Di Martino, Adriana and Dong, Hao-Ming and Fu, Xiaolan and Gong, Qiyong and Gorgolewski, Krzysztof J. and Han, Ying and He, Ye and He, Yong and Ho, Erica and Holmes, Avram and Hou, Xiao-Hui and Huckins, Jeremy and Jiang, Tianzi and Jiang, Yi and Kelley, William and Kelly, Clare and King, Margaret and LaConte, Stephen M. and Lainhart, Janet E. and Lei, Xu and Li, Hui-Jie and Li, Kaiming and Li, Kuncheng and Lin, Qixiang and Liu, Dongqiang and Liu, Jia and Liu, Xun and Liu, Yijun and Lu, Guangming and Lu, Jie and Luna, Beatriz and Luo, Jing and Lurie, Daniel and Mao, Ying and Margulies, Daniel S. and Mayer, Andrew R. and Meindl, Thomas and Meyerand, Mary E. and Nan, Weizhi and Nielsen, Jared A. and O'Connor, David and Paulsen, David and Prabhakaran, Vivek and Qi, Zhigang and Qiu, Jiang and Shao, Chunhong and Shehzad, Zarrar and Tang, Weijun and Villringer, Arno and Wang, Huiling and Wang, Kai and Wei, Dongtao and Wei, Gao-Xia and Weng, Xu-Chu and Wu, Xuehai and Xu, Ting and Yang, Ning and Yang, Zhi and Zang, Yu-Feng and Zhang, Lei and Zhang, Qinglin and Zhang, Zhe and Zhang, Zhiqiang and Zhao, Ke and Zhen, Zonglei and Zhou, Yuan and Zhu, Xing-Ting and Milham, Michael P.},
  year = 2014,
  month = dec,
  journal = {Sci Data},
  volume = {1},
  number = {1},
  pages = {140049},
  publisher = {Nature Publishing Group},
  issn = {2052-4463},
  urldate = {2024-11-05},
  copyright = {2014 The Author(s)},
  langid = {english}
}
