% Bibliography for SegMaST camera-ready submission
% File: midl26_NNN.bib

@article{marti2020survey,
  title={A survey on machine and statistical learning for longitudinal analysis of neuroimaging data in Alzheimer’s disease},
  author={Mart{\'\i}-Juan, Gerard and Sanroma-Guell, Gerard and Piella, Gemma},
  journal={Computer methods and programs in biomedicine},
  volume={189},
  pages={105348},
  year={2020},
  publisher={Elsevier}
}

@article{barkhof20252024,
  title={2024 MAGNIMS--CMSC--NAIMS consensus recommendations on the use of MRI for the diagnosis of multiple sclerosis},
  author={Barkhof, Frederik and Reich, Daniel S and Oh, Jiwon and Rocca, Maria A and Li, David KB and Sati, Pascal and Azevedo, Christina J and Bagnato, Francesca and Calabresi, Peter A and Ciccarelli, Olga and others},
  journal={The Lancet Neurology},
  volume={24},
  number={10},
  pages={866--879},
  year={2025},
  publisher={Elsevier}
}

@article{wen2023rano,
  title={RANO 2.0: update to the response assessment in neuro-oncology criteria for high-and low-grade gliomas in adults},
  author={Wen, Patrick Y and Van Den Bent, Martin and Youssef, Gilbert and Cloughesy, Timothy F and Ellingson, Benjamin M and Weller, Michael and Galanis, Evanthia and Barboriak, Daniel P and De Groot, John and Gilbert, Mark R and others},
  journal={Journal of Clinical Oncology},
  volume={41},
  number={33},
  pages={5187--5199},
  year={2023},
  publisher={Wolters Kluwer Health}
}

@inproceedings{ronneberger2015u,
  title={U-net: Convolutional networks for biomedical image segmentation},
  author={Ronneberger, Olaf and Fischer, Philipp and Brox, Thomas},
  booktitle={International Conference on Medical image computing and computer-assisted intervention},
  pages={234--241},
  year={2015},
  organization={Springer}
}

@inproceedings{hatamizadeh2021swin,
  title={Swin unetr: Swin transformers for semantic segmentation of brain tumors in mri images},
  author={Hatamizadeh, Ali and Nath, Vishwesh and Tang, Yucheng and Yang, Dong and Roth, Holger R and Xu, Daguang},
  booktitle={International MICCAI brainlesion workshop},
  pages={272--284},
  year={2021},
  organization={Springer}
}

@article{macar2021team,
  title={Team neuropoly: description of the pipelines for the MICCAI 2021 MS new lesions segmentation challenge},
  author={Macar, Uzay and Karthik, Enamundram Naga and Gros, Charley and Lemay, Andr{\'e}anne and Cohen-Adad, Julien},
  journal={arXiv preprint arXiv:2109.05409},
  year={2021}
}

@article{cabezas2021estimating,
  title={Estimating lesion activity through feature similarity: A dual path Unet approach for the MSSEG2 MICCAI challenge},
  author={Cabezas, Mariano and Luo, Yuling and Kyle, Kain and Ly, Linda and Wang, Chenyu and Barnett, Michael},
  journal={MSSEG-2 challenge proceedings: Multiple sclerosis new lesions segmentation challenge using a data management and processing infrastructure},
  volume={107},
  year={2021}
}

@article{seghedplus,
  title={SegHeD+: Segmentation of Heterogeneous Data for Multiple Sclerosis Lesions with Anatomical Constraints and Lesion-aware Augmentation},
  author={Doga Basaran, Berke and Matthews, Paul M and Bai, Wenjia},
  journal={arXiv e-prints},
  pages={arXiv--2412},
  year={2024}
}

@inproceedings{denner2020spatio,
  title={Spatio-temporal learning from longitudinal data for multiple sclerosis lesion segmentation},
  author={Denner, Stefan and Khakzar, Ashkan and Sajid, Moiz and Saleh, Mahdi and Spiclin, Ziga and Kim, Seong Tae and Navab, Nassir},
  booktitle={International MICCAI Brainlesion Workshop},
  pages={111--121},
  year={2020},
  organization={Springer}
}

@inproceedings{wu2023coactseg,
  title={Coactseg: Learning from heterogeneous data for new multiple sclerosis lesion segmentation},
  author={Wu, Yicheng and Wu, Zhonghua and Shi, Hengcan and Picker, Bjoern and Chong, Winston and Cai, Jianfei},
  booktitle={International conference on medical image computing and computer-assisted intervention},
  pages={3--13},
  year={2023},
  organization={Springer}
}

@article{aslani2019multi,
  title={Multi-branch convolutional neural network for multiple sclerosis lesion segmentation},
  author={Aslani, Shahab and Dayan, Michael and Storelli, Loredana and Filippi, Massimo and Murino, Vittorio and Rocca, Maria A and Sona, Diego},
  journal={NeuroImage},
  volume={196},
  pages={1--15},
  year={2019},
  publisher={Elsevier}
}

@article{isensee2021nnu,
  title={nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation},
  author={Isensee, Fabian and Jaeger, Paul F and Kohl, Simon AA and Petersen, Jens and Maier-Hein, Klaus H},
  journal={Nature methods},
  volume={18},
  number={2},
  pages={203--211},
  year={2021},
  publisher={Nature Publishing Group US New York}
}

@inproceedings{rokuss2024longitudinal,
  title={Longitudinal segmentation of ms lesions via temporal difference weighting},
  author={Rokuss, Maximilian R and Kirchhoff, Yannick and Roy, Saikat and Kovacs, Balint and Ulrich, Constantin and Wald, Tassilo and Zenk, Maximilian and Denner, Stefan and Isensee, Fabian and Vollmuth, Philipp and others},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={64--74},
  year={2024},
  organization={Springer}
}

@article{carass2017longitudinal,
  title={Longitudinal multiple sclerosis lesion segmentation: resource and challenge},
  author={Carass, Aaron and Roy, Snehashis and Jog, Amod and Cuzzocreo, Jennifer L and Magrath, Elizabeth and Gherman, Adrian and Button, Julia and Nguyen, James and Prados, Ferran and Sudre, Carole H and others},
  journal={NeuroImage},
  volume={148},
  pages={77--102},
  year={2017},
  publisher={Elsevier}
}

@inproceedings{wei2021consistent,
  title={Consistent segmentation of longitudinal brain MR images with spatio-temporal constrained networks},
  author={Wei, Jie and Shi, Feng and Cui, Zhiming and Pan, Yongsheng and Xia, Yong and Shen, Dinggang},
  booktitle={International conference on medical image computing and computer-assisted intervention},
  pages={89--98},
  year={2021},
  organization={Springer}
}

@inproceedings{commowick2021msseg,
  title={MSSEG-2 challenge proceedings: Multiple sclerosis new lesions segmentation challenge using a data management and processing infrastructure},
  author={Commowick, Olivier and Cervenansky, Fr{\'e}d{\'e}ric and Cotton, Fran{\c{c}}ois and Dojat, Michel},
  booktitle={MICCAI 2021-24th international conference on medical image computing and computer assisted intervention},
  pages={126},
  year={2021}
}

@inproceedings{tahghighi2024enhancing,
  title={Enhancing new multiple sclerosis lesion segmentation via self-supervised pre-training and synthetic lesion integration},
  author={Tahghighi, Peyman and Zhang, Yunyan and Souza, Roberto and Komeili, Amin},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={263--272},
  year={2024},
  organization={Springer}
}

@article{xie2021segformer,
  title={SegFormer: Simple and efficient design for semantic segmentation with transformers},
  author={Xie, Enze and Wang, Wenhai and Yu, Zhiding and Anandkumar, Anima and Alvarez, Jose M and Luo, Ping},
  journal={Advances in neural information processing systems},
  volume={34},
  pages={12077--12090},
  year={2021}
}

@article{yang2024vivim,
  title={Vivim: A video vision mamba for medical video segmentation},
  author={Yang, Yijun and Xing, Zhaohu and Yu, Lequan and Huang, Chunwang and Fu, Huazhu and Zhu, Lei},
  journal={arXiv preprint arXiv:2401.14168},
  year={2024}
}

@article{gu2023mamba,
  title={Mamba: Linear-time sequence modeling with selective state spaces},
  author={Gu, Albert and Dao, Tri},
  journal={arXiv preprint arXiv:2312.00752},
  year={2023}
}

@article{karimian2018gd,
  title={Gd contrast administration is dispensable in patients with MS without new T2 lesions on follow-up MRI},
  author={Karimian-Jazi, Kianush and Wildemann, Brigitte and Diem, Ricarda and Schwarz, Daniel and Hielscher, Thomas and Wick, Wolfgang and Bendszus, Martin and Breckwoldt, Michael O},
  journal={Neurology: Neuroimmunology \& Neuroinflammation},
  volume={5},
  number={5},
  pages={e480},
  year={2018},
  publisher={Lippincott Williams \& Wilkins Hagerstown, MD}
}

@article{bayas2024prospective,
  author  = {Bayas, Antonios and others},
  title   = {Prospective study validating a multidimensional treatment decision score predicting the 24-month outcome in untreated patients with clinically isolated syndrome and early relapsing--remitting multiple sclerosis, the {ProVal-MS} study},
  journal = {Neurological Research and Practice},
  volume  = {6},
  number  = {1},
  pages   = {15},
  year    = {2024}
}

@article{fields2024university,
  title={The university of california san francisco adult longitudinal post-treatment diffuse glioma mri dataset},
  author={Fields, Brandon KK and Calabrese, Evan and Mongan, John and Cha, Soonmee and Hess, Christopher P and Sugrue, Leo P and Chang, Susan M and Luks, Tracy L and Villanueva-Meyer, Javier E and Rauschecker, Andreas M and others},
  journal={Radiology: Artificial Intelligence},
  volume={6},
  number={4},
  pages={e230182},
  year={2024},
  publisher={Radiological Society of North America}
}

@article{tustison2010n4itk,
  title={N4ITK: improved N3 bias correction},
  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},
  journal={IEEE transactions on medical imaging},
  volume={29},
  number={6},
  pages={1310--1320},
  year={2010},
  publisher={IEEE}
}

@article{isensee2019automated,
  title={Automated brain extraction of multisequence MRI using artificial neural networks},
  author={Isensee, Fabian and Schell, Marianne and Pflueger, Irada and Brugnara, Gianluca and Bonekamp, David and Neuberger, Ulf and Wick, Antje and Schlemmer, Heinz-Peter and Heiland, Sabine and Wick, Wolfgang and others},
  journal={Human brain mapping},
  volume={40},
  number={17},
  pages={4952--4964},
  year={2019},
  publisher={Wiley Online Library}
}

@article{rohlfing2010sri24,
  title={The SRI24 multichannel atlas of normal adult human brain structure},
  author={Rohlfing, Torsten and Zahr, Natalie M and Sullivan, Edith V and Pfefferbaum, Adolf},
  journal={Human brain mapping},
  volume={31},
  number={5},
  pages={798--819},
  year={2010},
  publisher={Wiley Online Library}
}

@article{zhang2022qsmrim,
  title={QSMRim-Net: Imbalance-aware learning for identification of chronic active multiple sclerosis lesions on quantitative susceptibility maps},
  author={Zhang, Hang and Nguyen, Thanh D and Zhang, Jinwei and Marcille, Melanie and Spincemaille, Pascal and Wang, Yi and Gauthier, Susan A and Sweeney, Elizabeth M},
  journal={NeuroImage: Clinical},
  volume={34},
  pages={102979},
  year={2022},
  publisher={Elsevier}
}

@misc{brats2023,
  author       = {Saluja, R.},
  title        = {{BraTS-2023-Metrics}},
  howpublished = {GitHub},
  year         = {2023},
  note         = {Available: https://github.com/rachitsaluja/BraTS-2023-Metrics}
}

@article{loshchilov2017decoupled,
  title={Decoupled weight decay regularization},
  author={Loshchilov, Ilya and Hutter, Frank},
  journal={arXiv preprint arXiv:1711.05101},
  year={2017}
}

@article{loshchilov2016sgdr,
  title={Sgdr: Stochastic gradient descent with warm restarts},
  author={Loshchilov, Ilya and Hutter, Frank},
  journal={arXiv preprint arXiv:1608.03983},
  year={2016}
}

@article{goyal2017accurate,
  title={Accurate, large minibatch sgd: Training imagenet in 1 hour},
  author={Goyal, Priya and Doll{\'a}r, Piotr and Girshick, Ross and Noordhuis, Pieter and Wesolowski, Lukasz and Kyrola, Aapo and Tulloch, Andrew and Jia, Yangqing and He, Kaiming},
  journal={arXiv preprint arXiv:1706.02677},
  year={2017}
}

@article{maier2022metrics,
  title={Metrics reloaded: Pitfalls and recommendations for image analysis validation},
  author={Maier-Hein, Lena and Reinke, Annika and Christodoulou, Evangelia and Glocker, Ben and Godau, Patrick and Isensee, Fabian and Kleesiek, Jens and Kozubek, Michal and Reyes, Mauricio and Riegler, Michael A and others},
  journal={arXiv. org},
  year={2022},
  publisher={arXiv. org}
}

@article{wattjes20212021,
  title={2021 MAGNIMS--CMSC--NAIMS consensus recommendations on the use of MRI in patients with multiple sclerosis},
  author={Wattjes, Mike P and Ciccarelli, Olga and Reich, Daniel S and Banwell, Brenda and De Stefano, Nicola and Enzinger, Christian and Fazekas, Franz and Filippi, Massimo and Frederiksen, Jette and Gasperini, Claudio and others},
  journal={The Lancet Neurology},
  volume={20},
  number={8},
  pages={653--670},
  year={2021},
  publisher={Elsevier}
}
@article{commowick2018objective,
  title={Objective evaluation of multiple sclerosis lesion segmentation using a data management and processing infrastructure},
  author={Commowick, Olivier and Istace, Audrey and Kain, Michael and Laurent, Baptiste and Leray, Florent and Simon, Mathieu and Pop, Sorina Camarasu and Girard, Pascal and Ameli, Roxana and Ferr{\'e}, Jean-Christophe and others},
  journal={Scientific reports},
  volume={8},
  number={1},
  pages={13650},
  year={2018},
  publisher={Nature Publishing Group UK London}
}