@inproceedings{Swin-UNETR,
  title={Self-supervised pre-training of swin transformers for 3d medical image analysis},
  author={Tang, Yucheng and Yang, Dong and Li, Wenqi and Roth, Holger R and Landman, Bennett and Xu, Daguang and Nath, Vishwesh and Hatamizadeh, Ali},
  booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
  pages={20730--20740},
  year={2022}
}

@inproceedings{Unet-3D,
  title={3D U-Net: learning dense volumetric segmentation from sparse annotation},
  author={{\c{C}}i{\c{c}}ek, {\"O}zg{\"u}n and Abdulkadir, Ahmed and Lienkamp, Soeren S and Brox, Thomas and Ronneberger, Olaf},
  booktitle={Medical Image Computing and Computer-Assisted Intervention--MICCAI 2016: 19th International Conference, Athens, Greece, October 17-21, 2016, Proceedings, Part II 19},
  pages={424--432},
  year={2016},
  organization={Springer}
}


@article{DnCNN3D,
  title={Poststack seismic data denoising based on 3-D convolutional neural network},
  author={Liu, Dawei and Wang, Wei and Wang, Xiaokai and Wang, Cheng and Pei, Jiangyun and Chen, Wenchao},
  journal={IEEE Transactions on Geoscience and Remote Sensing},
  volume={58},
  number={3},
  pages={1598--1629},
  year={2019},
  publisher={IEEE}
}

@article{DnCNN,
  title={Beyond a gaussian denoiser: Residual learning of deep cnn for image denoising},
  author={Zhang, Kai and Zuo, Wangmeng and Chen, Yunjin and Meng, Deyu and Zhang, Lei},
  journal={IEEE transactions on image processing},
  volume={26},
  number={7},
  pages={3142--3155},
  year={2017},
  publisher={IEEE}
}

@article{Tractseg,
  title={TractSeg-Fast and accurate white matter tract segmentation},
  author={Wasserthal, Jakob and Neher, Peter and Maier-Hein, Klaus H},
  journal={NeuroImage},
  volume={183},
  pages={239--253},
  year={2018},
  publisher={Elsevier}
}

@article{Itzik_Avital,
  title={Neural segmentation of seeding ROIs (sROIs) for pre-surgical brain tractography},
  author={Avital, Itzik and Nelkenbaum, Ilya and Tsarfaty, Galia and Konen, Eli and Kiryati, Nahum and Mayer, Arnaldo},
  journal={IEEE Transactions on Medical Imaging},
  volume={39},
  number={5},
  pages={1655--1667},
  year={2019},
  publisher={IEEE}
}

@inproceedings{Ilya_nelkenbaum,
  title={Automatic segmentation of white matter tracts using multiple brain MRI sequences},
  author={Nelkenbaum, Ilya and Tsarfaty, Galia and Kiryati, Nahum and Konen, Eli and Mayer, Arnaldo},
  booktitle={2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI)},
  pages={368--371},
  year={2020},
  organization={IEEE}
}

@article{FSL_FLIRT_1,
  title={A global optimisation method for robust affine registration of brain images},
  author={Jenkinson, Mark and Smith, Stephen},
  journal={Medical image analysis},
  volume={5},
  number={2},
  pages={143--156},
  year={2001},
  publisher={Elsevier}
}

@article{FSL_FLIRT_2,
  title={Improved optimization for the robust and accurate linear registration and motion correction of brain images},
  author={Jenkinson, Mark and Bannister, Peter and Brady, Michael and Smith, Stephen},
  journal={Neuroimage},
  volume={17},
  number={2},
  pages={825--841},
  year={2002},
  publisher={Elsevier}
}

% 2nd
@article{Brain_extraction,
  author={Cullen, Nicholas and Avants, Brian},
  title={Convolutional neural networks for rapid and simultaneous brain extraction and tissue segmentation},
  journal={Brain Morphometry},
  publisher={Springer},
  address={New York, NY, USA},
  year={2018},
  pages={13--34}
}


@article{Sinisa_and_Pierpaoli_DEC_map,
  title={Color schemes to represent the orientation of anisotropic tissues from diffusion tensor data: application to white matter fiber tract mapping in the human brain},
  author={Pajevic, Sinisa and Pierpaoli, Carlo},
  journal={Magnetic Resonance in Medicine: An Official Journal of the International Society for Magnetic Resonance in Medicine},
  volume={42},
  number={3},
  pages={526--540},
  year={1999},
  publisher={Wiley Online Library}
}

@article{dipy,
  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 and Dipy Contributors},
  journal={Frontiers in neuroinformatics},
  volume={8},
  pages={8},
  year={2014},
  publisher={Frontiers Media SA}
}

@inproceedings{Noa_ECCV,
  title={Neural Registration and Segmentation of White Matter Tracts in Multi-modal Brain MRI},
  author={Barzilay, Noa and Nelkenbaum, Ilya and Konen, Eli and Kiryati, Nahum and Mayer, Arnaldo},
  booktitle={European Conference on Computer Vision},
  pages={252--267},
  year={2022},
  organization={Springer}
}

@article{kmeans,
  title={Concept decompositions for large sparse text data using clustering},
  author={Dhillon, Inderjit S and Modha, Dharmendra S},
  journal={Machine learning},
  volume={42},
  pages={143--175},
  year={2001},
  publisher={Springer}
}

@article{SnDTI,
  title={SDnDTI: Self-supervised deep learning-based denoising for diffusion tensor MRI},
  author={Tian, Qiyuan and Li, Ziyu and Fan, Qiuyun and Polimeni, Jonathan R and Bilgic, Berkin and Salat, David H and Huang, Susie Y},
  journal={Neuroimage},
  volume={253},
  pages={119033},
  year={2022},
  publisher={Elsevier}
}

@article{DeepDTI,
  title={DeepDTI: High-fidelity six-direction diffusion tensor imaging using deep learning},
  author={Tian, Qiyuan and Bilgic, Berkin and Fan, Qiuyun and Liao, Congyu and Ngamsombat, Chanon and Hu, Yuxin and Witzel, Thomas and Setsompop, Kawin and Polimeni, Jonathan R and Huang, Susie Y},
  journal={NeuroImage},
  volume={219},
  pages={117017},
  year={2020},
  publisher={Elsevier}
}

@article{SuperDTI,
  title={SuperDTI: Ultrafast DTI and fiber tractography with deep learning},
  author={Li, Hongyu and Liang, Zifei and Zhang, Chaoyi and Liu, Ruiying and Li, Jing and Zhang, Weihong and Liang, Dong and Shen, Bowen and Zhang, Xiaoliang and Ge, Yulin and others},
  journal={Magnetic resonance in medicine},
  volume={86},
  number={6},
  pages={3334--3347},
  year={2021},
  publisher={Wiley Online Library}
}
@article{HCP,
  title={The Human Connectome Project: a data acquisition perspective},
  author={Van Essen, David C and Ugurbil, Kamil and Auerbach, Edward and Barch, Deanna and Behrens, Timothy EJ and Bucholz, Richard and Chang, Acer and Chen, Liyong and Corbetta, Maurizio and Curtiss, Sandra W and others},
  journal={Neuroimage},
  volume={62},
  number={4},
  pages={2222--2231},
  year={2012},
  publisher={Elsevier}
}
@article{Effect_NDGD,
  title={Effects of number of diffusion gradient directions on derived diffusion tensor imaging indices in human brain},
  author={Ni, H and Kavcic, V and Zhu, T and Ekholm, S and Zhong, Jianhui},
  journal={American Journal of Neuroradiology},
  volume={27},
  number={8},
  pages={1776--1781},
  year={2006},
  publisher={Am Soc Neuroradiology}
}
@article{BasserDTI,
  title={MR diffusion tensor spectroscopy and imaging},
  author={Basser, Peter J and Mattiello, James and LeBihan, Denis},
  journal={Biophysical journal},
  volume={66},
  number={1},
  pages={259--267},
  year={1994},
  publisher={Elsevier}
}
@article{AngresDTI,
  title={How does angular resolution affect diffusion imaging measures?},
  author={Zhan, Liang and Leow, Alex D and Jahanshad, Neda and Chiang, Ming-Chang and Barysheva, Marina and Lee, Agatha D and Toga, Arthur W and McMahon, Katie L and De Zubicaray, Greig I and Wright, Margaret J and others},
  journal={neuroimage},
  volume={49},
  number={2},
  pages={1357--1371},
  year={2010},
  publisher={Elsevier}
}
@article{contrack,
  title={ConTrack: finding the most likely pathways between brain regions using diffusion tractography},
  author={Sherbondy, Anthony J and Dougherty, Robert F and Ben-Shachar, Michal and Napel, Sandy and Wandell, Brian A},
  journal={Journal of vision},
  volume={8},
  number={9},
  pages={15--15},
  year={2008},
  publisher={The Association for Research in Vision and Ophthalmology}
}
@article{diceloss,
  title={Robust liver vessel extraction using 3D U-Net with variant dice loss function},
  author={Huang, Qing and Sun, Jinfeng and Ding, Hui and Wang, Xiaodong and Wang, Guangzhi},
  journal={Computers in biology and medicine},
  volume={101},
  pages={153--162},
  year={2018},
  publisher={Elsevier}
}

@inproceedings{omri_miccai,
  title={Fast Acquisition for Diffusion Tensor Tractography},
  author={Leshem, Omri and Kiryati, Nahum and Green, Michael and Nelkenbaum, Ilya and Roizen, Dani and Mayer, Arnaldo},
  booktitle={International Workshop on Computational Diffusion MRI},
  pages={118--128},
  year={2023},
  organization={Springer}
}

@article{BraTS21_Benchmark,
  title={The rsna-asnr-miccai brats 2021 benchmark on brain tumor segmentation and radiogenomic classification},
  author={Baid, Ujjwal and Ghodasara, Satyam and Mohan, Suyash and Bilello, Michel and Calabrese, Evan and Colak, Errol and Farahani, Keyvan and Kalpathy-Cramer, Jayashree and Kitamura, Felipe C and Pati, Sarthak and others},
  journal={arXiv preprint arXiv:2107.02314},
  year={2021}
}

@article{Synthesizing_DTI_from_fMRI,
  title={Synthesizing diffusion tensor imaging from functional MRI using fully convolutional networks},
  author={Son, Seong-Jin and Park, Bo-yong and Byeon, Kyoungseob and Park, Hyunjin},
  journal={Computers in biology and medicine},
  volume={115},
  pages={103528},
  year={2019},
  publisher={Elsevier}
}

@article{DTI_predicts_fMRI_lexical_sublexical_reading,
  title={Structural connectivity predicts functional activation during lexical and sublexical reading},
  author={Ekstrand, Chelsea and Neudorf, Josh and Kress, Shaylyn and Borowsky, Ron},
  journal={NeuroImage},
  volume={218},
  pages={117008},
  year={2020},
  publisher={Elsevier}
}

@article{Structurl_predicts_individual_fMRI,
  title={Structural brain imaging predicts individual-level task activation maps using deep learning},
  author={Ellis, David G and Aizenberg, Michele R},
  journal={Frontiers in Neuroimaging},
  volume={1},
  pages={834883},
  year={2022},
  publisher={Frontiers Media SA}
}

@article{BrainVoyager,
  title={Analysis of functional image analysis contest (FIAC) data with brainvoyager QX: From single-subject to cortically aligned group general linear model analysis and self-organizing group independent component analysis},
  author={Goebel, Rainer and Esposito, Fabrizio and Formisano, Elia},
  journal={Human brain mapping},
  volume={27},
  number={5},
  pages={392--401},
  year={2006},
  publisher={Wiley Online Library}
}

@incollection{3d_slicer,
  title={3D Slicer: a platform for subject-specific image analysis, visualization, and clinical support},
  author={Kikinis, Ron and Pieper, Steve D and Vosburgh, Kirby G},
  booktitle={Intraoperative imaging and image-guided therapy},
  pages={277--289},
  year={2013},
  publisher={Springer}
}

@article{The_anatomy_of_language,
  title={The anatomy of language: contributions from functional neuroimaging},
  author={Price, Cathy J},
  journal={The Journal of Anatomy},
  volume={197},
  number={3},
  pages={335--359},
  year={2000},
  publisher={Cambridge University Press}
}

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

@article{attention_unet,
  title={Attention u-net: Learning where to look for the pancreas},
  author={Oktay, Ozan and Schlemper, Jo and Folgoc, Loic Le and Lee, Matthew and Heinrich, Mattias and Misawa, Kazunari and Mori, Kensaku and McDonagh, Steven and Hammerla, Nils Y and Kainz, Bernhard and others},
  journal={arXiv preprint arXiv:1804.03999},
  year={2018}
}

@article{edema_effect_DTI,
  title={The impact of edema and fiber crossing on diffusion MRI metrics assessed in an ex vivo nerve phantom: Multi-tensor model vs. diffusion orientation distribution function},
  author={Ye, Zezhong and Gary, Sam E and Sun, Peng and Mustafi, Sourajit Mitra and Glenn, George Russell and Yeh, Fang-Cheng and Merisaari, Harri and Song, Chunyu and Yang, Ruimeng and Huang, Guo-Shu and others},
  journal={NMR in Biomedicine},
  volume={34},
  number={1},
  pages={e4414},
  year={2021},
  publisher={Wiley Online Library}
}

@article{MR_modalities_showcase_arnaldo,
  title={An adaptive mean-shift framework for MRI brain segmentation},
  author={Mayer, Arnaldo and Greenspan, Hayit},
  journal={IEEE transactions on medical imaging},
  volume={28},
  number={8},
  pages={1238--1250},
  year={2009},
  publisher={IEEE}
}

@article{MR_modalities_showcase,
  title={Teratoma-associated anti-NMDAR encephalitis: two cases report and literature review},
  author={Liang, Zhigang and Yang, Shaowan and Sun, Xuwen and Li, Bing and Li, Wei and Liu, Zhuli and Yu, Guoping},
  journal={Medicine},
  volume={96},
  number={49},
  pages={e9177},
  year={2017},
  publisher={LWW}
}

@article{medical_segmentation_multi-modality_review,
  title={A review: Deep learning for medical image segmentation using multi-modality fusion},
  author={Zhou, Tongxue and Ruan, Su and Canu, St{\'e}phane},
  journal={Array},
  volume={3},
  pages={100004},
  year={2019},
  publisher={Elsevier}
}

@article{segmamba,
  title={Segmamba: Long-range sequential modeling mamba for 3d medical image segmentation},
  author={Xing, Zhaohu and Ye, Tian and Yang, Yijun and Liu, Guang and Zhu, Lei},
  journal={arXiv preprint arXiv:2401.13560},
  year={2024}
}

@book{The_emotional_brain,
  title={The emotional brain: The mysterious underpinnings of emotional life},
  author={LeDoux, Joseph E},
  year={1998},
  page={165},
  publisher={Simon and Schuster}
}

@article{Deterministic_and_Probabilistic_Tractography_TMI,
  title={Deterministic and probabilistic tractography based on complex fibre orientation distributions},
  author={Descoteaux, Maxime and Deriche, Rachid and Knosche, Thomas R and Anwander, Alfred},
  journal={IEEE transactions on medical imaging},
  volume={28},
  number={2},
  pages={269--286},
  year={2008},
  publisher={IEEE}
}

@inproceedings{qualitativ_quantitative_analysis_probabilistic_deterministic_tractography,
  title={Qualitative and quantitative analysis of probabilistic and deterministic fiber tracking},
  author={Klein, Jan and Gr{\"o}tsch, Adrian and Betz, Daniel and Barbieri, Sebastiano and Friman, Ola and Stieltjes, Bram and Hildebrandt, Helmut and Hahn, Horst K},
  booktitle={Medical Imaging 2010: Image Processing},
  volume={7623},
  pages={720--727},
  year={2010},
  organization={SPIE}
}

@article{multimodal_self_attention_aware_net,
  title={Multi-modality self-attention aware deep network for 3D biomedical segmentation},
  author={Jia, Xibin and Liu, Yunfeng and Yang, Zhenghan and Yang, Dawei},
  journal={BMC Medical Informatics and Decision Making},
  volume={20},
  pages={1--7},
  year={2020},
  publisher={Springer}
}

@inproceedings{V-net,
  title={V-net: Fully convolutional neural networks for volumetric medical image segmentation},
  author={Milletari, Fausto and Navab, Nassir and Ahmadi, Seyed-Ahmad},
  booktitle={2016 fourth international conference on 3D vision (3DV)},
  pages={565--571},
  year={2016},
  organization={Ieee}
}

@article{3d_slice_seg_1,
  title={Automatic semantic segmentation of brain gliomas from MRI images using a deep cascaded neural network},
  author={Cui, Shaoguo and Mao, Lei and Jiang, Jingfeng and Liu, Chang and Xiong, Shuyu},
  journal={Journal of healthcare engineering},
  volume={2018},
  number={1},
  pages={4940593},
  year={2018},
  publisher={Wiley Online Library}
}

@inproceedings{3d_slice_seg_2,
  title={IVD-Net: Intervertebral disc localization and segmentation in MRI with a multi-modal UNet},
  author={Dolz, Jose and Desrosiers, Christian and Ben Ayed, Ismail},
  booktitle={International workshop and challenge on computational methods and clinical applications for spine imaging},
  pages={130--143},
  year={2018},
  organization={Springer}
}

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

@article{Postoperative_Language_Outcome_in_Glioma_Patients,
  title={Speech and language errors during awake brain surgery and postoperative language outcome in glioma patients: a systematic review},
  author={Collee, Ellen and Vincent, Arnaud and Dirven, Clemens and Satoer, Djaina},
  journal={Cancers},
  volume={14},
  number={21},
  pages={5466},
  year={2022},
  publisher={MDPI}
}

@article{functional_outcome_language_mapping,
  title={Functional outcome after language mapping for glioma resection},
  author={Sanai, Nader and Mirzadeh, Zaman and Berger, Mitchel S},
  journal={New England Journal of Medicine},
  volume={358},
  number={1},
  pages={18--27},
  year={2008},
  publisher={Mass Medical Soc}
}

@article{fMRI_challenges_real-world_applications,
  title={fMRI in translation: the challenges facing real-world applications},
  author={Schleim, Stephan and Roiser, Jonathan P},
  journal={Frontiers in Human Neuroscience},
  volume={3},
  pages={845},
  year={2009},
  publisher={Frontiers}
}

% 1st
@article{Challenges_in_fMRI,
  title={Challenges in fMRI and its limitations},
  author={Constable, R Todd},
  journal={Functional neuroradiology: principles and clinical applications},
  pages={497--510},
  year={2023},
  publisher={Springer}
}

@article{noise_in_fMRI,
  title={Noise contributions to the fMRI signal: An overview},
  author={Liu, Thomas T},
  journal={NeuroImage},
  volume={143},
  pages={141--151},
  year={2016},
  publisher={Elsevier}
}

@inproceedings{unet_2d_original,
  title={U-net: Convolutional networks for biomedical image segmentation},
  author={Ronneberger, Olaf and Fischer, Philipp and Brox, Thomas},
  booktitle={Medical image computing and computer-assisted intervention--MICCAI 2015: 18th international conference, Munich, Germany, October 5-9, 2015, proceedings, part III 18},
  pages={234--241},
  year={2015},
  organization={Springer}
}

@article{hausdorff_distance_loss,
  title={Reducing the hausdorff distance in medical image segmentation with convolutional neural networks},
  author={Karimi, Davood and Salcudean, Septimiu E},
  journal={IEEE Transactions on medical imaging},
  volume={39},
  number={2},
  pages={499--513},
  year={2019},
  publisher={IEEE}
}

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

@article{itk_snap,
  author = {Paul A. Yushkevich and Joseph Piven and Cody Hazlett, Heather and
    Gimpel Smith, Rachel and Sean Ho and James C. Gee and Guido Gerig},
  title = {User-Guided {3D} Active Contour Segmentation of
    Anatomical Structures: Significantly Improved Efficiency and Reliability},
  journal = {Neuroimage},
  year = {2006},
  volume = {31},
  number = {3},
  pages = {1116--1128},
}

@article{lesion_activation_distance_relationship,
  title={Characterizing the relationship between lesion-activation distance using fMRI and verbal measures in brain tumor patients},
  author={Riley, Sean P and Chu, Daniel Y and Nair, Veena A and Baskaya, Mustafa K and Kuo, John S and Meyerand, Mary Elizabeth and Prabhakaran, Vivek},
  journal={Interdisciplinary Neurosurgery},
  volume={27},
  pages={101391},
  year={2022},
  publisher={Elsevier}
}

@article{fMRI_tolerance_5mm,
  title={One-staged in situ embolization combined with surgical resection for eloquence protection of AVM},
  author={Wang, Mingze and Qiu, Hancheng and Cao, Yong and Wang, Shuo and Zhao, Jizong},
  journal={Neurosurgical Review},
  volume={42},
  pages={783--790},
  year={2019},
  publisher={Springer}
}

@article{DiceCE_Loss,
  title={Combo loss: Handling input and output imbalance in multi-organ segmentation},
  author={Taghanaki, Saeid Asgari and Zheng, Yefeng and Zhou, S Kevin and Georgescu, Bogdan and Sharma, Puneet and Xu, Daguang and Comaniciu, Dorin and Hamarneh, Ghassan},
  journal={Computerized Medical Imaging and Graphics},
  volume={75},
  pages={24--33},
  year={2019},
  publisher={Elsevier}
}

@article{SENSAAS_functional_atlas,
  title={A SENtence Supramodal Areas AtlaS (SENSAAS) based on multiple task-induced activation mapping and graph analysis of intrinsic connectivity in 144 healthy right-handers},
  author={Labache, Loic and Joliot, Marc and Saracco, J{\'e}r{\^o}me and Jobard, Ga{\"e}l and Hesling, Isabelle and Zago, Laure and Mellet, Emmanuel and Petit, Laurent and Crivello, Fabrice and Mazoyer, Bernard and others},
  journal={Brain Structure and Function},
  volume={224},
  number={2},
  pages={859--882},
  year={2019},
  publisher={Springer}
}

@article{SimpleITK_registration,
  title={Image segmentation, registration and characterization in R with SimpleITK},
  author={Beare, Richard and Lowekamp, Bradley and Yaniv, Ziv},
  journal={Journal of statistical software},
  volume={86},
  pages={1--35},
  year={2018}
}

@article{PyTorch,
  title={Pytorch: An imperative style, high-performance deep learning library},
  author={Paszke, Adam and Gross, Sam and Massa, Francisco and Lerer, Adam and Bradbury, James and Chanan, Gregory and Killeen, Trevor and Lin, Zeming and Gimelshein, Natalia and Antiga, Luca and others},
  journal={Advances in neural information processing systems},
  volume={32},
  year={2019}
}

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

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