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72 changes: 46 additions & 26 deletions paper_JOSS/paper.bib
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@@ -1,22 +1,29 @@
@article{avants2011reproducible, title={
A reproducible evaluation of ANTs similarity metric performance in brain image registration}, author={Avants, BB and Tustison, NJ and Song, G and Cook, PA and Klein, A and Gee, JC}, journal={NeuroImage}, volume={54}, pages={2033--2044}, year={2011}, publisher={Elsevier}, doi={10.1016/j.neuroimage.2010.09.025} }
A reproducible evaluation of ANTs similarity metric performance in brain image registration}, author={Avants, BB and Tustison, NJ and others},
fullauthor={Avants, BB and Tustison, NJ and Song, G and Cook, PA and Klein, A and Gee, JC},
journal={NeuroImage}, volume={54}, pages={2033--2044}, year={2011}, publisher={Elsevier}, doi={10.1016/j.neuroimage.2010.09.025} }

@article{balbastre2017primatologist, title={
Primatologist: A modular segmentation pipeline for macaque brain morphometry}, author={Balbastre, Y and others}, journal={NeuroImage}, volume={162}, pages={306--321}, year={2017}, publisher={Elsevier} , doi={10.1016/j.neuroimage.2017.09.007}}

@article{cieslak2021qsiprep, title={
QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data}, author={Cieslak, M and others}, journal={Nature methods}, volume={18}, number={7}, pages={775--778}, year={2021}, publisher={Nature Publishing Group} , doi={10.1038/s41592-021-01185-5}}

@article{esteban2019fmriprep, title={
fMRIPrep: a robust preprocessing pipeline for functional MRI}, author={Esteban, O and others}, journal={Nature methods}, volume={16}, number={1}, pages={111--116}, year={2019}, publisher={Nature Publishing Group} , doi={10.1038/s41592-018-0235-4}
@article{esteban2019fmriprep,
title={fMRIPrep: a robust preprocessing pipeline for functional MRI}, author={Esteban, O and Birman, D and others},
fullauthor={Esteban, O and Birman, D and Schaer, M and Koyejo, OO and Poldrack, RA and Gorgolewski, KJ},
journal={Nature methods}, volume={16}, number={1}, pages={111--116}, year={2019}, publisher={Nature Publishing Group} , doi={10.1038/s41592-018-0235-4}
}

@article{cox1996afni, title={
AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages}, author={Cox, RW}, journal={Computers and Biomedical Research}, volume={29}, pages={162--173}, year={1996}, publisher={Elsevier}, doi={10.1006/cbmr.1996.0014}
}

@article{esteban2017mriqc, title={
MRIQC: advancing the automatic prediction of image quality in MRI from unseen sites}, author={Esteban, O and Birman, D and Schaer, M and Koyejo, OO and Poldrack, RA and Gorgolewski, KJ}, journal={PLoS One}, volume={12}, pages={1--21}, year={2017}, publisher={Public Library of Science}, doi={10.1371/journal.pone.0184661}
@article{esteban2017mriqc,
title={ MRIQC: advancing the automatic prediction of image quality in MRI from unseen sites},
author={Esteban, O and Birman, D and others},
fullauthor={Esteban, O and Birman, D and Schaer, M and Koyejo, OO and Poldrack, RA and Gorgolewski, KJ},
journal={PLoS One}, volume={12}, pages={1--21}, year={2017}, publisher={Public Library of Science}, doi={10.1371/journal.pone.0184661}
}

@article{fischl2012freesurfer, title={
Expand All @@ -28,40 +35,47 @@ @book{frackowiak1997human
}

@article{garcia2021preemacs, title={
PREEMACS: Pipeline for preprocessing and extraction of the macaque brain surface}, author={Garcia-Saldivar, P and Garimella, A and Garza-Villarreal, EA and Mendez, FA and Concha, L and Merchant, H}, journal={NeuroImage}, volume={227}, pages={117671}, year={2021}, publisher={Elsevier}, doi={10.1016/j.neuroimage.2020.117671}
}

@article{gorgolewski2011nipype, title={
Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python}, author={Gorgolewski, K and others}, journal={Front. Neuroimform.}, volume={5}, pages={13}, year={2011}, publisher={Frontiers Media SA}, doi={10.3389/fninf.2011.00013}
}

@article{gorgolewski2016brain, title={
The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments}, author={Gorgolewski, K and others}, journal={Sci Data}, volume={3}, pages={160044}, year={2016}, publisher={Nature Publishing Group} , doi={10.1038/sdata.2016.44}
}

@article{Isensee2019hdbet, 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 Bendszus, Martin and Maier-Hein, Klaus H. and Kickingereder, Philipp},journal = {Human Brain Mapping},volume = {40},number = {17},pages = {4952-4964},keywords = {artificial neural networks, brain extraction, deep learning, magnetic resonance imaging, neuroimaging, skull stripping},doi = {10.1002/hbm.24750},year = {2019}
}
PREEMACS: Pipeline for preprocessing and extraction of the macaque brain surface}, author={Garcia-Saldivar, P and Garimella, A and others}, fullauthor={Garcia-Saldivar, P and Garimella, A and Garza-Villarreal, EA and Mendez, FA and Concha, L and Merchant, H}, journal={NeuroImage}, volume={227}, pages={117671}, year={2021}, publisher={Elsevier}, doi={10.1016/j.neuroimage.2020.117671}
}
@article{gorgolewski2011nipype,
title={Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python},
author={Gorgolewski, K and Burns, Christopher and others}, journal={Front. Neuroimform.}, volume={5}, pages={13}, year={2011}, publisher={Frontiers Media SA}, doi={10.3389/fninf.2011.00013} }

@article{gorgolewski2016brain, title={The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments}, author={Gorgolewski, K and others}, journal={Sci Data}, volume={3}, pages={160044}, year={2016}, publisher={Nature Publishing Group} }

@article{Isensee2019hdbet,
author = {Isensee, Fabian and Schell, Marianne and others},
fullauthor = {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 Bendszus, Martin and Maier-Hein, Klaus H. and Kickingereder, Philipp},
title = {Automated brain extraction of multisequence MRI using artificial neural networks},
journal = {Human Brain Mapping},
volume = {40},
number = {17},
pages = {4952-4964},
keywords = {artificial neural networks, brain extraction, deep learning, magnetic resonance imaging, neuroimaging, skull stripping},
doi = {10.1002/hbm.24750},
year = {2019}
}

@article{lepage2021civet, title={
CIVET-Macaque: An automated pipeline for MRI-based cortical surface generation and cortical thickness in macaques}, author={Lepage, C and Wagstyl, K and Jung, B and Seidlitz, J and Sponheim, C and Ungerleider, L and Wang, X and Evans, AC and Messinger, A}, journal={Neuroimage}, volume={227}, pages={117622}, year={2021}, publisher={Elsevier}, doi={10.1016/j.neuroimage.2020.117622}
CIVET-Macaque: An automated pipeline for MRI-based cortical surface generation and cortical thickness in macaques}, author={Lepage, C and Wagstyl, K and others}, fullauthor={Lepage, C and Wagstyl, K and Jung, B and Seidlitz, J and Sponheim, C and Ungerleider, L and Wang, X and Evans, AC and Messinger, A}, journal={Neuroimage}, volume={227}, pages={117622}, year={2021}, publisher={Elsevier}, doi={10.1016/j.neuroimage.2020.117622}
}

@article{liu2021marmoset, title={
Marmoset Brain Mapping V3: Population multi-modal standard volumetric and surface-based templates}, author={Liu, C and others}, journal={Neuroimage}, year={2021}, publisher={Elsevier}, doi={10.1016/j.neuroimage.2020.117620}
}

@article{lohmeier2019atlasbrex, title={
AtlasBREX: Automated template-derived brain extraction in animal MRI}, author={Lohmeier, J and others}, journal={Sci Rep}, volume={9}, number={1}, pages={12219}, year={2019}, publisher={Nature Publishing Group}, doi={10.1038/s41598-019-48489-3}
AtlasBREX: Automated template-derived brain extraction in animal MRI}, author={Lohmeier, J and Kaneko, T and others},
fullauthor = {Lohmeier, J, and Kaneko , T and Hamm , Bernd and Makowski , Marcus R. and Okano, Hideyuki}, journal={Sci Rep}, volume={9}, number={1}, pages={12219}, year={2019}, publisher={Nature Publishing Group}, doi={10.1038/s41598-019-48489-3}
}

@article{love2016average, title={The average baboon brain: MRI templates and tissue probability maps from 89 individuals}, author={Love, S and others}, journal={NeuroImage}, volume={132}, year={2016}, publisher={Elsevier}, doi={10.1016/j.neuroimage.2016.03.018} }

@article{messinger2021collaborative, title={
A Collaborative Resource Platform for Non-Human Primate Neuroimaging}, author={Messinger, A and others}, journal={NeuroImage}, volume={226}, pages={117519}, year={2021}, publisher={Elsevier}, doi ={10.1101/2020.07.31.230185}
A Collaborative Resource Platform for Non-Human Primate Neuroimaging}, author={Messinger, A and Sirmpilatze , Nikoloz and others}, journal={NeuroImage}, volume={226}, pages={117519}, year={2021}, publisher={Elsevier}, doi ={10.1101/2020.07.31.230185}
}

@article{milham2018open, title={An Open Resource for Non-Human Primate Imaging}, author={Milham, MP and Ai, L and Koo, B and Xu, T and Amiez, C and Balezeau, F and Baxter, MG and Blezer, ELA and Brochier, T and Chen, A and others}, journal={Neuron}, volume={100}, pages={61--74}, year={2018}, publisher={Cell Press}, doi={10.1016/j.neuron.2018.08.039} }
@article{milham2018open, title={An Open Resource for Non-Human Primate Imaging}, author={Milham, MP and Ai, L and others}, fullauthor={Milham, MP and Ai, L and Koo, B and Xu, T and Amiez, C and Balezeau, F and Baxter, MG and Blezer, ELA and Brochier, T and Chen, A and others}, journal={Neuron}, volume={100}, pages={61--74}, year={2018}, publisher={Cell Press}, doi={10.1016/j.neuron.2018.08.039} }

@article{routier2021clinica, title={
Clinica: an open source software platform for reproducible clinical neuroscience studies}, author={Routier, A and others}, journal={Frontiers in Neuroinformatics}, volume={15}, pages={689675}, year={2021}, publisher={Frontiers Media SA} ,doi={10.3389/fninf.2021.689675}
Expand All @@ -72,15 +86,18 @@ @article{seidlitz2018population
}

@article{smith2004advances, title={
Advances in functional and structural MR image analysis and implementation as FSL}, author={Smith, SM and Jenkinson, M and Woolrich, MW and Beckmann, CF and Behrens, TEJ and Johansen-Berg, H and Bannister, PR and De Luca, M and Drobnjak, I and Flitney, DE and Niazy, RK and Saunders, J and Vickers, J and Zhang, Y and De Stefano, N and Brady, JM and Matthews, PM}, journal={NeuroImage}, volume={23}, pages={208--219}, year={2004}, publisher={Elsevier}, doi={10.1016/j.neuroimage.2004.07.051}
Advances in functional and structural MR image analysis and implementation as FSL}, author={Smith, SM and Jenkinson, M and others},fullauthor={Smith, SM and Jenkinson, M and Woolrich, MW and Beckmann, CF and Behrens, TEJ and Johansen-Berg, H and Bannister, PR and De Luca, M and Drobnjak, I and Flitney, DE and Niazy, RK and Saunders, J and Vickers, J and Zhang, Y and De Stefano, N and Brady, JM and Matthews, PM}, journal={NeuroImage}, volume={23}, pages={208--219}, year={2004}, publisher={Elsevier}, doi={10.1016/j.neuroimage.2004.07.051}
}

@article{tasserie2019pypreclin, title={
Pypreclin: An automatic pipeline for macaque functional MRI preprocessing}, author={Tasserie, J and others}, journal={NeuroImage}, year={2019}, publisher={Elsevier} , doi ={10.1016/j.neuroimage.2019.116353 }
}

@article{tournier2019mrtrix3, title={
MRtrix3: a fast, flexible and open software framework for medical image processing and visualisation}, author={Tournier, J-D and Smith, R and Raffelt, D and Tabbara, R and Dhollander, T and Pietsch, M and Christiaens, D and Jeurissen, B and Yeh, C-H and Connelly, A}, journal={NeuroImage}, volume={202}, pages={116--137}, year={2019}, publisher={Elsevier}, doi={10.1016/j.neuroimage.2019.116137}
MRtrix3: a fast, flexible and open software framework for medical image processing and visualisation},
author={Tournier, J-D and Smith, R and others},
fullauthor={Tournier, J-D and Smith, R and Raffelt, D and Tabbara, R and Dhollander, T and Pietsch, M and Christiaens, D and Jeurissen, B and Yeh, C-H and Connelly, A},
journal={NeuroImage}, volume={202}, pages={116--137}, year={2019}, publisher={Elsevier}, doi={10.1016/j.neuroimage.2019.116137}
}

@article{vickery2020chimpanzee, title={
Expand Down Expand Up @@ -111,5 +128,8 @@ @article{ZHONG2021117649
}

@article{ZHONG2024120652,title = {
nBEST: Deep-learning-based non-human primates Brain Extraction and Segmentation Toolbox across ages, sites and species},journal = {NeuroImage},volume = {295},pages = {120652},year = {2024},issn = {1053-8119},doi = {10.1016/j.neuroimage.2024.120652},url = {https://www.sciencedirect.com/science/article/pii/S1053811924001472},author = {Tao Zhong and Xueyang Wu and Shujun Liang and Zhenyuan Ning and Li Wang and Yuyu Niu and Shihua Yang and Zhuang Kang and Qianjin Feng and Gang Li and Yu Zhang}
nBEST: Deep-learning-based non-human primates Brain Extraction and Segmentation Toolbox across ages, sites and species},journal = {NeuroImage},volume = {295},pages = {120652},year = {2024},issn = {1053-8119},doi = {10.1016/j.neuroimage.2024.120652},url = {https://www.sciencedirect.com/science/article/pii/S1053811924001472},

author = {Tao Zhong and Xueyang Wu and others},
fullauthor = {Tao Zhong and Xueyang Wu and Shujun Liang and Zhenyuan Ning and Li Wang and Yuyu Niu and Shihua Yang and Zhuang Kang and Qianjin Feng and Gang Li and Yu Zhang}
}
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