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1,568 changes: 1,568 additions & 0 deletions paper/sea-neuro/Frontiers-Harvard.bst

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956 changes: 956 additions & 0 deletions paper/sea-neuro/FrontiersinHarvard.cls

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91 changes: 48 additions & 43 deletions paper/sea-neuro/biblio.bib
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@article{hayot2022sea,
title={Sea: A lightweight data-placement library for Big Data scientific computing},
author={Hayot-Sasson, Val{\'e}rie and Dugr{\'e}, Mathieu and Glatard, Tristan},
journal={arXiv preprint arXiv:2207.01737},
year={2022}
title = {Sea: A lightweight data-placement library for Big Data scientific computing},
author = {Hayot-Sasson, Val{\'e}rie and Dugr{\'e}, Mathieu and Glatard, Tristan},
journal = {arXiv preprint arXiv:2207.01737},
year = {2022}
}

@article{gorgolewski2016brain,
title={The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments},
author={Gorgolewski, Krzysztof J and Auer, Tibor and Calhoun, Vince D and Craddock, R Cameron and Das, Samir and Duff, Eugene P and Flandin, Guillaume and Ghosh, Satrajit S and Glatard, Tristan and Halchenko, Yaroslav O and others},
journal={Scientific data},
volume={3},
number={1},
pages={1--9},
year={2016},
publisher={Nature Publishing Group}
title = {{The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments}},
author = {Gorgolewski, Krzysztof J and Auer, Tibor and Calhoun, Vince D and Craddock, R Cameron and Das, Samir and Duff, Eugene P and Flandin, Guillaume and Ghosh, Satrajit S and Glatard, Tristan and Halchenko, Yaroslav O and others},
journal = {Scientific data},
volume = {3},
number = {1},
pages = {1--9},
year = {2016},
publisher = {Nature Publishing Group}
}

@article{henschel2020fastsurfer,
title={Fastsurfer-a fast and accurate deep learning based neuroimaging pipeline},
author={Henschel, Leonie and Conjeti, Sailesh and Estrada, Santiago and Diers, Kersten and Fischl, Bruce and Reuter, Martin},
journal={NeuroImage},
volume={219},
pages={117012},
year={2020},
publisher={Elsevier}
title = {{Fastsurfer-a fast and accurate deep learning based neuroimaging pipeline}},
author = {Henschel, Leonie and Conjeti, Sailesh and Estrada, Santiago and Diers, Kersten and Fischl, Bruce and Reuter, Martin},
journal = {NeuroImage},
volume = {219},
pages = {117012},
year = {2020},
publisher = {Elsevier}
}

@article{hoffmann2021synthmorph,
title={SynthMorph: learning contrast-invariant registration without acquired images},
author={Hoffmann, Malte and Billot, Benjamin and Greve, Douglas N and Iglesias, Juan Eugenio and Fischl, Bruce and Dalca, Adrian V},
journal={IEEE transactions on medical imaging},
volume={41},
number={3},
pages={543--558},
year={2021},
publisher={IEEE}
title = {{SynthMorph: learning contrast-invariant registration without acquired images}},
author = {Hoffmann, Malte and Billot, Benjamin and Greve, Douglas N and Iglesias, Juan Eugenio and Fischl, Bruce and Dalca, Adrian V},
journal = {IEEE transactions on medical imaging},
volume = {41},
number = {3},
pages = {543--558},
year = {2021},
publisher = {IEEE}
}

@article{HCP,
Expand Down Expand Up @@ -69,7 +69,7 @@ @article{zaharia2016apache
}

@inproceedings{rocklin2015dask,
title = {Dask: Parallel computation with blocked algorithms and task scheduling},
title = {{Dask: Parallel computation with blocked algorithms and task scheduling}},
author = {Rocklin, Matthew},
booktitle = {Proc. of the 14th Python in Science Conference},
pages = {130-136},
Expand All @@ -78,7 +78,7 @@ @inproceedings{rocklin2015dask
}

@misc{rokem2021pan,
title = {Pan-neuro: interactive computing at scale with BRAIN datasets},
title = {{Pan-neuro: interactive computing at scale with BRAIN datasets}},
author = {Rokem, Ariel and Dichter, Ben and Holdgraf, Christopher and Ghosh, Satrajit},
year = {2021},
publisher = {OSF Preprints}
Expand Down Expand Up @@ -113,7 +113,7 @@ @article{nipype
issn = {1662-5196},
journal = {Frontiers in Neuroinformatics},
pages = {13},
title = {Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python},
title = {{Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python}},
url = {https://www.frontiersin.org/article/10.3389/fninf.2011.00013},
volume = {5},
year = {2011},
Expand All @@ -122,14 +122,14 @@ @article{nipype
bdsk-file-1 = {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}
}
@article{joblib,
title = {Joblib: running python function as pipeline jobs},
title = {{Joblib: running python function as pipeline jobs}},
author = {Varoquaux, Ga{\"e}l and Grisel, O},
journal = {packages. python. org/joblib},
year = {2009}
}

@article{halchenko2021datalad,
title = {DataLad: distributed system for joint management of code, data, and their relationship},
title = {{DataLad: distributed system for joint management of code, data, and their relationship}},
author = {Halchenko, Yaroslav O and Meyer, Kyle and Poldrack, Benjamin and Solanky, Debanjum Singh and Wagner, Adina S and Gors, Jason and MacFarlane, Dave and Pustina, Dorian and Sochat, Vanessa and Ghosh, Satrajit S and others},
journal = {Journal of Open Source Software},
volume = {6},
Expand All @@ -140,7 +140,7 @@ @article{halchenko2021datalad


@article{wagner2021fairly,
title = {FAIRly big: A framework for computationally reproducible processing of large-scale data},
title = {{FAIRly big: A framework for computationally reproducible processing of large-scale data}},
author = {Wagner, Adina S and Waite, Laura K and Wierzba, Ma{\l}gorzata and Hoffstaedter, Felix and Waite, Alexander Q and Poldrack, Benjamin and Eickhoff, Simon B and Hanke, Michael},
journal = {bioRxiv},
year = {2021},
Expand All @@ -158,7 +158,7 @@ @article{amunts2013bigbrain
publisher = {American Association for the Advancement of Science}
}
@inproceedings{huang2020ooops,
title = {OOOPS: an innovative tool for IO workload management on supercomputers},
title = {{OOOPS: an innovative tool for IO workload management on supercomputers}},
author = {Huang, Lei and Liu, Si},
booktitle = {2020 IEEE 26th International Conference on Parallel and Distributed Systems (ICPADS)},
pages = {486--493},
Expand All @@ -167,7 +167,7 @@ @inproceedings{huang2020ooops
}

@article{bb,
title = {Performance characterization of scientific workflows for the optimal use of Burst Buffers},
title = {{Performance characterization of scientific workflows for the optimal use of Burst Buffers}},
journal = {Future Generation Computer Systems},
volume = {110},
pages = {468-480},
Expand All @@ -182,7 +182,7 @@ @article{bb
@inproceedings{burstfs,
author = {Wang, Teng and Mohror, Kathryn and Moody, Adam and Sato, Kento and Yu, Weikuan},
booktitle = {SC '16: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
title = {An Ephemeral Burst-Buffer File System for Scientific Applications},
title = {{An Ephemeral Burst-Buffer File System for Scientific Applications}},
year = {2016},
volume = {},
number = {},
Expand All @@ -194,7 +194,7 @@ @inproceedings{burstfs
@inproceedings{gekkofs,
author = {Vef, Marc-André and Moti, Nafiseh and Süß, Tim and Tocci, Tommaso and Nou, Ramon and Miranda, Alberto and Cortes, Toni and Brinkmann, André},
booktitle = {2018 IEEE International Conference on Cluster Computing (CLUSTER)},
title = {GekkoFS - A Temporary Distributed File System for HPC Applications},
title = {{GekkoFS - A Temporary Distributed File System for HPC Applications}},
year = {2018},
volume = {},
number = {},
Expand All @@ -212,7 +212,7 @@ @article{xtreemfs

@misc{ds001545,
author = {Aly, M. and Chen, J. and Turk-Browne, N.B. and Hasson, U.},
title = {"Learning Naturalistic Temporal Structure in the Posterior Medial Network"},
title = {{"Learning Naturalistic Temporal Structure in the Posterior Medial Network"}},
year = {2019},
doi = {10.18112/openneuro.ds001545.v1.1.1},
publisher = {OpenNeuro}
Expand Down Expand Up @@ -244,7 +244,7 @@ @article{fsl
}

@article{cox1996afni,
title = {AFNI: software for analysis and visualization of functional magnetic resonance neuroimages},
title = {{AFNI: software for analysis and visualization of functional magnetic resonance neuroimages}},
author = {Cox, Robert W},
journal = {Computers and Biomedical research},
volume = {29},
Expand All @@ -253,14 +253,19 @@ @article{cox1996afni
year = {1996},
publisher = {Elsevier}
}
@misc{spm,
title = {SPM},
howpublished = {\url{https://www.fil.ion.ucl.ac.uk/spm/software/}}

@article{spm,
title = {Statistical parametric mapping},
author = {Friston, Karl J},
journal = {Neuroscience databases: a practical guide},
pages = {237--250},
year = {2003},
publisher = {Springer}
}


@article{haitas2021age,
title = {Age-preserved semantic memory and the CRUNCH effect manifested as differential semantic control networks: An fMRI study},
title = {{Age-preserved semantic memory and the CRUNCH effect manifested as differential semantic control networks: An fMRI study}},
author = {Haitas, Niobe and Amiri, Mahnoush and Wilson, Maximiliano and Joanette, Yves and Steffener, Jason},
journal = {Plos one},
volume = {16},
Expand Down
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