diff --git a/paper.bib b/paper.bib index 1b1e493..192f33e 100644 --- a/paper.bib +++ b/paper.bib @@ -49,7 +49,8 @@ @ARTICLE{Dieringer2014-qz pages = "e91318", month = mar, year = 2014, - language = "en" + language = "en", + doi = {10.1371/journal.pone.0091318} } @ARTICLE{Stanisz2005-qg, @@ -72,6 +73,7 @@ @ARTICLE{Stanisz2005-qg to 10\%. Collectively, these results provide a useful reference for optimization of pulse sequence parameters for MRI at 3 T.", journal = "Magn. Reson. Med.", + doi = {10.1002/mrm.20605}, volume = 54, number = 3, pages = "507--512", @@ -90,6 +92,7 @@ @INCOLLECTION{Kluyver2016-nl and Hamrick, Jessica and Grout, Jason and Corlay, Sylvain and Ivanov, Paul and Abdalla, Safia and Willing, Carol", publisher = "IOS Press", + doi = {10.3233/978-1-61499-649-1-87}, pages = "87--90", year = 2016, address = "Amsterdam, NY" @@ -125,6 +128,7 @@ @ARTICLE{Barral2010-qm number = 4, pages = "1057--1067", month = oct, + doi = {10.1002/mrm.22497}, year = 2010, language = "en" } @@ -164,6 +168,7 @@ @ARTICLE{Bottomley1984-qx techniques are identified as major sources of data irreproducibility.", journal = "Med. Phys.", + doi = {10.1118/1.595535}, volume = 11, number = 4, pages = "425--448", @@ -171,27 +176,31 @@ @ARTICLE{Bottomley1984-qx language = "en" } -@UNPUBLISHED{Karakuzu2022-xq, - title = "{NeuroLibre} : A preprint server for full-fledged reproducible - neuroscience", - author = "Karakuzu, Agah and DuPre, Elizabeth and Tetrel, Loic and - Bermudez, Patrick and Boudreau, Mathieu and Chin, Mary and - Poline, Jean-Baptiste and Das, Samir and Bellec, Pierre and - Stikov, Nikola", - abstract = "NeuroLibre is a preprint server for neuroscience Jupyter Books, - blending code, visualization and narrative text into one - document. NeuroLibre archives the environment, code and data and - also implements a technical review to ensure readers can - reproduce the work. NeuroLibre offers an online platform where - readers can reproduce or modify each preprint from a web browser, - without any installation required. We hope that NeuroLibre will - contribute to usher the research community in a new area of open - and reproducible neuroscience. The preprint server is built with - open source components, and can be freely adapted to meet the - needs of other communities in the future as well.", - month = apr, - year = 2022, - keywords = "Communication; Open Science; Publishing; Reproducibility" +@article{Karakuzu2022-xq, + abstract = {NeuroLibre is a preprint server for neuroscience Jupyter Books, +blending code, visualization and narrative text into one +document. NeuroLibre archives the environment, code and data and +also implements a technical review to ensure readers can +reproduce the work. NeuroLibre offers an online platform where +readers can reproduce or modify each preprint from a web browser, +without any installation required. We hope that NeuroLibre will +contribute to usher the research community in a new area of open +and reproducible neuroscience. The preprint server is built with +open source components, and can be freely adapted to meet the +needs of other communities in the future as well.}, + author = {Karakuzu, Agah and DuPre, Elizabeth and Tetrel, Loic and +Bermudez, Patrick and Boudreau, Mathieu and Chin, Mary and +Poline, Jean-Baptiste and Das, Samir and Bellec, Pierre and +Stikov, Nikola}, + journal = {OSF preprints}, + keywords = {Communication; Open Science; Publishing; Reproducibility}, + language = {en}, + month = {April}, + publisher = {Open Science Framework}, + title = {{NeuroLibre} : A preprint server for full-fledged reproducible +neuroscience}, + doi = {10.31219/osf.io/h89js}, + year = {2022} } @ARTICLE{Cabana2015-zg, @@ -207,6 +216,7 @@ @ARTICLE{Cabana2015-zg publisher = "Wiley", volume = "44A", number = 5, + doi = {10.1002/cmr.a.21357}, pages = "263--277", month = sep, year = 2015, @@ -248,6 +258,7 @@ @ARTICLE{Karakuzu2022-af volume = 88, number = 3, pages = "1212--1228", + doi = {10.1002/mrm.29292}, month = sep, year = 2022, keywords = "magnetization transfer; multicenter; open source; qMRI; @@ -296,7 +307,8 @@ @ARTICLE{Keenan2018-px month = jan, year = 2018, keywords = "phantom; quality assurance; quantitative; system consistency", - language = "en" + language = "en", + doi = {10.1002/mrm.26982}, } @ARTICLE{Avants2009-cw, @@ -305,6 +317,7 @@ @ARTICLE{Avants2009-cw journal = "Insight J.", volume = 2, number = 365, + doi = {10.54294/uvnhin}, pages = "1--35", year = 2009 } @@ -363,6 +376,7 @@ @ARTICLE{Piechnik2010-be pages = "69", month = nov, year = 2010, + doi = {10.1186/1532-429X-12-69}, language = "en" } @@ -401,6 +415,7 @@ @ARTICLE{Lazari2021-oy pages = "117744", month = apr, year = 2021, + doi = {10.1016/j.neuroimage.2021.117744}, keywords = "Diffusion; Histology; MRI; Magnetization transfer; Microstructural imaging; Myelin; Relaxometry; Validation", language = "en" @@ -431,6 +446,7 @@ @ARTICLE{Mancini2020-sv journal = "Elife", volume = 9, month = oct, + doi = {10.55458/neurolibre.00004}, year = 2020, keywords = "MRI; brain; central nervous system; histology; human; meta-analysis; mouse; myelin; neuroscience; rat;Myelin", @@ -446,6 +462,7 @@ @ARTICLE{Pykett1978-mk pages = "961--967", month = sep, year = 1978, + doi = {10.1097/00004728-197904000-00056}, language = "en" } @@ -476,6 +493,7 @@ @ARTICLE{Bojorquez2017-xh pages = "69--80", month = jan, year = 2017, + doi = {10.1016/j.mri.2016.08.021}, keywords = "3 tesla; Relaxation times; T(1); T(2)", language = "en" } @@ -587,6 +605,7 @@ @MISC{Hahn1949-wf author = "Hahn, Erwin L", journal = "Physical Review", volume = 76, + doi = {10.1103/PhysRev.76.145}, number = 1, pages = "145--146", year = 1949 @@ -620,6 +639,7 @@ @ARTICLE{Boettiger2015-vd pages = "71--79", month = jan, year = 2015, + doi = {10.1145/2723872.2723882}, address = "New York, NY, USA" } @@ -642,6 +662,7 @@ @ARTICLE{Sled2001-fz journal = "Magn. Reson. Med.", volume = 46, number = 5, + doi = {10.1002/mrm.1278}, pages = "923--931", month = nov, year = 2001, @@ -654,6 +675,7 @@ @MISC{Deoni2003-qc author = "Deoni, Sean C L and Rutt, Brian K and Peters, Terry M", journal = "Magnetic Resonance in Medicine", volume = 49, + doi = {10.1002/mrm.10407}, number = 3, pages = "515--526", year = 2003 @@ -677,6 +699,7 @@ @ARTICLE{Karakuzu2020-ul journal = "J. Open Source Softw.", publisher = "The Open Journal", volume = 5, + doi = {10.21105/joss.02343}, number = 53, pages = "2343", month = sep, @@ -714,7 +737,8 @@ @ARTICLE{Beg2021-ps volume = 23, pages = "36--46", month = mar, - year = 2021 + year = 2021, + doi = {10.1109/MCSE.2021.3052101}, } @INPROCEEDINGS{Project_Jupyter2018-ll, @@ -742,7 +766,8 @@ @INPROCEEDINGS{Project_Jupyter2018-ll year = 2018, language = "en", conference = "Python in Science Conference", - location = "Austin, Texas" + location = "Austin, Texas", + doi = { 10.25080/Majora-4af1f417-011 } } @ARTICLE{Marques2013-yg, @@ -771,6 +796,7 @@ @ARTICLE{Marques2013-yg number = 7, pages = "e69294", month = jul, + doi = {10.1371/journal.pone.0069294}, year = 2013, language = "en" } @@ -788,6 +814,7 @@ @ARTICLE{Redpath1994-sb delineation of the cerebral cortex.", journal = "Br. J. Radiol.", volume = 67, + doi = {10.1259/0007-1285-67-804-1258}, number = 804, pages = "1258--1263", month = dec, @@ -815,6 +842,7 @@ @ARTICLE{Keenan2019-ni pages = "e26--e39", month = jun, year = 2019, + doi = {10.1002/jmri.26598}, keywords = "phantom; quantitative MRI; reference objects; standards; validation", language = "en" @@ -864,6 +892,7 @@ @ARTICLE{Stupic2021-hu volume = 86, number = 3, pages = "1194--1211", + doi = {10.1002/mrm.28779}, month = sep, year = 2021, keywords = "MRI standards; phantom; quality assurance; quantitative MRI", @@ -930,6 +959,7 @@ @ARTICLE{Captur2016-xn number = 1, pages = "58", month = sep, + doi = {10.1186/s12968-016-0280-z}, year = 2016, keywords = "Phantom; Standardization; T1 mapping", language = "en" @@ -988,6 +1018,7 @@ @ARTICLE{Bane2018-wt pages = "2564--2575", month = may, year = 2018, + doi = {10.1002/mrm.26903}, keywords = "DCE-MRI; T1 mapping; multicenter; phantom", language = "en" } @@ -1013,6 +1044,7 @@ @ARTICLE{Look1970-no journal = "Rev. Sci. Instrum.", publisher = "AIP Publishing", volume = 41, + doi = {10.1063/1.1684482}, number = 2, pages = "250--251", month = feb, @@ -1040,6 +1072,7 @@ @ARTICLE{Damadian1971-sc journal = "Science", volume = 171, number = 3976, + doi = {10.1126/science.171.3976.1151}, pages = "1151--1153", month = mar, year = 1971, @@ -1107,6 +1140,7 @@ @ARTICLE{Drain1949-yk journal = "Proc. Phys. Soc. A", publisher = "IOP Publishing", volume = 62, + doi = {10.1088/0370-1298/62/5/306}, number = 5, pages = "301", month = may, @@ -1148,6 +1182,7 @@ @ARTICLE{Messroghli2004-iv volume = 52, number = 1, pages = "141--146", + doi = {10.1002/mrm.20110}, month = jul, year = 2004, language = "en" @@ -1214,6 +1249,7 @@ @ARTICLE{Piechnik2013-xl accurate measure of T1, but that ShMOLLI is a stable and reproducible method for T1-mapping.", journal = "J. Cardiovasc. Magn. Reson.", + doi = {10.1186/1532-429X-15-13}, volume = 15, number = 1, pages = "13", @@ -1228,6 +1264,7 @@ @INCOLLECTION{Boudreau2020-jf author = "Boudreau, Mathieu and Keenan, Kathryn E and Stikov, Nikola", pages = "19--45", month = nov, + doi = {10.1016/b978-0-12-817057-1.00004-4}, year = 2020 } @@ -1235,6 +1272,7 @@ @MISC{McCarthy2019-qd title = "{FSLeyes}", author = "McCarthy, Paul", month = sep, + doi = {10.5281/zenodo.6511596}, year = 2019 } @@ -1260,6 +1298,7 @@ @ARTICLE{Tofts1997-ln (approximately in vitro value).", journal = "J. Magn. Reson. Imaging", volume = 7, + doi = {10.1002/jmri.1880070113}, number = 1, pages = "91--101", year = 1997, @@ -1314,6 +1353,7 @@ @ARTICLE{Keenan2021-ly number = 6, pages = "e0252966", month = jun, + doi = {10.1371/journal.pone.0252966}, year = 2021, keywords = "Multicenter;Phantoms", language = "en" @@ -1355,6 +1395,7 @@ @ARTICLE{Wansapura1999-tf volume = 9, number = 4, pages = "531--538", + doi = {10.1002/(SICI)1522-2586(199904)9:4<531::AID-JMRI4>3.0.CO;2-L}, month = apr, year = 1999, language = "en" @@ -1368,6 +1409,7 @@ @ARTICLE{Gracien2020-ak sequences and data analysis …", author = "{Gracien} and {Maiworm} and {Br{\"u}che} and {Shrestha} and {others}", + doi = {10.1016/j.neuroimage.2019.116364}, journal = "Neuroimage", year = 2020 } @@ -1408,6 +1450,7 @@ @ARTICLE{Yuan2012-xh pages = "245--253", month = dec, year = 2012, + doi = {10.3978/j.issn.2223-4292.2012.11.04}, keywords = "DCE-MRI; T1 mapping; Tofts model; dual-flip-angle method; head and neck", language = "en" @@ -1423,6 +1466,7 @@ @ARTICLE{Schweitzer2016-fl pages = "781--782", month = oct, year = 2016, + doi = {10.1002/jmri.25417}, language = "en" } @@ -1465,6 +1509,7 @@ @ARTICLE{A_G_Teixeira2020-bw volume = 84, number = 1, pages = "221--236", + doi = {10.1002/mrm.28109}, month = jul, year = 2020, keywords = "CSMT; DESPOT; JSR; T1 mapping; T2 mapping; magnetization @@ -1497,6 +1542,7 @@ @ARTICLE{Ernst1966-pp volume = 37, number = 1, pages = "93--102", + doi = {10.1063/1.1719961}, month = jan, year = 1966 } @@ -1539,6 +1585,7 @@ @ARTICLE{Layton2017-dy number = 4, pages = "1544--1552", month = apr, + doi = {10.1002/mrm.26235}, year = 2017, keywords = "Pulseq; open-source; platform independent; pulse sequence programming; rapid development", @@ -1570,6 +1617,7 @@ @ARTICLE{Fryback1991-sy volume = 11, number = 2, pages = "88--94", + doi = {10.1177/0272989X9101100203}, year = 1991, language = "en" } @@ -1583,6 +1631,7 @@ @MISC{Marques2010-po journal = "NeuroImage", volume = 49, number = 2, + doi = {10.1016/j.neuroimage.2009.10.002}, pages = "1271--1281", year = 2010 } @@ -1625,6 +1674,7 @@ @ARTICLE{Stikov2015-qj number = 2, pages = "514--522", year = 2015, + doi = {10.1002/mrm.25135}, keywords = "relaxometry T1 mapping quantitative MRI accuracy precision inversion recovery Look-Locker variable flip angle B1 mapping" } @@ -1646,6 +1696,7 @@ @ARTICLE{Fram1987-jj compared to partial saturation techniques.", journal = "Magn. Reson. Imaging", volume = 5, + doi = {10.1016/0730-725X(87)90021-X}, number = 3, pages = "201--208", year = 1987, @@ -1659,44 +1710,8 @@ @MISC{Cheng2006-qe author = "Cheng, Hai-Ling Margaret and Wright, Graham A", journal = "Magnetic Resonance in Medicine", volume = 55, + doi = {10.1002/mrm.20791}, number = 3, pages = "566--574", year = 2006 } - -@misc{Karakuzu2022-nlwf, - title={NeuroLibre : A preprint server for full-fledged reproducible neuroscience}, - url={osf.io/h89js}, - DOI={10.31219/osf.io/h89js}, - publisher={OSF Preprints}, - author={Karakuzu, Agah and DuPre, Elizabeth and Tetrel, Loic and Bermudez, Patrick and Boudreau, Mathieu and Chin, Mary and Poline, Jean-Baptiste and Das, Samir and Bellec, Pierre and Stikov, Nikola}, - year={2022}, - month={Apr} -} - -@article{Dupre2022-iro, - title={Beyond advertising: New infrastructures for publishing integrated research objects}, - author={DuPre, Elizabeth and Holdgraf, Chris and Karakuzu, Agah and Tetrel, Lo{\"\i}c and Bellec, Pierre and Stikov, Nikola and Poline, Jean-Baptiste}, - journal={PLOS Computational Biology}, - doi = {10.1371/journal.pcbi.1009651}, - volume={18}, - number={1}, - pages={e1009651}, - year={2022}, - publisher={Public Library of Science San Francisco, CA USA} -} - -@article{Harding2023-conp, - title = {The {Canadian} {Open} {Neuroscience} {Platform}—{An} open science framework for the neuroscience community}, - volume = {19}, - url = {10.1371/journal.pcbi.1011230}, - doi = {10.1371/journal.pcbi.1011230}, - abstract = {The Canadian Open Neuroscience Platform (CONP) takes a multifaceted approach to enabling open neuroscience, aiming to make research, data, and tools accessible to everyone, with the ultimate objective of accelerating discovery. Its core infrastructure is the CONP Portal, a repository with a decentralized design, where datasets and analysis tools across disparate platforms can be browsed, searched, accessed, and shared in accordance with FAIR principles. Another key piece of CONP infrastructure is NeuroLibre, a preprint server capable of creating and hosting executable and fully reproducible scientific publications that embed text, figures, and code. As part of its holistic approach, the CONP has also constructed frameworks and guidance for ethics and data governance, provided support and developed resources to help train the next generation of neuroscientists, and has fostered and grown an engaged community through outreach and communications. In this manuscript, we provide a high-level overview of this multipronged platform and its vision of lowering the barriers to the practice of open neuroscience and yielding the associated benefits for both individual researchers and the wider community.}, - number = {7}, - journal = {PLOS Computational Biology}, - author = {Harding, Rachel J. and Bermudez, Patrick and Bernier, Alexander and Beauvais, Michael and Bellec, Pierre and Hill, Sean and Karakuzu, Agah and Knoppers, Bartha M. and Pavlidis, Paul and Poline, Jean-Baptiste and Roskams, Jane and Stikov, Nikola and Stone, Jessica and Strother, Stephen and Consortium, CONP and Evans, Alan C.}, - month = jul, - year = {2023}, - note = {Publisher: Public Library of Science}, - pages = {1--14}, -} \ No newline at end of file