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100644 content/publications/zhao-2023/index.md diff --git a/content/publications/abrams-2021/cite.bib b/content/publications/abrams-2021/cite.bib new file mode 100644 index 0000000..5c9d48d --- /dev/null +++ b/content/publications/abrams-2021/cite.bib @@ -0,0 +1,23 @@ +@article{abrams_2021, + author = {Abrams, Mathew Birdsall and Bjaalie, Jan G. and Das, Samir +and Egan, Gary F. and Ghosh, Satrajit S. and Goscinski, +Wojtek J. and Grethe, Jeffrey S. and Kotaleski, Jeanette +Hellgren and Ho, Eric Tatt Wei and Kennedy, David N. and +Lanyon, Linda J. and Leergaard, Trygve B. and Mayberg, +Helen S. and Milanesi, Luciano and Mouček, Roman and +Poline, J. B. and Roy, Prasun K. and Strother, Stephen C. +and Tang, Tong Boon and Tiesinga, Paul and Wachtler, Thomas +and Wójcik, Daniel K. and Martone, Maryann E.}, + doi = {10.1007/s12021-020-09509-0}, + issn = {1559-0089}, + journal = {Neuroinformatics}, + month = {January}, + number = {1}, + pages = {25–36}, + publisher = {Springer Science and Business Media LLC}, + title = {A Standards Organization for Open and FAIR Neuroscience: +the International Neuroinformatics Coordinating Facility}, + url = {http://dx.doi.org/10.1007/s12021-020-09509-0}, + volume = {20}, + year = {2021} +} diff --git a/content/publications/abrams-2021/index.md b/content/publications/abrams-2021/index.md new file mode 100644 index 0000000..081817d --- /dev/null +++ b/content/publications/abrams-2021/index.md @@ -0,0 +1,37 @@ +--- +title: 'A Standards Organization for Open and FAIR Neuroscience: the International + Neuroinformatics Coordinating Facility' +authors: +- Mathew Birdsall Abrams +- Jan G. Bjaalie +- Samir Das +- Gary F. Egan +- Satrajit S. Ghosh +- Wojtek J. Goscinski +- Jeffrey S. Grethe +- Jeanette Hellgren Kotaleski +- Eric Tatt Wei Ho +- David N. Kennedy +- Linda J. Lanyon +- Trygve B. Leergaard +- Helen S. Mayberg +- Luciano Milanesi +- Roman Mouček +- J. B. Poline +- Prasun K. Roy +- Stephen C. Strother +- Tong Boon Tang +- Paul Tiesinga +- Thomas Wachtler +- Daniel K. Wójcik +- Maryann E. Martone +date: '2021-01-01' +publishDate: '2024-12-19T23:16:36.346376Z' +publication_types: +- article-journal +publication: '*Neuroinformatics*' +doi: 10.1007/s12021-020-09509-0 +links: +- name: URL + url: http://dx.doi.org/10.1007/s12021-020-09509-0 +--- diff --git a/content/publications/bandrowski-2016/cite.bib b/content/publications/bandrowski-2016/cite.bib new file mode 100644 index 0000000..275e7da --- /dev/null +++ b/content/publications/bandrowski-2016/cite.bib @@ -0,0 +1,15 @@ +@article{bandrowski_2016, + author = {Bandrowski, Anita E. and Martone, Maryann E.}, + doi = {10.1016/j.neuron.2016.04.030}, + issn = {0896-6273}, + journal = {Neuron}, + month = {May}, + number = {3}, + pages = {434–436}, + publisher = {Elsevier BV}, + title = {RRIDs: A Simple Step toward Improving Reproducibility +through Rigor and Transparency of Experimental Methods}, + url = {http://dx.doi.org/10.1016/j.neuron.2016.04.030}, + volume = {90}, + year = {2016} +} diff --git a/content/publications/bandrowski-2016/index.md b/content/publications/bandrowski-2016/index.md new file mode 100644 index 0000000..05f31d4 --- /dev/null +++ b/content/publications/bandrowski-2016/index.md @@ -0,0 +1,16 @@ +--- +title: 'RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency + of Experimental Methods' +authors: +- Anita E. Bandrowski +- Maryann E. Martone +date: '2016-05-01' +publishDate: '2024-12-19T23:16:36.352565Z' +publication_types: +- article-journal +publication: '*Neuron*' +doi: 10.1016/j.neuron.2016.04.030 +links: +- name: URL + url: http://dx.doi.org/10.1016/j.neuron.2016.04.030 +--- diff --git a/content/publications/bannier-2021/cite.bib b/content/publications/bannier-2021/cite.bib new file mode 100644 index 0000000..0fa812c --- /dev/null +++ b/content/publications/bannier-2021/cite.bib @@ -0,0 +1,29 @@ +@article{bannier_2021, + author = {Bannier, Elise and Barker, Gareth and Borghesani, +Valentina and Broeckx, Nils and Clement, Patricia and +Emblem, Kyrre E. and Ghosh, Satrajit and Glerean, Enrico +and Gorgolewski, Krzysztof J. and Havu, Marko and +Halchenko, Yaroslav O. and Herholz, Peer and Hespel, Anne +and Heunis, Stephan and Hu, Yue and Hu, Chuan‐Peng and +Huijser, Dorien and de la Iglesia Vayá, María and +Jancalek, Radim and Katsaros, Vasileios K. and Kieseler, +Marie‐Luise and Maumet, Camille and Moreau, Clara A. and +Mutsaerts, Henk‐Jan and Oostenveld, Robert and +Ozturk‐Isik, Esin and Pascual Leone Espinosa, Nicolas and +Pellman, John and Pernet, Cyril R and Pizzini, Francesca +Benedetta and Trbalić, Amira Šerifović and Toussaint, +Paule‐Joanne and Visconti di Oleggio Castello, Matteo and +Wang, Fengjuan and Wang, Cheng and Zhu, Hua}, + doi = {10.1002/hbm.25351}, + issn = {1097-0193}, + journal = {Human Brain Mapping}, + month = {February}, + number = {7}, + pages = {1945–1951}, + publisher = {Wiley}, + title = {The Open Brain Consent: Informing research participants +and obtaining consent to share brain imaging data}, + url = {http://dx.doi.org/10.1002/hbm.25351}, + volume = {42}, + year = {2021} +} diff --git a/content/publications/bannier-2021/index.md b/content/publications/bannier-2021/index.md new file mode 100644 index 0000000..05e639a --- /dev/null +++ b/content/publications/bannier-2021/index.md @@ -0,0 +1,50 @@ +--- +title: 'The Open Brain Consent: Informing research participants and obtaining consent + to share brain imaging data' +authors: +- Elise Bannier +- Gareth Barker +- Valentina Borghesani +- Nils Broeckx +- Patricia Clement +- Kyrre E. Emblem +- Satrajit Ghosh +- Enrico Glerean +- Krzysztof J. Gorgolewski +- Marko Havu +- Yaroslav O. Halchenko +- Peer Herholz +- Anne Hespel +- Stephan Heunis +- Yue Hu +- Chuan‐Peng Hu +- Dorien Huijser +- María de la Iglesia Vayá +- Radim Jancalek +- Vasileios K. Katsaros +- Marie‐Luise Kieseler +- Camille Maumet +- Clara A. Moreau +- Henk‐Jan Mutsaerts +- Robert Oostenveld +- Esin Ozturk‐Isik +- Nicolas Pascual Leone Espinosa +- John Pellman +- Cyril R Pernet +- Francesca Benedetta Pizzini +- Amira Šerifović Trbalić +- Paule‐Joanne Toussaint +- Matteo Visconti di Oleggio Castello +- Fengjuan Wang +- Cheng Wang +- Hua Zhu +date: '2021-02-01' +publishDate: '2024-12-19T23:16:36.356531Z' +publication_types: +- article-journal +publication: '*Human Brain Mapping*' +doi: 10.1002/hbm.25351 +links: +- name: URL + url: http://dx.doi.org/10.1002/hbm.25351 +--- diff --git a/content/publications/baranger-2021/cite.bib b/content/publications/baranger-2021/cite.bib new file mode 100644 index 0000000..8b1dc54 --- /dev/null +++ b/content/publications/baranger-2021/cite.bib @@ -0,0 +1,15 @@ +@article{baranger_2021, + author = {Baranger, David A.A. and Halchenko, Yaroslav O. and Satz, +Skye and Ragozzino, Rachel and Iyengar, Satish and Swartz, +Holly A. and Manelis, Anna}, + doi = {10.1016/j.mex.2021.101595}, + issn = {2215-0161}, + journal = {MethodsX}, + pages = {101595}, + publisher = {Elsevier BV}, + title = {Protocol for a machine learning algorithm predicting +depressive disorders using the T1w/T2w ratio}, + url = {http://dx.doi.org/10.1016/j.mex.2021.101595}, + volume = {8}, + year = {2021} +} diff --git a/content/publications/baranger-2021/index.md b/content/publications/baranger-2021/index.md new file mode 100644 index 0000000..2c28ca0 --- /dev/null +++ b/content/publications/baranger-2021/index.md @@ -0,0 +1,21 @@ +--- +title: Protocol for a machine learning algorithm predicting depressive disorders using + the T1w/T2w ratio +authors: +- David A.A. Baranger +- Yaroslav O. Halchenko +- Skye Satz +- Rachel Ragozzino +- Satish Iyengar +- Holly A. Swartz +- Anna Manelis +date: '2021-01-01' +publishDate: '2024-12-19T23:16:36.361403Z' +publication_types: +- article-journal +publication: '*MethodsX*' +doi: 10.1016/j.mex.2021.101595 +links: +- name: URL + url: http://dx.doi.org/10.1016/j.mex.2021.101595 +--- diff --git a/content/publications/bazeille-2021/cite.bib b/content/publications/bazeille-2021/cite.bib new file mode 100644 index 0000000..dc3fdba --- /dev/null +++ b/content/publications/bazeille-2021/cite.bib @@ -0,0 +1,15 @@ +@article{bazeille_2021, + author = {Bazeille, Thomas and DuPre, Elizabeth and Richard, Hugo +and Poline, Jean-Baptiste and Thirion, Bertrand}, + doi = {10.1016/j.neuroimage.2021.118683}, + issn = {1053-8119}, + journal = {NeuroImage}, + month = {December}, + pages = {118683}, + publisher = {Elsevier BV}, + title = {An empirical evaluation of functional alignment using +inter-subject decoding}, + url = {http://dx.doi.org/10.1016/j.neuroimage.2021.118683}, + volume = {245}, + year = {2021} +} diff --git a/content/publications/bazeille-2021/index.md b/content/publications/bazeille-2021/index.md new file mode 100644 index 0000000..5b7b99f --- /dev/null +++ b/content/publications/bazeille-2021/index.md @@ -0,0 +1,18 @@ +--- +title: An empirical evaluation of functional alignment using inter-subject decoding +authors: +- Thomas Bazeille +- Elizabeth DuPre +- Hugo Richard +- Jean-Baptiste Poline +- Bertrand Thirion +date: '2021-12-01' +publishDate: '2024-12-19T23:16:36.365494Z' +publication_types: +- article-journal +publication: '*NeuroImage*' +doi: 10.1016/j.neuroimage.2021.118683 +links: +- name: URL + url: http://dx.doi.org/10.1016/j.neuroimage.2021.118683 +--- diff --git a/content/publications/bhagwat-2021/cite.bib b/content/publications/bhagwat-2021/cite.bib new file mode 100644 index 0000000..0388aae --- /dev/null +++ b/content/publications/bhagwat-2021/cite.bib @@ -0,0 +1,18 @@ +@article{bhagwat_2021, + author = {Bhagwat, Nikhil and Barry, Amadou and Dickie, Erin W and +Brown, Shawn T and Devenyi, Gabriel A and Hatano, Koji and +DuPre, Elizabeth and Dagher, Alain and Chakravarty, Mallar +and Greenwood, Celia M T and Misic, Bratislav and Kennedy, +David N and Poline, Jean-Baptiste}, + doi = {10.1093/gigascience/giaa155}, + issn = {2047-217X}, + journal = {GigaScience}, + month = {January}, + number = {1}, + publisher = {Oxford University Press (OUP)}, + title = {Understanding the impact of preprocessing pipelines on +neuroimaging cortical surface analyses}, + url = {http://dx.doi.org/10.1093/gigascience/giaa155}, + volume = {10}, + year = {2021} +} diff --git a/content/publications/bhagwat-2021/index.md b/content/publications/bhagwat-2021/index.md new file mode 100644 index 0000000..320948e --- /dev/null +++ b/content/publications/bhagwat-2021/index.md @@ -0,0 +1,27 @@ +--- +title: Understanding the impact of preprocessing pipelines on neuroimaging cortical + surface analyses +authors: +- Nikhil Bhagwat +- Amadou Barry +- Erin W Dickie +- Shawn T Brown +- Gabriel A Devenyi +- Koji Hatano +- Elizabeth DuPre +- Alain Dagher +- Mallar Chakravarty +- Celia M T Greenwood +- Bratislav Misic +- David N Kennedy +- Jean-Baptiste Poline +date: '2021-01-01' +publishDate: '2024-12-19T23:16:36.369515Z' +publication_types: +- article-journal +publication: '*GigaScience*' +doi: 10.1093/gigascience/giaa155 +links: +- name: URL + url: http://dx.doi.org/10.1093/gigascience/giaa155 +--- diff --git a/content/publications/boaro-2022/cite.bib b/content/publications/boaro-2022/cite.bib new file mode 100644 index 0000000..6e60e70 --- /dev/null +++ b/content/publications/boaro-2022/cite.bib @@ -0,0 +1,19 @@ +@article{boaro_2022, + author = {Boaro, Alessandro and Kaczmarzyk, Jakub R. and Kavouridis, +Vasileios K. and Harary, Maya and Mammi, Marco and Dawood, +Hassan and Shea, Alice and Cho, Elise Y. and Juvekar, +Parikshit and Noh, Thomas and Rana, Aakanksha and Ghosh, +Satrajit and Arnaout, Omar}, + doi = {10.1038/s41598-022-19356-5}, + issn = {2045-2322}, + journal = {Scientific Reports}, + month = {September}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {Deep neural networks allow expert-level brain meningioma +segmentation and present potential for improvement of +clinical practice}, + url = {http://dx.doi.org/10.1038/s41598-022-19356-5}, + volume = {12}, + year = {2022} +} diff --git a/content/publications/boaro-2022/index.md b/content/publications/boaro-2022/index.md new file mode 100644 index 0000000..9142a09 --- /dev/null +++ b/content/publications/boaro-2022/index.md @@ -0,0 +1,27 @@ +--- +title: Deep neural networks allow expert-level brain meningioma segmentation and present + potential for improvement of clinical practice +authors: +- Alessandro Boaro +- Jakub R. Kaczmarzyk +- Vasileios K. Kavouridis +- Maya Harary +- Marco Mammi +- Hassan Dawood +- Alice Shea +- Elise Y. Cho +- Parikshit Juvekar +- Thomas Noh +- Aakanksha Rana +- Satrajit Ghosh +- Omar Arnaout +date: '2022-09-01' +publishDate: '2024-12-19T23:16:36.373740Z' +publication_types: +- article-journal +publication: '*Scientific Reports*' +doi: 10.1038/s41598-022-19356-5 +links: +- name: URL + url: http://dx.doi.org/10.1038/s41598-022-19356-5 +--- diff --git a/content/publications/bollmann-2023/cite.bib b/content/publications/bollmann-2023/cite.bib new file mode 100644 index 0000000..6541c53 --- /dev/null +++ b/content/publications/bollmann-2023/cite.bib @@ -0,0 +1,26 @@ +@article{bollmann_2023, + author = {Bollmann, Steffen and Renton, Angela and Dao, Thuy and +Johnstone, Tom and Civier, Oren and Sullivan, Ryan and +White, David and Lyons, Paris and Slade, Benjamin and +Abbott, David and Amos, Toluwani and Bollmann, Saskia and +Botting, Andy and Campbell, Megan and Chang, Jeryn and +Close, Thomas and Eckstein, Korbinian and Egan, Gary and +Evas, Stefanie and Flandin, Guillaume and Garner, Kelly and +Garrido, Marta and Ghosh, Satrajit and Grignard, Martin and +Hannan, Anthony and Huber, Laurentius (Renzo) and +Kaczmarzyk, Jakub and Kasper, Lars and Kuhlmann, Levin and +Lou, Kexin and Mantilla-Ramos, Yorguin-Jose and Mattingley, +Jason and Morris, Jo and Narayanan, Akshaiy and Pestilli, +Franco and Puce, Aina and Ribeiro, Fernanda and Rogasch, +Nigel and Rorden, Chris and Schira, Mark and Shaw, Thomas +and Sowman, Paul and Spitz, Gershon and Stewart, Ashley and +Ye, Xincheng and Zhu, Judy and Hughes, Matthew and +Narayanan, Aswin}, + doi = {10.21203/rs.3.rs-2649734/v1}, + month = {March}, + publisher = {Research Square Platform LLC}, + title = {Neurodesk: An accessible, flexible, and portable data +analysis environment for reproducible neuroimaging}, + url = {http://dx.doi.org/10.21203/rs.3.rs-2649734/v1}, + year = {2023} +} diff --git a/content/publications/bollmann-2023/index.md b/content/publications/bollmann-2023/index.md new file mode 100644 index 0000000..0c9c64b --- /dev/null +++ b/content/publications/bollmann-2023/index.md @@ -0,0 +1,62 @@ +--- +title: 'Neurodesk: An accessible, flexible, and portable data analysis environment + for reproducible neuroimaging' +authors: +- Steffen Bollmann +- Angela Renton +- Thuy Dao +- Tom Johnstone +- Oren Civier +- Ryan Sullivan +- David White +- Paris Lyons +- Benjamin Slade +- David Abbott +- Toluwani Amos +- Saskia Bollmann +- Andy Botting +- Megan Campbell +- Jeryn Chang +- Thomas Close +- Korbinian Eckstein +- Gary Egan +- Stefanie Evas +- Guillaume Flandin +- Kelly Garner +- Marta Garrido +- Satrajit Ghosh +- Martin Grignard +- Anthony Hannan +- Laurentius (Renzo) Huber +- Jakub Kaczmarzyk +- Lars Kasper +- Levin Kuhlmann +- Kexin Lou +- Yorguin-Jose Mantilla-Ramos +- Jason Mattingley +- Jo Morris +- Akshaiy Narayanan +- Franco Pestilli +- Aina Puce +- Fernanda Ribeiro +- Nigel Rogasch +- Chris Rorden +- Mark Schira +- Thomas Shaw +- Paul Sowman +- Gershon Spitz +- Ashley Stewart +- Xincheng Ye +- Judy Zhu +- Matthew Hughes +- Aswin Narayanan +date: '2023-03-01' +publishDate: '2024-12-19T23:16:36.377908Z' +publication_types: +- article-journal +publication: '*Research Square Platform LLC*' +doi: 10.21203/rs.3.rs-2649734/v1 +links: +- name: URL + url: http://dx.doi.org/10.21203/rs.3.rs-2649734/v1 +--- diff --git a/content/publications/botvinik-nezer-2020/cite.bib b/content/publications/botvinik-nezer-2020/cite.bib new file mode 100644 index 0000000..d40ccb2 --- /dev/null +++ b/content/publications/botvinik-nezer-2020/cite.bib @@ -0,0 +1,90 @@ +@article{botvinik_nezer_2020, + author = {Botvinik-Nezer, Rotem and Holzmeister, Felix and Camerer, +Colin F. and Dreber, Anna and Huber, Juergen and +Johannesson, Magnus and Kirchler, Michael and Iwanir, Roni +and Mumford, Jeanette A. and Adcock, R. Alison and Avesani, +Paolo and Baczkowski, Blazej M. and Bajracharya, Aahana and +Bakst, Leah and Ball, Sheryl and Barilari, Marco and Bault, +Nadège and Beaton, Derek and Beitner, Julia and Benoit, +Roland G. and Berkers, Ruud M. W. J. and Bhanji, Jamil P. +and Biswal, Bharat B. and Bobadilla-Suarez, Sebastian and +Bortolini, Tiago and Bottenhorn, Katherine L. and Bowring, +Alexander and Braem, Senne and Brooks, Hayley R. and +Brudner, Emily G. and Calderon, Cristian B. and Camilleri, +Julia A. and Castrellon, Jaime J. and Cecchetti, Luca and +Cieslik, Edna C. and Cole, Zachary J. and Collignon, +Olivier and Cox, Robert W. and Cunningham, William A. and +Czoschke, Stefan and Dadi, Kamalaker and Davis, Charles P. +and Luca, Alberto De and Delgado, Mauricio R. and +Demetriou, Lysia and Dennison, Jeffrey B. and Di, Xin and +Dickie, Erin W. and Dobryakova, Ekaterina and Donnat, +Claire L. and Dukart, Juergen and Duncan, Niall W. and +Durnez, Joke and Eed, Amr and Eickhoff, Simon B. and +Erhart, Andrew and Fontanesi, Laura and Fricke, G. Matthew +and Fu, Shiguang and Galván, Adriana and Gau, Remi and +Genon, Sarah and Glatard, Tristan and Glerean, Enrico and +Goeman, Jelle J. and Golowin, Sergej A. E. and +González-García, Carlos and Gorgolewski, Krzysztof J. and +Grady, Cheryl L. and Green, Mikella A. and Guassi Moreira, +João F. and Guest, Olivia and Hakimi, Shabnam and +Hamilton, J. Paul and Hancock, Roeland and Handjaras, +Giacomo and Harry, Bronson B. and Hawco, Colin and Herholz, +Peer and Herman, Gabrielle and Heunis, Stephan and +Hoffstaedter, Felix and Hogeveen, Jeremy and Holmes, Susan +and Hu, Chuan-Peng and Huettel, Scott A. and Hughes, +Matthew E. and Iacovella, Vittorio and Iordan, Alexandru D. +and Isager, Peder M. and Isik, Ayse I. and Jahn, Andrew and +Johnson, Matthew R. and Johnstone, Tom and Joseph, Michael +J. E. and Juliano, Anthony C. and Kable, Joseph W. and +Kassinopoulos, Michalis and Koba, Cemal and Kong, +Xiang-Zhen and Koscik, Timothy R. and Kucukboyaci, Nuri +Erkut and Kuhl, Brice A. and Kupek, Sebastian and Laird, +Angela R. and Lamm, Claus and Langner, Robert and +Lauharatanahirun, Nina and Lee, Hongmi and Lee, Sangil and +Leemans, Alexander and Leo, Andrea and Lesage, Elise and +Li, Flora and Li, Monica Y. C. and Lim, Phui Cheng and +Lintz, Evan N. and Liphardt, Schuyler W. and Losecaat +Vermeer, Annabel B. and Love, Bradley C. and Mack, Michael +L. and Malpica, Norberto and Marins, Theo and Maumet, +Camille and McDonald, Kelsey and McGuire, Joseph T. and +Melero, Helena and Méndez Leal, Adriana S. and Meyer, +Benjamin and Meyer, Kristin N. and Mihai, Glad and Mitsis, +Georgios D. and Moll, Jorge and Nielson, Dylan M. and +Nilsonne, Gustav and Notter, Michael P. and Olivetti, +Emanuele and Onicas, Adrian I. and Papale, Paolo and Patil, +Kaustubh R. and Peelle, Jonathan E. and Pérez, Alexandre +and Pischedda, Doris and Poline, Jean-Baptiste and +Prystauka, Yanina and Ray, Shruti and Reuter-Lorenz, +Patricia A. and Reynolds, Richard C. and Ricciardi, +Emiliano and Rieck, Jenny R. and Rodriguez-Thompson, Anais +M. and Romyn, Anthony and Salo, Taylor and Samanez-Larkin, +Gregory R. and Sanz-Morales, Emilio and Schlichting, +Margaret L. and Schultz, Douglas H. and Shen, Qiang and +Sheridan, Margaret A. and Silvers, Jennifer A. and +Skagerlund, Kenny and Smith, Alec and Smith, David V. and +Sokol-Hessner, Peter and Steinkamp, Simon R. and Tashjian, +Sarah M. and Thirion, Bertrand and Thorp, John N. and +Tinghög, Gustav and Tisdall, Loreen and Tompson, Steven H. +and Toro-Serey, Claudio and Torre Tresols, Juan Jesus and +Tozzi, Leonardo and Truong, Vuong and Turella, Luca and van +‘t Veer, Anna E. and Verguts, Tom and Vettel, Jean M. and +Vijayarajah, Sagana and Vo, Khoi and Wall, Matthew B. and +Weeda, Wouter D. and Weis, Susanne and White, David J. and +Wisniewski, David and Xifra-Porxas, Alba and Yearling, +Emily A. and Yoon, Sangsuk and Yuan, Rui and Yuen, Kenneth +S. L. and Zhang, Lei and Zhang, Xu and Zosky, Joshua E. and +Nichols, Thomas E. and Poldrack, Russell A. and Schonberg, +Tom}, + doi = {10.1038/s41586-020-2314-9}, + issn = {1476-4687}, + journal = {Nature}, + month = {May}, + number = {7810}, + pages = {84–88}, + publisher = {Springer Science and Business Media LLC}, + title = {Variability in the analysis of a single neuroimaging +dataset by many teams}, + url = {http://dx.doi.org/10.1038/s41586-020-2314-9}, + volume = {582}, + year = {2020} +} diff --git a/content/publications/botvinik-nezer-2020/index.md b/content/publications/botvinik-nezer-2020/index.md new file mode 100644 index 0000000..25fab64 --- /dev/null +++ b/content/publications/botvinik-nezer-2020/index.md @@ -0,0 +1,210 @@ +--- +title: Variability in the analysis of a single neuroimaging dataset by many teams +authors: +- Rotem Botvinik-Nezer +- Felix Holzmeister +- Colin F. Camerer +- Anna Dreber +- Juergen Huber +- Magnus Johannesson +- Michael Kirchler +- Roni Iwanir +- Jeanette A. Mumford +- R. Alison Adcock +- Paolo Avesani +- Blazej M. Baczkowski +- Aahana Bajracharya +- Leah Bakst +- Sheryl Ball +- Marco Barilari +- Nadège Bault +- Derek Beaton +- Julia Beitner +- Roland G. Benoit +- Ruud M. W. J. Berkers +- Jamil P. Bhanji +- Bharat B. Biswal +- Sebastian Bobadilla-Suarez +- Tiago Bortolini +- Katherine L. Bottenhorn +- Alexander Bowring +- Senne Braem +- Hayley R. Brooks +- Emily G. Brudner +- Cristian B. Calderon +- Julia A. Camilleri +- Jaime J. Castrellon +- Luca Cecchetti +- Edna C. Cieslik +- Zachary J. Cole +- Olivier Collignon +- Robert W. Cox +- William A. Cunningham +- Stefan Czoschke +- Kamalaker Dadi +- Charles P. Davis +- Alberto De Luca +- Mauricio R. Delgado +- Lysia Demetriou +- Jeffrey B. Dennison +- Xin Di +- Erin W. Dickie +- Ekaterina Dobryakova +- Claire L. Donnat +- Juergen Dukart +- Niall W. Duncan +- Joke Durnez +- Amr Eed +- Simon B. Eickhoff +- Andrew Erhart +- Laura Fontanesi +- G. Matthew Fricke +- Shiguang Fu +- Adriana Galván +- Remi Gau +- Sarah Genon +- Tristan Glatard +- Enrico Glerean +- Jelle J. Goeman +- Sergej A. E. Golowin +- Carlos González-García +- Krzysztof J. Gorgolewski +- Cheryl L. Grady +- Mikella A. Green +- João F. Guassi Moreira +- Olivia Guest +- Shabnam Hakimi +- J. Paul Hamilton +- Roeland Hancock +- Giacomo Handjaras +- Bronson B. Harry +- Colin Hawco +- Peer Herholz +- Gabrielle Herman +- Stephan Heunis +- Felix Hoffstaedter +- Jeremy Hogeveen +- Susan Holmes +- Chuan-Peng Hu +- Scott A. Huettel +- Matthew E. Hughes +- Vittorio Iacovella +- Alexandru D. Iordan +- Peder M. Isager +- Ayse I. Isik +- Andrew Jahn +- Matthew R. Johnson +- Tom Johnstone +- Michael J. E. Joseph +- Anthony C. Juliano +- Joseph W. Kable +- Michalis Kassinopoulos +- Cemal Koba +- Xiang-Zhen Kong +- Timothy R. Koscik +- Nuri Erkut Kucukboyaci +- Brice A. Kuhl +- Sebastian Kupek +- Angela R. Laird +- Claus Lamm +- Robert Langner +- Nina Lauharatanahirun +- Hongmi Lee +- Sangil Lee +- Alexander Leemans +- Andrea Leo +- Elise Lesage +- Flora Li +- Monica Y. C. Li +- Phui Cheng Lim +- Evan N. Lintz +- Schuyler W. Liphardt +- Annabel B. Losecaat Vermeer +- Bradley C. Love +- Michael L. Mack +- Norberto Malpica +- Theo Marins +- Camille Maumet +- Kelsey McDonald +- Joseph T. McGuire +- Helena Melero +- Adriana S. Méndez Leal +- Benjamin Meyer +- Kristin N. Meyer +- Glad Mihai +- Georgios D. Mitsis +- Jorge Moll +- Dylan M. Nielson +- Gustav Nilsonne +- Michael P. Notter +- Emanuele Olivetti +- Adrian I. Onicas +- Paolo Papale +- Kaustubh R. Patil +- Jonathan E. Peelle +- Alexandre Pérez +- Doris Pischedda +- Jean-Baptiste Poline +- Yanina Prystauka +- Shruti Ray +- Patricia A. Reuter-Lorenz +- Richard C. Reynolds +- Emiliano Ricciardi +- Jenny R. Rieck +- Anais M. Rodriguez-Thompson +- Anthony Romyn +- Taylor Salo +- Gregory R. Samanez-Larkin +- Emilio Sanz-Morales +- Margaret L. Schlichting +- Douglas H. Schultz +- Qiang Shen +- Margaret A. Sheridan +- Jennifer A. Silvers +- Kenny Skagerlund +- Alec Smith +- David V. Smith +- Peter Sokol-Hessner +- Simon R. Steinkamp +- Sarah M. Tashjian +- Bertrand Thirion +- John N. Thorp +- Gustav Tinghög +- Loreen Tisdall +- Steven H. Tompson +- Claudio Toro-Serey +- Juan Jesus Torre Tresols +- Leonardo Tozzi +- Vuong Truong +- Luca Turella +- Anna E. van ‘t Veer +- Tom Verguts +- Jean M. Vettel +- Sagana Vijayarajah +- Khoi Vo +- Matthew B. Wall +- Wouter D. Weeda +- Susanne Weis +- David J. White +- David Wisniewski +- Alba Xifra-Porxas +- Emily A. Yearling +- Sangsuk Yoon +- Rui Yuan +- Kenneth S. L. Yuen +- Lei Zhang +- Xu Zhang +- Joshua E. Zosky +- Thomas E. Nichols +- Russell A. Poldrack +- Tom Schonberg +date: '2020-05-01' +publishDate: '2024-12-19T23:16:36.382775Z' +publication_types: +- article-journal +publication: '*Nature*' +doi: 10.1038/s41586-020-2314-9 +links: +- name: URL + url: http://dx.doi.org/10.1038/s41586-020-2314-9 +--- diff --git a/content/publications/burdinski-2024/cite.bib b/content/publications/burdinski-2024/cite.bib new file mode 100644 index 0000000..2125a8d --- /dev/null +++ b/content/publications/burdinski-2024/cite.bib @@ -0,0 +1,12 @@ +@article{burdinski_2024, + author = {Burdinski, Debbie and Kodibagkar, Alisha and Potter, Kevin +and Schuster, Randi and Evins, A. Eden and Ghosh, Satrajit +and Gilman, Jodi}, + doi = {10.1101/2024.04.29.24306516}, + month = {May}, + publisher = {Cold Spring Harbor Laboratory}, + title = {Impact of year-long cannabis use for medical symptoms on +brain activation during cognitive processes}, + url = {http://dx.doi.org/10.1101/2024.04.29.24306516}, + year = {2024} +} diff --git a/content/publications/burdinski-2024/index.md b/content/publications/burdinski-2024/index.md new file mode 100644 index 0000000..8692f74 --- /dev/null +++ b/content/publications/burdinski-2024/index.md @@ -0,0 +1,21 @@ +--- +title: Impact of year-long cannabis use for medical symptoms on brain activation during + cognitive processes +authors: +- Debbie Burdinski +- Alisha Kodibagkar +- Kevin Potter +- Randi Schuster +- A. Eden Evins +- Satrajit Ghosh +- Jodi Gilman +date: '2024-05-01' +publishDate: '2024-12-19T23:16:36.390525Z' +publication_types: +- article-journal +publication: '*Cold Spring Harbor Laboratory*' +doi: 10.1101/2024.04.29.24306516 +links: +- name: URL + url: http://dx.doi.org/10.1101/2024.04.29.24306516 +--- diff --git a/content/publications/charles-2020/cite.bib b/content/publications/charles-2020/cite.bib new file mode 100644 index 0000000..a01c2fb --- /dev/null +++ b/content/publications/charles-2020/cite.bib @@ -0,0 +1,19 @@ +@article{charles_2020, + author = {Charles, Adam S. and Falk, Benjamin and Turner, Nicholas +and Pereira, Talmo D. and Tward, Daniel and Pedigo, +Benjamin D. and Chung, Jaewon and Burns, Randal and Ghosh, +Satrajit S. and Kebschull, Justus M. and Silversmith, +William and Vogelstein, Joshua T.}, + doi = {10.1146/annurev-neuro-100119-110036}, + issn = {1545-4126}, + journal = {Annual Review of Neuroscience}, + month = {July}, + number = {1}, + pages = {441–464}, + publisher = {Annual Reviews}, + title = {Toward Community-Driven Big Open Brain Science: Open Big +Data and Tools for Structure, Function, and Genetics}, + url = {http://dx.doi.org/10.1146/annurev-neuro-100119-110036}, + volume = {43}, + year = {2020} +} diff --git a/content/publications/charles-2020/index.md b/content/publications/charles-2020/index.md new file mode 100644 index 0000000..fb3db14 --- /dev/null +++ b/content/publications/charles-2020/index.md @@ -0,0 +1,26 @@ +--- +title: 'Toward Community-Driven Big Open Brain Science: Open Big Data and Tools for + Structure, Function, and Genetics' +authors: +- Adam S. Charles +- Benjamin Falk +- Nicholas Turner +- Talmo D. Pereira +- Daniel Tward +- Benjamin D. Pedigo +- Jaewon Chung +- Randal Burns +- Satrajit S. Ghosh +- Justus M. Kebschull +- William Silversmith +- Joshua T. Vogelstein +date: '2020-07-01' +publishDate: '2024-12-19T23:16:36.394656Z' +publication_types: +- article-journal +publication: '*Annual Review of Neuroscience*' +doi: 10.1146/annurev-neuro-100119-110036 +links: +- name: URL + url: http://dx.doi.org/10.1146/annurev-neuro-100119-110036 +--- diff --git a/content/publications/cheng-2020/cite.bib b/content/publications/cheng-2020/cite.bib new file mode 100644 index 0000000..4d51d96 --- /dev/null +++ b/content/publications/cheng-2020/cite.bib @@ -0,0 +1,14 @@ +@article{cheng_2020, + author = {Cheng, Christopher P. and Halchenko, Yaroslav O.}, + doi = {10.12688/f1000research.24544.1}, + issn = {2046-1402}, + journal = {F1000Research}, + month = {September}, + pages = {1131}, + publisher = {F1000 Research Ltd}, + title = {A new virtue of phantom MRI data: explaining variance in +human participant data}, + url = {http://dx.doi.org/10.12688/f1000research.24544.1}, + volume = {9}, + year = {2020} +} diff --git a/content/publications/cheng-2020/index.md b/content/publications/cheng-2020/index.md new file mode 100644 index 0000000..0c7139a --- /dev/null +++ b/content/publications/cheng-2020/index.md @@ -0,0 +1,16 @@ +--- +title: 'A new virtue of phantom MRI data: explaining variance in human participant + data' +authors: +- Christopher P. Cheng +- Yaroslav O. Halchenko +date: '2020-09-01' +publishDate: '2024-12-19T23:16:36.398756Z' +publication_types: +- article-journal +publication: '*F1000Research*' +doi: 10.12688/f1000research.24544.1 +links: +- name: URL + url: http://dx.doi.org/10.12688/f1000research.24544.1 +--- diff --git a/content/publications/ciric-2022/cite.bib b/content/publications/ciric-2022/cite.bib new file mode 100644 index 0000000..26ee77d --- /dev/null +++ b/content/publications/ciric-2022/cite.bib @@ -0,0 +1,19 @@ +@article{ciric_2022, + author = {Ciric, Rastko and Thompson, William H. and Lorenz, Romy +and Goncalves, Mathias and MacNicol, Eilidh E. and +Markiewicz, Christopher J. and Halchenko, Yaroslav O. and +Ghosh, Satrajit S. and Gorgolewski, Krzysztof J. and +Poldrack, Russell A. and Esteban, Oscar}, + doi = {10.1038/s41592-022-01681-2}, + issn = {1548-7105}, + journal = {Nature Methods}, + month = {December}, + number = {12}, + pages = {1568–1571}, + publisher = {Springer Science and Business Media LLC}, + title = {TemplateFlow: FAIR-sharing of multi-scale, multi-species +brain models}, + url = {http://dx.doi.org/10.1038/s41592-022-01681-2}, + volume = {19}, + year = {2022} +} diff --git a/content/publications/ciric-2022/index.md b/content/publications/ciric-2022/index.md new file mode 100644 index 0000000..f82e59f --- /dev/null +++ b/content/publications/ciric-2022/index.md @@ -0,0 +1,24 @@ +--- +title: 'TemplateFlow: FAIR-sharing of multi-scale, multi-species brain models' +authors: +- Rastko Ciric +- William H. Thompson +- Romy Lorenz +- Mathias Goncalves +- Eilidh E. MacNicol +- Christopher J. Markiewicz +- Yaroslav O. Halchenko +- Satrajit S. Ghosh +- Krzysztof J. Gorgolewski +- Russell A. Poldrack +- Oscar Esteban +date: '2022-12-01' +publishDate: '2024-12-19T23:16:36.402766Z' +publication_types: +- article-journal +publication: '*Nature Methods*' +doi: 10.1038/s41592-022-01681-2 +links: +- name: URL + url: http://dx.doi.org/10.1038/s41592-022-01681-2 +--- diff --git a/content/publications/cruces-2022/cite.bib b/content/publications/cruces-2022/cite.bib new file mode 100644 index 0000000..9872b58 --- /dev/null +++ b/content/publications/cruces-2022/cite.bib @@ -0,0 +1,20 @@ +@article{cruces_2022, + author = {Cruces, Raúl R. and Royer, Jessica and Herholz, Peer and +Larivière, Sara and Vos de Wael, Reinder and Paquola, +Casey and Benkarim, Oualid and Park, Bo-yong and +Degré-Pelletier, Janie and Nelson, Mark C. and DeKraker, +Jordan and Leppert, Ilana R. and Tardif, Christine and +Poline, Jean-Baptiste and Concha, Luis and Bernhardt, Boris +C.}, + doi = {10.1016/j.neuroimage.2022.119612}, + issn = {1053-8119}, + journal = {NeuroImage}, + month = {November}, + pages = {119612}, + publisher = {Elsevier BV}, + title = {Micapipe: A pipeline for multimodal neuroimaging and +connectome analysis}, + url = {http://dx.doi.org/10.1016/j.neuroimage.2022.119612}, + volume = {263}, + year = {2022} +} diff --git a/content/publications/cruces-2022/index.md b/content/publications/cruces-2022/index.md new file mode 100644 index 0000000..80fa0c5 --- /dev/null +++ b/content/publications/cruces-2022/index.md @@ -0,0 +1,29 @@ +--- +title: 'Micapipe: A pipeline for multimodal neuroimaging and connectome analysis' +authors: +- Raúl R. Cruces +- Jessica Royer +- Peer Herholz +- Sara Larivière +- Reinder Vos de Wael +- Casey Paquola +- Oualid Benkarim +- Bo-yong Park +- Janie Degré-Pelletier +- Mark C. Nelson +- Jordan DeKraker +- Ilana R. Leppert +- Christine Tardif +- Jean-Baptiste Poline +- Luis Concha +- Boris C. Bernhardt +date: '2022-11-01' +publishDate: '2024-12-19T23:16:36.407061Z' +publication_types: +- article-journal +publication: '*NeuroImage*' +doi: 10.1016/j.neuroimage.2022.119612 +links: +- name: URL + url: http://dx.doi.org/10.1016/j.neuroimage.2022.119612 +--- diff --git a/content/publications/de-la-vega-2022/cite.bib b/content/publications/de-la-vega-2022/cite.bib new file mode 100644 index 0000000..7dc8786 --- /dev/null +++ b/content/publications/de-la-vega-2022/cite.bib @@ -0,0 +1,16 @@ +@article{de_la_vega_2022, + author = {de la Vega, Alejandro and Rocca, Roberta and Blair, Ross W +and Markiewicz, Christopher J and Mentch, Jeff and Kent, +James D and Herholz, Peer and Ghosh, Satrajit S and +Poldrack, Russell A and Yarkoni, Tal}, + doi = {10.7554/elife.79277}, + issn = {2050-084X}, + journal = {eLife}, + month = {August}, + publisher = {eLife Sciences Publications, Ltd}, + title = {Neuroscout, a unified platform for generalizable and +reproducible fMRI research}, + url = {http://dx.doi.org/10.7554/elife.79277}, + volume = {11}, + year = {2022} +} diff --git a/content/publications/de-la-vega-2022/index.md b/content/publications/de-la-vega-2022/index.md new file mode 100644 index 0000000..cc7ba08 --- /dev/null +++ b/content/publications/de-la-vega-2022/index.md @@ -0,0 +1,23 @@ +--- +title: Neuroscout, a unified platform for generalizable and reproducible fMRI research +authors: +- Alejandro de la Vega +- Roberta Rocca +- Ross W Blair +- Christopher J Markiewicz +- Jeff Mentch +- James D Kent +- Peer Herholz +- Satrajit S Ghosh +- Russell A Poldrack +- Tal Yarkoni +date: '2022-08-01' +publishDate: '2024-12-19T23:16:36.411316Z' +publication_types: +- article-journal +publication: '*eLife*' +doi: 10.7554/elife.79277 +links: +- name: URL + url: http://dx.doi.org/10.7554/elife.79277 +--- diff --git a/content/publications/dock-s-2021/cite.bib b/content/publications/dock-s-2021/cite.bib new file mode 100644 index 0000000..36437f7 --- /dev/null +++ b/content/publications/dock-s-2021/cite.bib @@ -0,0 +1,15 @@ +@article{dock_s_2021, + author = {Dockès, Jérôme and Varoquaux, Gaël and Poline, +Jean-Baptiste}, + doi = {10.1093/gigascience/giab055}, + issn = {2047-217X}, + journal = {GigaScience}, + month = {September}, + number = {9}, + publisher = {Oxford University Press (OUP)}, + title = {Preventing dataset shift from breaking machine-learning +biomarkers}, + url = {http://dx.doi.org/10.1093/gigascience/giab055}, + volume = {10}, + year = {2021} +} diff --git a/content/publications/dock-s-2021/index.md b/content/publications/dock-s-2021/index.md new file mode 100644 index 0000000..98532a1 --- /dev/null +++ b/content/publications/dock-s-2021/index.md @@ -0,0 +1,16 @@ +--- +title: Preventing dataset shift from breaking machine-learning biomarkers +authors: +- Jérôme Dockès +- Gaël Varoquaux +- Jean-Baptiste Poline +date: '2021-09-01' +publishDate: '2024-12-19T23:16:36.415505Z' +publication_types: +- article-journal +publication: '*GigaScience*' +doi: 10.1093/gigascience/giab055 +links: +- name: URL + url: http://dx.doi.org/10.1093/gigascience/giab055 +--- diff --git a/content/publications/dupre-2020/cite.bib b/content/publications/dupre-2020/cite.bib new file mode 100644 index 0000000..2aaedb9 --- /dev/null +++ b/content/publications/dupre-2020/cite.bib @@ -0,0 +1,15 @@ +@article{dupre_2020, + author = {DuPre, Elizabeth and Hanke, Michael and Poline, +Jean-Baptiste}, + doi = {10.1016/j.neuroimage.2019.116330}, + issn = {1053-8119}, + journal = {NeuroImage}, + month = {August}, + pages = {116330}, + publisher = {Elsevier BV}, + title = {Nature abhors a paywall: How open science can realize the +potential of naturalistic stimuli}, + url = {http://dx.doi.org/10.1016/j.neuroimage.2019.116330}, + volume = {216}, + year = {2020} +} diff --git a/content/publications/dupre-2020/index.md b/content/publications/dupre-2020/index.md new file mode 100644 index 0000000..60b4862 --- /dev/null +++ b/content/publications/dupre-2020/index.md @@ -0,0 +1,17 @@ +--- +title: 'Nature abhors a paywall: How open science can realize the potential of naturalistic + stimuli' +authors: +- Elizabeth DuPre +- Michael Hanke +- Jean-Baptiste Poline +date: '2020-08-01' +publishDate: '2024-12-19T23:16:36.419456Z' +publication_types: +- article-journal +publication: '*NeuroImage*' +doi: 10.1016/j.neuroimage.2019.116330 +links: +- name: URL + url: http://dx.doi.org/10.1016/j.neuroimage.2019.116330 +--- diff --git a/content/publications/dupre-2022/cite.bib b/content/publications/dupre-2022/cite.bib new file mode 100644 index 0000000..b934aa5 --- /dev/null +++ b/content/publications/dupre-2022/cite.bib @@ -0,0 +1,18 @@ +@article{dupre_2022, + author = {DuPre, Elizabeth and Holdgraf, Chris and Karakuzu, Agah +and Tetrel, Loïc and Bellec, Pierre and Stikov, Nikola and +Poline, Jean-Baptiste}, + doi = {10.1371/journal.pcbi.1009651}, + editor = {Mac Gabhann, Feilim}, + issn = {1553-7358}, + journal = {PLOS Computational Biology}, + month = {January}, + number = {1}, + pages = {e1009651}, + publisher = {Public Library of Science (PLoS)}, + title = {Beyond advertising: New infrastructures for publishing +integrated research objects}, + url = {http://dx.doi.org/10.1371/journal.pcbi.1009651}, + volume = {18}, + year = {2022} +} diff --git a/content/publications/dupre-2022/index.md b/content/publications/dupre-2022/index.md new file mode 100644 index 0000000..36f2c41 --- /dev/null +++ b/content/publications/dupre-2022/index.md @@ -0,0 +1,21 @@ +--- +title: 'Beyond advertising: New infrastructures for publishing integrated research + objects' +authors: +- Elizabeth DuPre +- Chris Holdgraf +- Agah Karakuzu +- Loïc Tetrel +- Pierre Bellec +- Nikola Stikov +- Jean-Baptiste Poline +date: '2022-01-01' +publishDate: '2024-12-19T23:16:36.423494Z' +publication_types: +- article-journal +publication: '*PLOS Computational Biology*' +doi: 10.1371/journal.pcbi.1009651 +links: +- name: URL + url: http://dx.doi.org/10.1371/journal.pcbi.1009651 +--- diff --git a/content/publications/eglen-2017/cite.bib b/content/publications/eglen-2017/cite.bib new file mode 100644 index 0000000..0b9e3ff --- /dev/null +++ b/content/publications/eglen-2017/cite.bib @@ -0,0 +1,19 @@ +@article{eglen_2017, + author = {Eglen, Stephen J and Marwick, Ben and Halchenko, Yaroslav +O and Hanke, Michael and Sufi, Shoaib and Gleeson, Padraig +and Silver, R Angus and Davison, Andrew P and Lanyon, Linda +and Abrams, Mathew and Wachtler, Thomas and Willshaw, David +J and Pouzat, Christophe and Poline, Jean-Baptiste}, + doi = {10.1038/nn.4550}, + issn = {1546-1726}, + journal = {Nature Neuroscience}, + month = {June}, + number = {6}, + pages = {770–773}, + publisher = {Springer Science and Business Media LLC}, + title = {Toward standard practices for sharing computer code and +programs in neuroscience}, + url = {http://dx.doi.org/10.1038/nn.4550}, + volume = {20}, + year = {2017} +} diff --git a/content/publications/eglen-2017/index.md b/content/publications/eglen-2017/index.md new file mode 100644 index 0000000..b72301e --- /dev/null +++ b/content/publications/eglen-2017/index.md @@ -0,0 +1,27 @@ +--- +title: Toward standard practices for sharing computer code and programs in neuroscience +authors: +- Stephen J Eglen +- Ben Marwick +- Yaroslav O Halchenko +- Michael Hanke +- Shoaib Sufi +- Padraig Gleeson +- R Angus Silver +- Andrew P Davison +- Linda Lanyon +- Mathew Abrams +- Thomas Wachtler +- David J Willshaw +- Christophe Pouzat +- Jean-Baptiste Poline +date: '2017-06-01' +publishDate: '2024-12-19T23:16:36.427626Z' +publication_types: +- article-journal +publication: '*Nature Neuroscience*' +doi: 10.1038/nn.4550 +links: +- name: URL + url: http://dx.doi.org/10.1038/nn.4550 +--- diff --git a/content/publications/eke-2022/cite.bib b/content/publications/eke-2022/cite.bib new file mode 100644 index 0000000..f8f4b82 --- /dev/null +++ b/content/publications/eke-2022/cite.bib @@ -0,0 +1,18 @@ +@article{eke_2022, + author = {Eke, Damian O. and Bernard, Amy and Bjaalie, Jan G. and +Chavarriaga, Ricardo and Hanakawa, Takashi and Hannan, +Anthony J. and Hill, Sean L. and Martone, Maryann E. and +McMahon, Agnes and Ruebel, Oliver and Crook, Sharon and +Thiels, Edda and Pestilli, Franco}, + doi = {10.1016/j.neuron.2021.11.017}, + issn = {0896-6273}, + journal = {Neuron}, + month = {February}, + number = {4}, + pages = {600–612}, + publisher = {Elsevier BV}, + title = {International data governance for neuroscience}, + url = {http://dx.doi.org/10.1016/j.neuron.2021.11.017}, + volume = {110}, + year = {2022} +} diff --git a/content/publications/eke-2022/index.md b/content/publications/eke-2022/index.md new file mode 100644 index 0000000..401a289 --- /dev/null +++ b/content/publications/eke-2022/index.md @@ -0,0 +1,26 @@ +--- +title: International data governance for neuroscience +authors: +- Damian O. Eke +- Amy Bernard +- Jan G. Bjaalie +- Ricardo Chavarriaga +- Takashi Hanakawa +- Anthony J. Hannan +- Sean L. Hill +- Maryann E. Martone +- Agnes McMahon +- Oliver Ruebel +- Sharon Crook +- Edda Thiels +- Franco Pestilli +date: '2022-02-01' +publishDate: '2024-12-19T23:16:36.432048Z' +publication_types: +- article-journal +publication: '*Neuron*' +doi: 10.1016/j.neuron.2021.11.017 +links: +- name: URL + url: http://dx.doi.org/10.1016/j.neuron.2021.11.017 +--- diff --git a/content/publications/esteban-2020/cite.bib b/content/publications/esteban-2020/cite.bib new file mode 100644 index 0000000..f6e91d6 --- /dev/null +++ b/content/publications/esteban-2020/cite.bib @@ -0,0 +1,25 @@ +@article{esteban_2020, + author = {Esteban, Oscar and Ciric, Rastko and Finc, Karolina and +Blair, Ross W. and Markiewicz, Christopher J. and Moodie, +Craig A. and Kent, James D. and Goncalves, Mathias and +DuPre, Elizabeth and Gomez, Daniel E. P. and Ye, Zhifang +and Salo, Taylor and Valabregue, Romain and Amlien, Inge K. +and Liem, Franziskus and Jacoby, Nir and Stojić, Hrvoje +and Cieslak, Matthew and Urchs, Sebastian and Halchenko, +Yaroslav O. and Ghosh, Satrajit S. and De La Vega, +Alejandro and Yarkoni, Tal and Wright, Jessey and Thompson, +William H. and Poldrack, Russell A. and Gorgolewski, +Krzysztof J.}, + doi = {10.1038/s41596-020-0327-3}, + issn = {1750-2799}, + journal = {Nature Protocols}, + month = {June}, + number = {7}, + pages = {2186–2202}, + publisher = {Springer Science and Business Media LLC}, + title = {Analysis of task-based functional MRI data preprocessed +with fMRIPrep}, + url = {http://dx.doi.org/10.1038/s41596-020-0327-3}, + volume = {15}, + year = {2020} +} diff --git a/content/publications/esteban-2020/index.md b/content/publications/esteban-2020/index.md new file mode 100644 index 0000000..2c6b91b --- /dev/null +++ b/content/publications/esteban-2020/index.md @@ -0,0 +1,40 @@ +--- +title: Analysis of task-based functional MRI data preprocessed with fMRIPrep +authors: +- Oscar Esteban +- Rastko Ciric +- Karolina Finc +- Ross W. Blair +- Christopher J. Markiewicz +- Craig A. Moodie +- James D. Kent +- Mathias Goncalves +- Elizabeth DuPre +- Daniel E. P. Gomez +- Zhifang Ye +- Taylor Salo +- Romain Valabregue +- Inge K. Amlien +- Franziskus Liem +- Nir Jacoby +- Hrvoje Stojić +- Matthew Cieslak +- Sebastian Urchs +- Yaroslav O. Halchenko +- Satrajit S. Ghosh +- Alejandro De La Vega +- Tal Yarkoni +- Jessey Wright +- William H. Thompson +- Russell A. Poldrack +- Krzysztof J. Gorgolewski +date: '2020-06-01' +publishDate: '2024-12-19T23:16:36.436338Z' +publication_types: +- article-journal +publication: '*Nature Protocols*' +doi: 10.1038/s41596-020-0327-3 +links: +- name: URL + url: http://dx.doi.org/10.1038/s41596-020-0327-3 +--- diff --git a/content/publications/fenner-2019/cite.bib b/content/publications/fenner-2019/cite.bib new file mode 100644 index 0000000..aa4ad01 --- /dev/null +++ b/content/publications/fenner-2019/cite.bib @@ -0,0 +1,16 @@ +@article{fenner_2019, + author = {Fenner, Martin and Crosas, Mercè and Grethe, Jeffrey S. +and Kennedy, David and Hermjakob, Henning and Rocca-Serra, +Phillippe and Durand, Gustavo and Berjon, Robin and +Karcher, Sebastian and Martone, Maryann and Clark, Tim}, + doi = {10.1038/s41597-019-0031-8}, + issn = {2052-4463}, + journal = {Scientific Data}, + month = {April}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {A data citation roadmap for scholarly data repositories}, + url = {http://dx.doi.org/10.1038/s41597-019-0031-8}, + volume = {6}, + year = {2019} +} diff --git a/content/publications/fenner-2019/index.md b/content/publications/fenner-2019/index.md new file mode 100644 index 0000000..db4817b --- /dev/null +++ b/content/publications/fenner-2019/index.md @@ -0,0 +1,24 @@ +--- +title: A data citation roadmap for scholarly data repositories +authors: +- Martin Fenner +- Mercè Crosas +- Jeffrey S. Grethe +- David Kennedy +- Henning Hermjakob +- Phillippe Rocca-Serra +- Gustavo Durand +- Robin Berjon +- Sebastian Karcher +- Maryann Martone +- Tim Clark +date: '2019-04-01' +publishDate: '2024-12-19T23:16:36.441113Z' +publication_types: +- article-journal +publication: '*Scientific Data*' +doi: 10.1038/s41597-019-0031-8 +links: +- name: URL + url: http://dx.doi.org/10.1038/s41597-019-0031-8 +--- diff --git a/content/publications/ferris-2023/cite.bib b/content/publications/ferris-2023/cite.bib new file mode 100644 index 0000000..ea34d92 --- /dev/null +++ b/content/publications/ferris-2023/cite.bib @@ -0,0 +1,15 @@ +@article{ferris_2023, + author = {Ferris, Jennifer K. and Lo, Bethany P. and Khlif, Mohamed +Salah and Brodtmann, Amy and Boyd, Lara A. and Liew, +Sook-Lei}, + doi = {10.3389/fnimg.2023.1099301}, + issn = {2813-1193}, + journal = {Frontiers in Neuroimaging}, + month = {March}, + publisher = {Frontiers Media SA}, + title = {Optimizing automated white matter hyperintensity +segmentation in individuals with stroke}, + url = {http://dx.doi.org/10.3389/fnimg.2023.1099301}, + volume = {2}, + year = {2023} +} diff --git a/content/publications/ferris-2023/index.md b/content/publications/ferris-2023/index.md new file mode 100644 index 0000000..c999843 --- /dev/null +++ b/content/publications/ferris-2023/index.md @@ -0,0 +1,20 @@ +--- +title: Optimizing automated white matter hyperintensity segmentation in individuals + with stroke +authors: +- Jennifer K. Ferris +- Bethany P. Lo +- Mohamed Salah Khlif +- Amy Brodtmann +- Lara A. Boyd +- Sook-Lei Liew +date: '2023-03-01' +publishDate: '2024-12-19T23:16:36.445225Z' +publication_types: +- article-journal +publication: '*Frontiers in Neuroimaging*' +doi: 10.3389/fnimg.2023.1099301 +links: +- name: URL + url: http://dx.doi.org/10.3389/fnimg.2023.1099301 +--- diff --git a/content/publications/fitzpatrick-2019/cite.bib b/content/publications/fitzpatrick-2019/cite.bib new file mode 100644 index 0000000..27e76b3 --- /dev/null +++ b/content/publications/fitzpatrick-2019/cite.bib @@ -0,0 +1,14 @@ +@article{fitzpatrick_2019, + author = {Fitzpatrick, Paula and Mitchell, Teresa and Schmidt, R.C. +and Kennedy, David and Frazier, Jean A.}, + doi = {10.1016/j.neulet.2019.01.037}, + issn = {0304-3940}, + journal = {Neuroscience Letters}, + month = {April}, + pages = {24–30}, + publisher = {Elsevier BV}, + title = {Alpha band signatures of social synchrony}, + url = {http://dx.doi.org/10.1016/j.neulet.2019.01.037}, + volume = {699}, + year = {2019} +} diff --git a/content/publications/fitzpatrick-2019/index.md b/content/publications/fitzpatrick-2019/index.md new file mode 100644 index 0000000..6dd0cd9 --- /dev/null +++ b/content/publications/fitzpatrick-2019/index.md @@ -0,0 +1,18 @@ +--- +title: Alpha band signatures of social synchrony +authors: +- Paula Fitzpatrick +- Teresa Mitchell +- R.C. Schmidt +- David Kennedy +- Jean A. Frazier +date: '2019-04-01' +publishDate: '2024-12-19T23:16:36.449205Z' +publication_types: +- article-journal +publication: '*Neuroscience Letters*' +doi: 10.1016/j.neulet.2019.01.037 +links: +- name: URL + url: http://dx.doi.org/10.1016/j.neulet.2019.01.037 +--- diff --git a/content/publications/gan-or-2020/cite.bib b/content/publications/gan-or-2020/cite.bib new file mode 100644 index 0000000..4053c69 --- /dev/null +++ b/content/publications/gan-or-2020/cite.bib @@ -0,0 +1,25 @@ +@article{gan_or_2020, + author = {Gan-Or, Ziv and Rao, Trisha and Leveille, Etienne and +Degroot, Clotilde and Chouinard, Sylvain and Cicchetti, +Francesca and Dagher, Alain and Das, Samir and Desautels, +Alex and Drouin-Ouellet, Janelle and Durcan, Thomas and +Gagnon, Jean-François and Genge, Angela and Karamchandani, +Jason and Lafontaine, Anne-Louise and Sun, Sonia Lai Wing +and Langlois, Mélanie and Levesque, Martin and Melmed, +Calvin and Panisset, Michel and Parent, Martin and Poline, +Jean-Baptiste and Postuma, Ronald B. and Pourcher, +Emmanuelle and Rouleau, Guy A. and Sharp, Madeleine and +Monchi, Oury and Dupré, Nicolas and Fon, Edward A.}, + doi = {10.3233/jpd-191775}, + issn = {1877-718X}, + journal = {Journal of Parkinson’s Disease}, + month = {January}, + number = {1}, + pages = {301–313}, + publisher = {SAGE Publications}, + title = {The Quebec Parkinson Network: A Researcher-Patient +Matching Platform and Multimodal Biorepository}, + url = {http://dx.doi.org/10.3233/jpd-191775}, + volume = {10}, + year = {2020} +} diff --git a/content/publications/gan-or-2020/index.md b/content/publications/gan-or-2020/index.md new file mode 100644 index 0000000..e3d527a --- /dev/null +++ b/content/publications/gan-or-2020/index.md @@ -0,0 +1,43 @@ +--- +title: 'The Quebec Parkinson Network: A Researcher-Patient Matching Platform and Multimodal + Biorepository' +authors: +- Ziv Gan-Or +- Trisha Rao +- Etienne Leveille +- Clotilde Degroot +- Sylvain Chouinard +- Francesca Cicchetti +- Alain Dagher +- Samir Das +- Alex Desautels +- Janelle Drouin-Ouellet +- Thomas Durcan +- Jean-François Gagnon +- Angela Genge +- Jason Karamchandani +- Anne-Louise Lafontaine +- Sonia Lai Wing Sun +- Mélanie Langlois +- Martin Levesque +- Calvin Melmed +- Michel Panisset +- Martin Parent +- Jean-Baptiste Poline +- Ronald B. Postuma +- Emmanuelle Pourcher +- Guy A. Rouleau +- Madeleine Sharp +- Oury Monchi +- Nicolas Dupré +- Edward A. Fon +date: '2020-01-01' +publishDate: '2024-12-19T23:16:36.453155Z' +publication_types: +- article-journal +publication: '*Journal of Parkinson’s Disease*' +doi: 10.3233/jpd-191775 +links: +- name: URL + url: http://dx.doi.org/10.3233/jpd-191775 +--- diff --git a/content/publications/gau-2021/cite.bib b/content/publications/gau-2021/cite.bib new file mode 100644 index 0000000..5cb0220 --- /dev/null +++ b/content/publications/gau-2021/cite.bib @@ -0,0 +1,98 @@ +@article{gau_2021, + author = {Gau, Rémi and Noble, Stephanie and Heuer, Katja and +Bottenhorn, Katherine L. and Bilgin, Isil P. and Yang, +Yu-Fang and Huntenburg, Julia M. and Bayer, Johanna M.M. +and Bethlehem, Richard A.I. and Rhoads, Shawn A. and +Vogelbacher, Christoph and Borghesani, Valentina and +Levitis, Elizabeth and Wang, Hao-Ting and Van Den Bossche, +Sofie and Kobeleva, Xenia and Legarreta, Jon Haitz and +Guay, Samuel and Atay, Selim Melvin and Varoquaux, Gael P. +and Huijser, Dorien C. and Sandström, Malin S. and +Herholz, Peer and Nastase, Samuel A. and Badhwar, AmanPreet +and Dumas, Guillaume and Schwab, Simon and Moia, Stefano +and Dayan, Michael and Bassil, Yasmine and Brooks, Paula P. +and Mancini, Matteo and Shine, James M. and O’Connor, +David and Xie, Xihe and Poggiali, Davide and Friedrich, +Patrick and Heinsfeld, Anibal S. and Riedl, Lydia and Toro, +Roberto and Caballero-Gaudes, César and Eklund, Anders and +Garner, Kelly G. and Nolan, Christopher R. and Demeter, +Damion V. and Barrios, Fernando A. and Merchant, Junaid S. +and McDevitt, Elizabeth A. and Oostenveld, Robert and +Craddock, R. Cameron and Rokem, Ariel and Doyle, Andrew and +Ghosh, Satrajit S. and Nikolaidis, Aki and Stanley, Olivia +W. and Uruñuela, Eneko and Anousheh, Nasim and +Arnatkeviciute, Aurina and Auzias, Guillaume and Bachar, +Dipankar and Bannier, Elise and Basanisi, Ruggero and +Basavaraj, Arshitha and Bedini, Marco and Bellec, Pierre +and Benn, R. Austin and Berluti, Kathryn and Bollmann, +Steffen and Bollmann, Saskia and Bradley, Claire and Brown, +Jesse and Buchweitz, Augusto and Callahan, Patrick and +Chan, Micaela Y. and Chandio, Bramsh Q. and Cheng, Theresa +and Chopra, Sidhant and Chung, Ai Wern and Close, Thomas G. +and Combrisson, Etienne and Cona, Giorgia and Constable, R. +Todd and Cury, Claire and Dadi, Kamalaker and Damasceno, +Pablo F. and Das, Samir and De Vico Fallani, Fabrizio and +DeStasio, Krista and Dickie, Erin W. and Dorfschmidt, Lena +and Duff, Eugene P. and DuPre, Elizabeth and Dziura, Sarah +and Esper, Nathalia B. and Esteban, Oscar and Fadnavis, +Shreyas and Flandin, Guillaume and Flannery, Jessica E. and +Flournoy, John and Forkel, Stephanie J. and Franco, +Alexandre R. and Ganesan, Saampras and Gao, Siyuan and +García Alanis, José C. and Garyfallidis, Eleftherios and +Glatard, Tristan and Glerean, Enrico and Gonzalez-Castillo, +Javier and Gould van Praag, Cassandra D. and Greene, +Abigail S. and Gupta, Geetika and Hahn, Catherine Alice and +Halchenko, Yaroslav O. and Handwerker, Daniel and Hartmann, +Thomas S. and Hayot-Sasson, Valérie and Heunis, Stephan +and Hoffstaedter, Felix and Hohmann, Daniela M. and Horien, +Corey and Ioanas, Horea-Ioan and Iordan, Alexandru and +Jiang, Chao and Joseph, Michael and Kai, Jason and +Karakuzu, Agah and Kennedy, David N. and Keshavan, Anisha +and Khan, Ali R. and Kiar, Gregory and Klink, P. Christiaan +and Koppelmans, Vincent and Koudoro, Serge and Laird, +Angela R. and Langs, Georg and Laws, Marissa and Licandro, +Roxane and Liew, Sook-Lei and Lipic, Tomislav and Litinas, +Krisanne and Lurie, Daniel J. and Lussier, Désirée and +Madan, Christopher R. and Mais, Lea-Theresa and Mansour L, +Sina and Manzano-Patron, J.P. and Maoutsa, Dimitra and +Marcon, Matheus and Margulies, Daniel S. and Marinato, +Giorgio and Marinazzo, Daniele and Markiewicz, Christopher +J. and Maumet, Camille and Meneguzzi, Felipe and Meunier, +David and Milham, Michael P. and Mills, Kathryn L. and +Momi, Davide and Moreau, Clara A. and Motala, Aysha and +Moxon-Emre, Iska and Nichols, Thomas E. and Nielson, Dylan +M. and Nilsonne, Gustav and Novello, Lisa and O’Brien, +Caroline and Olafson, Emily and Oliver, Lindsay D. and +Onofrey, John A. and Orchard, Edwina R. and Oudyk, Kendra +and Park, Patrick J. and Parsapoor, Mahboobeh and Pasquini, +Lorenzo and Peltier, Scott and Pernet, Cyril R. and +Pienaar, Rudolph and Pinheiro-Chagas, Pedro and Poline, +Jean-Baptiste and Qiu, Anqi and Quendera, Tiago and Rice, +Laura C. and Rocha-Hidalgo, Joscelin and Rutherford, Saige +and Scharinger, Mathias and Scheinost, Dustin and Shariq, +Deena and Shaw, Thomas B. and Siless, Viviana and +Simmonite, Molly and Sirmpilatze, Nikoloz and Spence, Hayli +and Sprenger, Julia and Stajduhar, Andrija and Szinte, +Martin and Takerkart, Sylvain and Tam, Angela and +Tejavibulya, Link and Thiebaut de Schotten, Michel and +Thome, Ina and Tomaz da Silva, Laura and Traut, Nicolas and +Uddin, Lucina Q. and Vallesi, Antonino and VanMeter, John +W. and Vijayakumar, Nandita and di Oleggio Castello, Matteo +Visconti and Vohryzek, Jakub and Vukojević, Jakša and +Whitaker, Kirstie Jane and Whitmore, Lucy and Wideman, +Steve and Witt, Suzanne T. and Xie, Hua and Xu, Ting and +Yan, Chao-Gan and Yeh, Fang-Cheng and Yeo, B.T. Thomas and +Zuo, Xi-Nian}, + doi = {10.1016/j.neuron.2021.04.001}, + issn = {0896-6273}, + journal = {Neuron}, + month = {June}, + number = {11}, + pages = {1769–1775}, + publisher = {Elsevier BV}, + title = {Brainhack: Developing a culture of open, inclusive, +community-driven neuroscience}, + url = {http://dx.doi.org/10.1016/j.neuron.2021.04.001}, + volume = {109}, + year = {2021} +} diff --git a/content/publications/gau-2021/index.md b/content/publications/gau-2021/index.md new file mode 100644 index 0000000..e8334ae --- /dev/null +++ b/content/publications/gau-2021/index.md @@ -0,0 +1,232 @@ +--- +title: 'Brainhack: Developing a culture of open, inclusive, community-driven neuroscience' +authors: +- Rémi Gau +- Stephanie Noble +- Katja Heuer +- Katherine L. Bottenhorn +- Isil P. Bilgin +- Yu-Fang Yang +- Julia M. Huntenburg +- Johanna M.M. Bayer +- Richard A.I. Bethlehem +- Shawn A. Rhoads +- Christoph Vogelbacher +- Valentina Borghesani +- Elizabeth Levitis +- Hao-Ting Wang +- Sofie Van Den Bossche +- Xenia Kobeleva +- Jon Haitz Legarreta +- Samuel Guay +- Selim Melvin Atay +- Gael P. Varoquaux +- Dorien C. Huijser +- Malin S. Sandström +- Peer Herholz +- Samuel A. Nastase +- AmanPreet Badhwar +- Guillaume Dumas +- Simon Schwab +- Stefano Moia +- Michael Dayan +- Yasmine Bassil +- Paula P. Brooks +- Matteo Mancini +- James M. Shine +- David O’Connor +- Xihe Xie +- Davide Poggiali +- Patrick Friedrich +- Anibal S. Heinsfeld +- Lydia Riedl +- Roberto Toro +- César Caballero-Gaudes +- Anders Eklund +- Kelly G. Garner +- Christopher R. Nolan +- Damion V. Demeter +- Fernando A. Barrios +- Junaid S. Merchant +- Elizabeth A. McDevitt +- Robert Oostenveld +- R. Cameron Craddock +- Ariel Rokem +- Andrew Doyle +- Satrajit S. Ghosh +- Aki Nikolaidis +- Olivia W. Stanley +- Eneko Uruñuela +- Nasim Anousheh +- Aurina Arnatkeviciute +- Guillaume Auzias +- Dipankar Bachar +- Elise Bannier +- Ruggero Basanisi +- Arshitha Basavaraj +- Marco Bedini +- Pierre Bellec +- R. Austin Benn +- Kathryn Berluti +- Steffen Bollmann +- Saskia Bollmann +- Claire Bradley +- Jesse Brown +- Augusto Buchweitz +- Patrick Callahan +- Micaela Y. Chan +- Bramsh Q. Chandio +- Theresa Cheng +- Sidhant Chopra +- Ai Wern Chung +- Thomas G. Close +- Etienne Combrisson +- Giorgia Cona +- R. Todd Constable +- Claire Cury +- Kamalaker Dadi +- Pablo F. Damasceno +- Samir Das +- Fabrizio De Vico Fallani +- Krista DeStasio +- Erin W. Dickie +- Lena Dorfschmidt +- Eugene P. Duff +- Elizabeth DuPre +- Sarah Dziura +- Nathalia B. Esper +- Oscar Esteban +- Shreyas Fadnavis +- Guillaume Flandin +- Jessica E. Flannery +- John Flournoy +- Stephanie J. Forkel +- Alexandre R. Franco +- Saampras Ganesan +- Siyuan Gao +- José C. García Alanis +- Eleftherios Garyfallidis +- Tristan Glatard +- Enrico Glerean +- Javier Gonzalez-Castillo +- Cassandra D. Gould van Praag +- Abigail S. Greene +- Geetika Gupta +- Catherine Alice Hahn +- Yaroslav O. Halchenko +- Daniel Handwerker +- Thomas S. Hartmann +- Valérie Hayot-Sasson +- Stephan Heunis +- Felix Hoffstaedter +- Daniela M. Hohmann +- Corey Horien +- Horea-Ioan Ioanas +- Alexandru Iordan +- Chao Jiang +- Michael Joseph +- Jason Kai +- Agah Karakuzu +- David N. Kennedy +- Anisha Keshavan +- Ali R. Khan +- Gregory Kiar +- P. Christiaan Klink +- Vincent Koppelmans +- Serge Koudoro +- Angela R. Laird +- Georg Langs +- Marissa Laws +- Roxane Licandro +- Sook-Lei Liew +- Tomislav Lipic +- Krisanne Litinas +- Daniel J. Lurie +- Désirée Lussier +- Christopher R. Madan +- Lea-Theresa Mais +- Sina Mansour L +- J.P. Manzano-Patron +- Dimitra Maoutsa +- Matheus Marcon +- Daniel S. Margulies +- Giorgio Marinato +- Daniele Marinazzo +- Christopher J. Markiewicz +- Camille Maumet +- Felipe Meneguzzi +- David Meunier +- Michael P. Milham +- Kathryn L. Mills +- Davide Momi +- Clara A. Moreau +- Aysha Motala +- Iska Moxon-Emre +- Thomas E. Nichols +- Dylan M. Nielson +- Gustav Nilsonne +- Lisa Novello +- Caroline O’Brien +- Emily Olafson +- Lindsay D. Oliver +- John A. Onofrey +- Edwina R. Orchard +- Kendra Oudyk +- Patrick J. Park +- Mahboobeh Parsapoor +- Lorenzo Pasquini +- Scott Peltier +- Cyril R. Pernet +- Rudolph Pienaar +- Pedro Pinheiro-Chagas +- Jean-Baptiste Poline +- Anqi Qiu +- Tiago Quendera +- Laura C. Rice +- Joscelin Rocha-Hidalgo +- Saige Rutherford +- Mathias Scharinger +- Dustin Scheinost +- Deena Shariq +- Thomas B. Shaw +- Viviana Siless +- Molly Simmonite +- Nikoloz Sirmpilatze +- Hayli Spence +- Julia Sprenger +- Andrija Stajduhar +- Martin Szinte +- Sylvain Takerkart +- Angela Tam +- Link Tejavibulya +- Michel Thiebaut de Schotten +- Ina Thome +- Laura Tomaz da Silva +- Nicolas Traut +- Lucina Q. Uddin +- Antonino Vallesi +- John W. VanMeter +- Nandita Vijayakumar +- Matteo Visconti di Oleggio Castello +- Jakub Vohryzek +- Jakša Vukojević +- Kirstie Jane Whitaker +- Lucy Whitmore +- Steve Wideman +- Suzanne T. Witt +- Hua Xie +- Ting Xu +- Chao-Gan Yan +- Fang-Cheng Yeh +- B.T. Thomas Yeo +- Xi-Nian Zuo +date: '2021-06-01' +publishDate: '2024-12-19T23:16:36.457619Z' +publication_types: +- article-journal +publication: '*Neuron*' +doi: 10.1016/j.neuron.2021.04.001 +links: +- name: URL + url: http://dx.doi.org/10.1016/j.neuron.2021.04.001 +--- diff --git a/content/publications/ghosh-2017/cite.bib b/content/publications/ghosh-2017/cite.bib new file mode 100644 index 0000000..8c7723b --- /dev/null +++ b/content/publications/ghosh-2017/cite.bib @@ -0,0 +1,15 @@ +@article{ghosh_2017, + author = {Ghosh, Satrajit S. and Poline, Jean-Baptiste and Keator, +David B. and Halchenko, Yaroslav O. and Thomas, Adam G. and +Kessler, Daniel A. and Kennedy, David N.}, + doi = {10.12688/f1000research.10783.2}, + issn = {2046-1402}, + journal = {F1000Research}, + month = {June}, + pages = {124}, + publisher = {F1000 Research Ltd}, + title = {A very simple, re-executable neuroimaging publication}, + url = {http://dx.doi.org/10.12688/f1000research.10783.2}, + volume = {6}, + year = {2017} +} diff --git a/content/publications/ghosh-2017/index.md b/content/publications/ghosh-2017/index.md new file mode 100644 index 0000000..63b5fa9 --- /dev/null +++ b/content/publications/ghosh-2017/index.md @@ -0,0 +1,20 @@ +--- +title: A very simple, re-executable neuroimaging publication +authors: +- Satrajit S. Ghosh +- Jean-Baptiste Poline +- David B. Keator +- Yaroslav O. Halchenko +- Adam G. Thomas +- Daniel A. Kessler +- David N. Kennedy +date: '2017-06-01' +publishDate: '2024-12-19T23:16:36.466026Z' +publication_types: +- article-journal +publication: '*F1000Research*' +doi: 10.12688/f1000research.10783.2 +links: +- name: URL + url: http://dx.doi.org/10.12688/f1000research.10783.2 +--- diff --git a/content/publications/gorgolewski-2016/cite.bib b/content/publications/gorgolewski-2016/cite.bib new file mode 100644 index 0000000..b89e473 --- /dev/null +++ b/content/publications/gorgolewski-2016/cite.bib @@ -0,0 +1,24 @@ +@article{gorgolewski_2016, + 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 Handwerker, +Daniel A. and Hanke, Michael and Keator, David and Li, +Xiangrui and Michael, Zachary and Maumet, Camille and +Nichols, B. Nolan and Nichols, Thomas E. and Pellman, John +and Poline, Jean-Baptiste and Rokem, Ariel and Schaefer, +Gunnar and Sochat, Vanessa and Triplett, William and +Turner, Jessica A. and Varoquaux, Gaël and Poldrack, +Russell A.}, + doi = {10.1038/sdata.2016.44}, + issn = {2052-4463}, + journal = {Scientific Data}, + month = {June}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {The brain imaging data structure, a format for organizing +and describing outputs of neuroimaging experiments}, + url = {http://dx.doi.org/10.1038/sdata.2016.44}, + volume = {3}, + year = {2016} +} diff --git a/content/publications/gorgolewski-2016/index.md b/content/publications/gorgolewski-2016/index.md new file mode 100644 index 0000000..7e0d326 --- /dev/null +++ b/content/publications/gorgolewski-2016/index.md @@ -0,0 +1,41 @@ +--- +title: The brain imaging data structure, a format for organizing and describing outputs + of neuroimaging experiments +authors: +- Krzysztof J. Gorgolewski +- Tibor Auer +- Vince D. Calhoun +- R. Cameron Craddock +- Samir Das +- Eugene P. Duff +- Guillaume Flandin +- Satrajit S. Ghosh +- Tristan Glatard +- Yaroslav O. Halchenko +- Daniel A. Handwerker +- Michael Hanke +- David Keator +- Xiangrui Li +- Zachary Michael +- Camille Maumet +- B. Nolan Nichols +- Thomas E. Nichols +- John Pellman +- Jean-Baptiste Poline +- Ariel Rokem +- Gunnar Schaefer +- Vanessa Sochat +- William Triplett +- Jessica A. Turner +- Gaël Varoquaux +- Russell A. Poldrack +date: '2016-06-01' +publishDate: '2024-12-19T23:16:36.470138Z' +publication_types: +- article-journal +publication: '*Scientific Data*' +doi: 10.1038/sdata.2016.44 +links: +- name: URL + url: http://dx.doi.org/10.1038/sdata.2016.44 +--- diff --git a/content/publications/gorgolewski-2017/cite.bib b/content/publications/gorgolewski-2017/cite.bib new file mode 100644 index 0000000..9be8487 --- /dev/null +++ b/content/publications/gorgolewski-2017/cite.bib @@ -0,0 +1,27 @@ +@article{gorgolewski_2017, + author = {Gorgolewski, Krzysztof J. and Alfaro-Almagro, Fidel and +Auer, Tibor and Bellec, Pierre and Capotă, Mihai and +Chakravarty, M. Mallar and Churchill, Nathan W. and Cohen, +Alexander Li and Craddock, R. Cameron and Devenyi, Gabriel +A. and Eklund, Anders and Esteban, Oscar and Flandin, +Guillaume and Ghosh, Satrajit S. and Guntupalli, J. Swaroop +and Jenkinson, Mark and Keshavan, Anisha and Kiar, Gregory +and Liem, Franziskus and Raamana, Pradeep Reddy and +Raffelt, David and Steele, Christopher J. and Quirion, +Pierre-Olivier and Smith, Robert E. and Strother, Stephen +C. and Varoquaux, Gaël and Wang, Yida and Yarkoni, Tal and +Poldrack, Russell A.}, + doi = {10.1371/journal.pcbi.1005209}, + editor = {Schneidman, Dina}, + issn = {1553-7358}, + journal = {PLOS Computational Biology}, + month = {March}, + number = {3}, + pages = {e1005209}, + publisher = {Public Library of Science (PLoS)}, + title = {BIDS apps: Improving ease of use, accessibility, and +reproducibility of neuroimaging data analysis methods}, + url = {http://dx.doi.org/10.1371/journal.pcbi.1005209}, + volume = {13}, + year = {2017} +} diff --git a/content/publications/gorgolewski-2017/index.md b/content/publications/gorgolewski-2017/index.md new file mode 100644 index 0000000..70a3c67 --- /dev/null +++ b/content/publications/gorgolewski-2017/index.md @@ -0,0 +1,43 @@ +--- +title: 'BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging + data analysis methods' +authors: +- Krzysztof J. Gorgolewski +- Fidel Alfaro-Almagro +- Tibor Auer +- Pierre Bellec +- Mihai Capotă +- M. Mallar Chakravarty +- Nathan W. Churchill +- Alexander Li Cohen +- R. Cameron Craddock +- Gabriel A. Devenyi +- Anders Eklund +- Oscar Esteban +- Guillaume Flandin +- Satrajit S. Ghosh +- J. Swaroop Guntupalli +- Mark Jenkinson +- Anisha Keshavan +- Gregory Kiar +- Franziskus Liem +- Pradeep Reddy Raamana +- David Raffelt +- Christopher J. Steele +- Pierre-Olivier Quirion +- Robert E. Smith +- Stephen C. Strother +- Gaël Varoquaux +- Yida Wang +- Tal Yarkoni +- Russell A. Poldrack +date: '2017-03-01' +publishDate: '2024-12-19T23:16:36.474509Z' +publication_types: +- article-journal +publication: '*PLOS Computational Biology*' +doi: 10.1371/journal.pcbi.1005209 +links: +- name: URL + url: http://dx.doi.org/10.1371/journal.pcbi.1005209 +--- diff --git a/content/publications/guell-2018/cite.bib b/content/publications/guell-2018/cite.bib new file mode 100644 index 0000000..0a9e01c --- /dev/null +++ b/content/publications/guell-2018/cite.bib @@ -0,0 +1,13 @@ +@article{guell_2018, + author = {Guell, Xavier and Schmahmann, Jeremy D and Gabrieli, John +DE and Ghosh, Satrajit S}, + doi = {10.7554/elife.36652}, + issn = {2050-084X}, + journal = {eLife}, + month = {August}, + publisher = {eLife Sciences Publications, Ltd}, + title = {Functional gradients of the cerebellum}, + url = {http://dx.doi.org/10.7554/elife.36652}, + volume = {7}, + year = {2018} +} diff --git a/content/publications/guell-2018/index.md b/content/publications/guell-2018/index.md new file mode 100644 index 0000000..dab3c6a --- /dev/null +++ b/content/publications/guell-2018/index.md @@ -0,0 +1,17 @@ +--- +title: Functional gradients of the cerebellum +authors: +- Xavier Guell +- Jeremy D Schmahmann +- John DE Gabrieli +- Satrajit S Ghosh +date: '2018-08-01' +publishDate: '2024-12-19T23:16:36.479002Z' +publication_types: +- article-journal +publication: '*eLife*' +doi: 10.7554/elife.36652 +links: +- name: URL + url: http://dx.doi.org/10.7554/elife.36652 +--- diff --git a/content/publications/guell-2019/cite.bib b/content/publications/guell-2019/cite.bib new file mode 100644 index 0000000..7a5eb68 --- /dev/null +++ b/content/publications/guell-2019/cite.bib @@ -0,0 +1,18 @@ +@article{guell_2019, + author = {Guell, Xavier and Goncalves, Mathias and Kaczmarzyk, Jakub +R. and Gabrieli, John D. E. and Schmahmann, Jeremy D. and +Ghosh, Satrajit S.}, + doi = {10.1371/journal.pone.0210028}, + editor = {Margulies, Daniel S.}, + issn = {1932-6203}, + journal = {PLOS ONE}, + month = {January}, + number = {1}, + pages = {e0210028}, + publisher = {Public Library of Science (PLoS)}, + title = {LittleBrain: A gradient-based tool for the topographical +interpretation of cerebellar neuroimaging findings}, + url = {http://dx.doi.org/10.1371/journal.pone.0210028}, + volume = {14}, + year = {2019} +} diff --git a/content/publications/guell-2019/index.md b/content/publications/guell-2019/index.md new file mode 100644 index 0000000..561a8ab --- /dev/null +++ b/content/publications/guell-2019/index.md @@ -0,0 +1,20 @@ +--- +title: 'LittleBrain: A gradient-based tool for the topographical interpretation of + cerebellar neuroimaging findings' +authors: +- Xavier Guell +- Mathias Goncalves +- Jakub R. Kaczmarzyk +- John D. E. Gabrieli +- Jeremy D. Schmahmann +- Satrajit S. Ghosh +date: '2019-01-01' +publishDate: '2024-12-19T23:16:36.482873Z' +publication_types: +- article-journal +publication: '*PLOS ONE*' +doi: 10.1371/journal.pone.0210028 +links: +- name: URL + url: http://dx.doi.org/10.1371/journal.pone.0210028 +--- diff --git a/content/publications/hagler-2019/cite.bib b/content/publications/hagler-2019/cite.bib new file mode 100644 index 0000000..e46cb9d --- /dev/null +++ b/content/publications/hagler-2019/cite.bib @@ -0,0 +1,67 @@ +@article{hagler_2019, + author = {Hagler, Donald J. and Hatton, SeanN. and Cornejo, M. +Daniela and Makowski, Carolina and Fair, Damien A. and +Dick, Anthony Steven and Sutherland, Matthew T. and Casey, +B.J. and Barch, Deanna M. and Harms, Michael P. and Watts, +Richard and Bjork, James M. and Garavan, Hugh P. and +Hilmer, Laura and Pung, Christopher J. and Sicat, Chelsea +S. and Kuperman, Joshua and Bartsch, Hauke and Xue, Feng +and Heitzeg, Mary M. and Laird, Angela R. and Trinh, Thanh +T. and Gonzalez, Raul and Tapert, Susan F. and Riedel, +Michael C. and Squeglia, Lindsay M. and Hyde, Luke W. and +Rosenberg, Monica D. and Earl, Eric A. and Howlett, Katia +D. and Baker, Fiona C. and Soules, Mary and Diaz, Jazmin +and de Leon, Octavio Ruiz and Thompson, Wesley K. and +Neale, Michael C. and Herting, Megan and Sowell, Elizabeth +R. and Alvarez, Ruben P. and Hawes, Samuel W. and Sanchez, +Mariana and Bodurka, Jerzy and Breslin, Florence J. and +Morris, Amanda Sheffield and Paulus, Martin P. and Simmons, +W. Kyle and Polimeni, Jonathan R. and van der Kouwe, Andre +and Nencka, Andrew S. and Gray, Kevin M. and Pierpaoli, +Carlo and Matochik, John A. and Noronha, Antonio and Aklin, +Will M. and Conway, Kevin and Glantz, Meyer and Hoffman, +Elizabeth and Little, Roger and Lopez, Marsha and +Pariyadath, Vani and Weiss, Susan RB. and Wolff-Hughes, +Dana L. and DelCarmen-Wiggins, Rebecca and Feldstein Ewing, +Sarah W. and Miranda-Dominguez, Oscar and Nagel, Bonnie J. +and Perrone, Anders J. and Sturgeon, Darrick T. and +Goldstone, Aimee and Pfefferbaum, Adolf and Pohl, Kilian M. +and Prouty, Devin and Uban, Kristina and Bookheimer, Susan +Y. and Dapretto, Mirella and Galvan, Adriana and Bagot, +Kara and Giedd, Jay and Infante, M. Alejandra and Jacobus, +Joanna and Patrick, Kevin and Shilling, Paul D. and +Desikan, Rahul and Li, Yi and Sugrue, Leo and Banich, Marie +T. and Friedman, Naomi and Hewitt, John K. and Hopfer, +Christian and Sakai, Joseph and Tanabe, Jody and Cottler, +Linda B. and Nixon, Sara Jo and Chang, Linda and Cloak, +Christine and Ernst, Thomas and Reeves, Gloria and Kennedy, +David N. and Heeringa, Steve and Peltier, Scott and +Schulenberg, John and Sripada, Chandra and Zucker, Robert +A. and Iacono, William G. and Luciana, Monica and Calabro, +Finnegan J. and Clark, Duncan B. and Lewis, David A. and +Luna, Beatriz and Schirda, Claudiu and Brima, Tufikameni +and Foxe, John J. and Freedman, Edward G. and Mruzek, +Daniel W. and Mason, Michael J. and Huber, Rebekah and +McGlade, Erin and Prescot, Andrew and Renshaw, Perry F. and +Yurgelun-Todd, Deborah A. and Allgaier, Nicholas A. and +Dumas, Julie A. and Ivanova, Masha and Potter, Alexandra +and Florsheim, Paul and Larson, Christine and Lisdahl, +Krista and Charness, Michael E. and Fuemmeler, Bernard and +Hettema, John M. and Maes, Hermine H. and Steinberg, Joel +and Anokhin, Andrey P. and Glaser, Paul and Heath, Andrew +C. and Madden, Pamela A. and Baskin-Sommers, Arielle and +Constable, R. Todd and Grant, Steven J. and Dowling, +Gayathri J. and Brown, Sandra A. and Jernigan, Terry L. and +Dale, Anders M.}, + doi = {10.1016/j.neuroimage.2019.116091}, + issn = {1053-8119}, + journal = {NeuroImage}, + month = {November}, + pages = {116091}, + publisher = {Elsevier BV}, + title = {Image processing and analysis methods for the Adolescent +Brain Cognitive Development Study}, + url = {http://dx.doi.org/10.1016/j.neuroimage.2019.116091}, + volume = {202}, + year = {2019} +} diff --git a/content/publications/hagler-2019/index.md b/content/publications/hagler-2019/index.md new file mode 100644 index 0000000..dd1fd8e --- /dev/null +++ b/content/publications/hagler-2019/index.md @@ -0,0 +1,157 @@ +--- +title: Image processing and analysis methods for the Adolescent Brain Cognitive Development + Study +authors: +- Donald J. Hagler +- SeanN. Hatton +- M. Daniela Cornejo +- Carolina Makowski +- Damien A. Fair +- Anthony Steven Dick +- Matthew T. Sutherland +- B.J. Casey +- Deanna M. Barch +- Michael P. Harms +- Richard Watts +- James M. Bjork +- Hugh P. Garavan +- Laura Hilmer +- Christopher J. Pung +- Chelsea S. Sicat +- Joshua Kuperman +- Hauke Bartsch +- Feng Xue +- Mary M. Heitzeg +- Angela R. Laird +- Thanh T. Trinh +- Raul Gonzalez +- Susan F. Tapert +- Michael C. Riedel +- Lindsay M. Squeglia +- Luke W. Hyde +- Monica D. Rosenberg +- Eric A. Earl +- Katia D. Howlett +- Fiona C. Baker +- Mary Soules +- Jazmin Diaz +- Octavio Ruiz de Leon +- Wesley K. Thompson +- Michael C. Neale +- Megan Herting +- Elizabeth R. Sowell +- Ruben P. Alvarez +- Samuel W. Hawes +- Mariana Sanchez +- Jerzy Bodurka +- Florence J. Breslin +- Amanda Sheffield Morris +- Martin P. Paulus +- W. Kyle Simmons +- Jonathan R. Polimeni +- Andre van der Kouwe +- Andrew S. Nencka +- Kevin M. Gray +- Carlo Pierpaoli +- John A. Matochik +- Antonio Noronha +- Will M. Aklin +- Kevin Conway +- Meyer Glantz +- Elizabeth Hoffman +- Roger Little +- Marsha Lopez +- Vani Pariyadath +- Susan RB. Weiss +- Dana L. Wolff-Hughes +- Rebecca DelCarmen-Wiggins +- Sarah W. Feldstein Ewing +- Oscar Miranda-Dominguez +- Bonnie J. Nagel +- Anders J. Perrone +- Darrick T. Sturgeon +- Aimee Goldstone +- Adolf Pfefferbaum +- Kilian M. Pohl +- Devin Prouty +- Kristina Uban +- Susan Y. Bookheimer +- Mirella Dapretto +- Adriana Galvan +- Kara Bagot +- Jay Giedd +- M. Alejandra Infante +- Joanna Jacobus +- Kevin Patrick +- Paul D. Shilling +- Rahul Desikan +- Yi Li +- Leo Sugrue +- Marie T. Banich +- Naomi Friedman +- John K. Hewitt +- Christian Hopfer +- Joseph Sakai +- Jody Tanabe +- Linda B. Cottler +- Sara Jo Nixon +- Linda Chang +- Christine Cloak +- Thomas Ernst +- Gloria Reeves +- David N. Kennedy +- Steve Heeringa +- Scott Peltier +- John Schulenberg +- Chandra Sripada +- Robert A. Zucker +- William G. Iacono +- Monica Luciana +- Finnegan J. Calabro +- Duncan B. Clark +- David A. Lewis +- Beatriz Luna +- Claudiu Schirda +- Tufikameni Brima +- John J. Foxe +- Edward G. Freedman +- Daniel W. Mruzek +- Michael J. Mason +- Rebekah Huber +- Erin McGlade +- Andrew Prescot +- Perry F. Renshaw +- Deborah A. Yurgelun-Todd +- Nicholas A. Allgaier +- Julie A. Dumas +- Masha Ivanova +- Alexandra Potter +- Paul Florsheim +- Christine Larson +- Krista Lisdahl +- Michael E. Charness +- Bernard Fuemmeler +- John M. Hettema +- Hermine H. Maes +- Joel Steinberg +- Andrey P. Anokhin +- Paul Glaser +- Andrew C. Heath +- Pamela A. Madden +- Arielle Baskin-Sommers +- R. Todd Constable +- Steven J. Grant +- Gayathri J. Dowling +- Sandra A. Brown +- Terry L. Jernigan +- Anders M. Dale +date: '2019-11-01' +publishDate: '2024-12-19T23:16:36.486880Z' +publication_types: +- article-journal +publication: '*NeuroImage*' +doi: 10.1016/j.neuroimage.2019.116091 +links: +- name: URL + url: http://dx.doi.org/10.1016/j.neuroimage.2019.116091 +--- diff --git a/content/publications/halchenko-2021/cite.bib b/content/publications/halchenko-2021/cite.bib new file mode 100644 index 0000000..841117e --- /dev/null +++ b/content/publications/halchenko-2021/cite.bib @@ -0,0 +1,25 @@ +@article{halchenko_2021, + author = {Halchenko, Yaroslav and Meyer, Kyle and Poldrack, Benjamin +and Solanky, Debanjum and Wagner, Adina and Gors, Jason and +MacFarlane, Dave and Pustina, Dorian and Sochat, Vanessa +and Ghosh, Satrajit and Mönch, Christian and Markiewicz, +Christopher and Waite, Laura and Shlyakhter, Ilya and de la +Vega, Alejandro and Hayashi, Soichi and Häusler, Christian +and Poline, Jean-Baptiste and Kadelka, Tobias and Skytén, +Kusti and Jarecka, Dorota and Kennedy, David and Strauss, +Ted and Cieslak, Matt and Vavra, Peter and Ioanas, +Horea-Ioan and Schneider, Robin and Pflüger, Mika and +Haxby, James and Eickhoff, Simon and Hanke, Michael}, + doi = {10.21105/joss.03262}, + issn = {2475-9066}, + journal = {Journal of Open Source Software}, + month = {July}, + number = {63}, + pages = {3262}, + publisher = {The Open Journal}, + title = {DataLad: distributed system for joint management of code, +data, and their relationship}, + url = {http://dx.doi.org/10.21105/joss.03262}, + volume = {6}, + year = {2021} +} diff --git a/content/publications/halchenko-2021/index.md b/content/publications/halchenko-2021/index.md new file mode 100644 index 0000000..ff7e501 --- /dev/null +++ b/content/publications/halchenko-2021/index.md @@ -0,0 +1,45 @@ +--- +title: 'DataLad: distributed system for joint management of code, data, and their + relationship' +authors: +- Yaroslav Halchenko +- Kyle Meyer +- Benjamin Poldrack +- Debanjum Solanky +- Adina Wagner +- Jason Gors +- Dave MacFarlane +- Dorian Pustina +- Vanessa Sochat +- Satrajit Ghosh +- Christian Mönch +- Christopher Markiewicz +- Laura Waite +- Ilya Shlyakhter +- Alejandro de la Vega +- Soichi Hayashi +- Christian Häusler +- Jean-Baptiste Poline +- Tobias Kadelka +- Kusti Skytén +- Dorota Jarecka +- David Kennedy +- Ted Strauss +- Matt Cieslak +- Peter Vavra +- Horea-Ioan Ioanas +- Robin Schneider +- Mika Pflüger +- James Haxby +- Simon Eickhoff +- Michael Hanke +date: '2021-07-01' +publishDate: '2024-12-19T23:16:36.493434Z' +publication_types: +- article-journal +publication: '*Journal of Open Source Software*' +doi: 10.21105/joss.03262 +links: +- name: URL + url: http://dx.doi.org/10.21105/joss.03262 +--- diff --git a/content/publications/halchenko-2024/cite.bib b/content/publications/halchenko-2024/cite.bib new file mode 100644 index 0000000..64bc0b6 --- /dev/null +++ b/content/publications/halchenko-2024/cite.bib @@ -0,0 +1,25 @@ +@article{halchenko_2024, + author = {Halchenko, Yaroslav O. and Goncalves, Mathias and Ghosh, +Satrajit and Velasco, Pablo and Visconti di Oleggio +Castello, Matteo and Salo, Taylor and Wodder, John T. and +Hanke, Michael and Sadil, Patrick and Gorgolewski, +Krzysztof Jacek and Ioanas, Horea-Ioan and Rorden, Chris +and Hendrickson, Timothy J. and Dayan, Michael and +Houlihan, Sean Dae and Kent, James and Strauss, Ted and +Lee, John and To, Isaac and Markiewicz, Christopher J. and +Lukas, Darren and Butler, Ellyn R. and Thompson, Todd and +Termenon, Maite and Smith, David V. and Macdonald, Austin +and Kennedy, David N.}, + doi = {10.21105/joss.05839}, + issn = {2475-9066}, + journal = {Journal of Open Source Software}, + month = {July}, + number = {99}, + pages = {5839}, + publisher = {The Open Journal}, + title = {HeuDiConv — flexible DICOM conversion into structured +directory layouts}, + url = {http://dx.doi.org/10.21105/joss.05839}, + volume = {9}, + year = {2024} +} diff --git a/content/publications/halchenko-2024/index.md b/content/publications/halchenko-2024/index.md new file mode 100644 index 0000000..bad91d1 --- /dev/null +++ b/content/publications/halchenko-2024/index.md @@ -0,0 +1,40 @@ +--- +title: HeuDiConv — flexible DICOM conversion into structured directory layouts +authors: +- Yaroslav O. Halchenko +- Mathias Goncalves +- Satrajit Ghosh +- Pablo Velasco +- Matteo Visconti di Oleggio Castello +- Taylor Salo +- John T. Wodder +- Michael Hanke +- Patrick Sadil +- Krzysztof Jacek Gorgolewski +- Horea-Ioan Ioanas +- Chris Rorden +- Timothy J. Hendrickson +- Michael Dayan +- Sean Dae Houlihan +- James Kent +- Ted Strauss +- John Lee +- Isaac To +- Christopher J. Markiewicz +- Darren Lukas +- Ellyn R. Butler +- Todd Thompson +- Maite Termenon +- David V. Smith +- Austin Macdonald +- David N. Kennedy +date: '2024-07-01' +publishDate: '2024-12-19T23:16:36.497843Z' +publication_types: +- article-journal +publication: '*Journal of Open Source Software*' +doi: 10.21105/joss.05839 +links: +- name: URL + url: http://dx.doi.org/10.21105/joss.05839 +--- diff --git a/content/publications/hanke-2021/cite.bib b/content/publications/hanke-2021/cite.bib new file mode 100644 index 0000000..533bff3 --- /dev/null +++ b/content/publications/hanke-2021/cite.bib @@ -0,0 +1,15 @@ +@article{hanke_2021, + author = {Hanke, Michael and Pestilli, Franco and Wagner, Adina S. +and Markiewicz, Christopher J. and Poline, Jean-Baptiste +and Halchenko, Yaroslav O.}, + doi = {10.1515/nf-2020-0037}, + issn = {0947-0875}, + journal = {Neuroforum}, + month = {January}, + number = {0}, + publisher = {Walter de Gruyter GmbH}, + title = {In defense of decentralized research data management}, + url = {http://dx.doi.org/10.1515/nf-2020-0037}, + volume = {0}, + year = {2021} +} diff --git a/content/publications/hanke-2021/index.md b/content/publications/hanke-2021/index.md new file mode 100644 index 0000000..6c30894 --- /dev/null +++ b/content/publications/hanke-2021/index.md @@ -0,0 +1,19 @@ +--- +title: In defense of decentralized research data management +authors: +- Michael Hanke +- Franco Pestilli +- Adina S. Wagner +- Christopher J. Markiewicz +- Jean-Baptiste Poline +- Yaroslav O. Halchenko +date: '2021-01-01' +publishDate: '2024-12-19T23:16:36.502232Z' +publication_types: +- article-journal +publication: '*Neuroforum*' +doi: 10.1515/nf-2020-0037 +links: +- name: URL + url: http://dx.doi.org/10.1515/nf-2020-0037 +--- diff --git a/content/publications/hodge-2021/cite.bib b/content/publications/hodge-2021/cite.bib new file mode 100644 index 0000000..81d355b --- /dev/null +++ b/content/publications/hodge-2021/cite.bib @@ -0,0 +1,15 @@ +@article{hodge_2021, + author = {Hodge, Steven M. and Haselgrove, Christian and Honor, Leah +and Kennedy, David N. and Frazier, Jean A.}, + doi = {10.12688/f1000research.25306.2}, + issn = {2046-1402}, + journal = {F1000Research}, + month = {March}, + pages = {1031}, + publisher = {F1000 Research Ltd}, + title = {An assessment of the autism neuroimaging literature for +the prospects of re-executability}, + url = {http://dx.doi.org/10.12688/f1000research.25306.2}, + volume = {9}, + year = {2021} +} diff --git a/content/publications/hodge-2021/index.md b/content/publications/hodge-2021/index.md new file mode 100644 index 0000000..7142ec5 --- /dev/null +++ b/content/publications/hodge-2021/index.md @@ -0,0 +1,18 @@ +--- +title: An assessment of the autism neuroimaging literature for the prospects of re-executability +authors: +- Steven M. Hodge +- Christian Haselgrove +- Leah Honor +- David N. Kennedy +- Jean A. Frazier +date: '2021-03-01' +publishDate: '2024-12-19T23:16:36.506182Z' +publication_types: +- article-journal +publication: '*F1000Research*' +doi: 10.12688/f1000research.25306.2 +links: +- name: URL + url: http://dx.doi.org/10.12688/f1000research.25306.2 +--- diff --git a/content/publications/honor-2016/cite.bib b/content/publications/honor-2016/cite.bib new file mode 100644 index 0000000..ac2d63c --- /dev/null +++ b/content/publications/honor-2016/cite.bib @@ -0,0 +1,14 @@ +@article{honor_2016, + author = {Honor, Leah B. and Haselgrove, Christian and Frazier, Jean +A. and Kennedy, David N.}, + doi = {10.3389/fninf.2016.00034}, + issn = {1662-5196}, + journal = {Frontiers in Neuroinformatics}, + month = {August}, + publisher = {Frontiers Media SA}, + title = {Data Citation in Neuroimaging: Proposed Best Practices for +Data Identification and Attribution}, + url = {http://dx.doi.org/10.3389/fninf.2016.00034}, + volume = {10}, + year = {2016} +} diff --git a/content/publications/honor-2016/index.md b/content/publications/honor-2016/index.md new file mode 100644 index 0000000..4b452fb --- /dev/null +++ b/content/publications/honor-2016/index.md @@ -0,0 +1,18 @@ +--- +title: 'Data Citation in Neuroimaging: Proposed Best Practices for Data Identification + and Attribution' +authors: +- Leah B. Honor +- Christian Haselgrove +- Jean A. Frazier +- David N. Kennedy +date: '2016-08-01' +publishDate: '2024-12-19T23:16:36.510083Z' +publication_types: +- article-journal +publication: '*Frontiers in Neuroinformatics*' +doi: 10.3389/fninf.2016.00034 +links: +- name: URL + url: http://dx.doi.org/10.3389/fninf.2016.00034 +--- diff --git a/content/publications/hubbard-2020/cite.bib b/content/publications/hubbard-2020/cite.bib new file mode 100644 index 0000000..169ee91 --- /dev/null +++ b/content/publications/hubbard-2020/cite.bib @@ -0,0 +1,20 @@ +@article{hubbard_2020, + author = {Hubbard, N.A. and Siless, V. and Frosch, I.R. and +Goncalves, M. and Lo, N. and Wang, J. and Bauer, C.C.C. and +Conroy, K. and Cosby, E. and Hay, A. and Jones, R. and +Pinaire, M. and Vaz De Souza, F. and Vergara, G. and Ghosh, +S. and Henin, A. and Hirshfeld-Becker, D.R. and Hofmann, +S.G. and Rosso, I.M. and Auerbach, R.P. and Pizzagalli, +D.A. and Yendiki, A. and Gabrieli, J.D.E. and +Whitfield-Gabrieli, S.}, + doi = {10.1016/j.nicl.2020.102240}, + issn = {2213-1582}, + journal = {NeuroImage: Clinical}, + pages = {102240}, + publisher = {Elsevier BV}, + title = {Brain function and clinical characterization in the Boston +adolescent neuroimaging of depression and anxiety study}, + url = {http://dx.doi.org/10.1016/j.nicl.2020.102240}, + volume = {27}, + year = {2020} +} diff --git a/content/publications/hubbard-2020/index.md b/content/publications/hubbard-2020/index.md new file mode 100644 index 0000000..d31121b --- /dev/null +++ b/content/publications/hubbard-2020/index.md @@ -0,0 +1,38 @@ +--- +title: Brain function and clinical characterization in the Boston adolescent neuroimaging + of depression and anxiety study +authors: +- N.A. Hubbard +- V. Siless +- I.R. Frosch +- M. Goncalves +- N. Lo +- J. Wang +- C.C.C. Bauer +- K. Conroy +- E. Cosby +- A. Hay +- R. Jones +- M. Pinaire +- F. Vaz De Souza +- G. Vergara +- S. Ghosh +- A. Henin +- D.R. Hirshfeld-Becker +- S.G. Hofmann +- I.M. Rosso +- R.P. Auerbach +- D.A. Pizzagalli +- A. Yendiki +- J.D.E. Gabrieli +- S. Whitfield-Gabrieli +date: '2020-01-01' +publishDate: '2024-12-19T23:16:36.513979Z' +publication_types: +- article-journal +publication: '*NeuroImage: Clinical*' +doi: 10.1016/j.nicl.2020.102240 +links: +- name: URL + url: http://dx.doi.org/10.1016/j.nicl.2020.102240 +--- diff --git a/content/publications/hubbard-2024/cite.bib b/content/publications/hubbard-2024/cite.bib new file mode 100644 index 0000000..23be62b --- /dev/null +++ b/content/publications/hubbard-2024/cite.bib @@ -0,0 +1,19 @@ +@article{hubbard_2024, + author = {Hubbard, N. A. and Bauer, C. C. C. and Siless, V. and +Auerbach, R. P. and Elam, J. S. and Frosch, I. R. and +Henin, A. and Hofmann, S. G. and Hodge, M. R. and Jones, R. +and Lenzini, P. and Lo, N. and Park, A. T. and Pizzagalli, +D. A. and Vaz-DeSouza, F. and Gabrieli, J. D. E. and +Whitfield-Gabrieli, S. and Yendiki, A. and Ghosh, S. S.}, + doi = {10.1038/s41597-024-03629-x}, + issn = {2052-4463}, + journal = {Scientific Data}, + month = {August}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {The Human Connectome Project of adolescent anxiety and +depression dataset}, + url = {http://dx.doi.org/10.1038/s41597-024-03629-x}, + volume = {11}, + year = {2024} +} diff --git a/content/publications/hubbard-2024/index.md b/content/publications/hubbard-2024/index.md new file mode 100644 index 0000000..a664614 --- /dev/null +++ b/content/publications/hubbard-2024/index.md @@ -0,0 +1,32 @@ +--- +title: The Human Connectome Project of adolescent anxiety and depression dataset +authors: +- N. A. Hubbard +- C. C. C. Bauer +- V. Siless +- R. P. Auerbach +- J. S. Elam +- I. R. Frosch +- A. Henin +- S. G. Hofmann +- M. R. Hodge +- R. Jones +- P. Lenzini +- N. Lo +- A. T. Park +- D. A. Pizzagalli +- F. Vaz-DeSouza +- J. D. E. Gabrieli +- S. Whitfield-Gabrieli +- A. Yendiki +- S. S. Ghosh +date: '2024-08-01' +publishDate: '2024-12-19T23:16:36.518197Z' +publication_types: +- article-journal +publication: '*Scientific Data*' +doi: 10.1038/s41597-024-03629-x +links: +- name: URL + url: http://dx.doi.org/10.1038/s41597-024-03629-x +--- diff --git a/content/publications/hung-2020/cite.bib b/content/publications/hung-2020/cite.bib new file mode 100644 index 0000000..0a4f39a --- /dev/null +++ b/content/publications/hung-2020/cite.bib @@ -0,0 +1,19 @@ +@article{hung_2020, + author = {Hung, Yuwen and Uchida, Mai and Gaillard, Schuyler L. and +Woodworth, Hilary and Kelberman, Caroline and Capella, +James and Kadlec, Kelly and Goncalves, Mathias and Ghosh, +Satrajit and Yendiki, Anastasia and Chai, Xiaoqian J. and +Hirshfeld-Becker, Dina R. and Whitfield-Gabrieli, Susan and +Gabrieli, John D.E. and Biederman, Joseph}, + doi = {10.1016/j.nicl.2020.102266}, + issn = {2213-1582}, + journal = {NeuroImage: Clinical}, + pages = {102266}, + publisher = {Elsevier BV}, + title = {Cingulum-Callosal white-matter microstructure associated +with emotional dysregulation in children: A diffusion +tensor imaging study}, + url = {http://dx.doi.org/10.1016/j.nicl.2020.102266}, + volume = {27}, + year = {2020} +} diff --git a/content/publications/hung-2020/index.md b/content/publications/hung-2020/index.md new file mode 100644 index 0000000..1a51c28 --- /dev/null +++ b/content/publications/hung-2020/index.md @@ -0,0 +1,29 @@ +--- +title: 'Cingulum-Callosal white-matter microstructure associated with emotional dysregulation + in children: A diffusion tensor imaging study' +authors: +- Yuwen Hung +- Mai Uchida +- Schuyler L. Gaillard +- Hilary Woodworth +- Caroline Kelberman +- James Capella +- Kelly Kadlec +- Mathias Goncalves +- Satrajit Ghosh +- Anastasia Yendiki +- Xiaoqian J. Chai +- Dina R. Hirshfeld-Becker +- Susan Whitfield-Gabrieli +- John D.E. Gabrieli +- Joseph Biederman +date: '2020-01-01' +publishDate: '2024-12-19T23:16:36.522387Z' +publication_types: +- article-journal +publication: '*NeuroImage: Clinical*' +doi: 10.1016/j.nicl.2020.102266 +links: +- name: URL + url: http://dx.doi.org/10.1016/j.nicl.2020.102266 +--- diff --git a/content/publications/huntenburg-2017/cite.bib b/content/publications/huntenburg-2017/cite.bib new file mode 100644 index 0000000..3e60d15 --- /dev/null +++ b/content/publications/huntenburg-2017/cite.bib @@ -0,0 +1,17 @@ +@article{huntenburg_2017, + author = {Huntenburg, Julia M. and Bazin, Pierre-Louis and Goulas, +Alexandros and Tardif, Christine L. and Villringer, Arno +and Margulies, Daniel S.}, + doi = {10.1093/cercor/bhx030}, + issn = {1460-2199}, + journal = {Cerebral Cortex}, + month = {February}, + number = {2}, + pages = {981–997}, + publisher = {Oxford University Press (OUP)}, + title = {A Systematic Relationship Between Functional Connectivity +and Intracortical Myelin in the Human Cerebral Cortex}, + url = {http://dx.doi.org/10.1093/cercor/bhx030}, + volume = {27}, + year = {2017} +} diff --git a/content/publications/huntenburg-2017/index.md b/content/publications/huntenburg-2017/index.md new file mode 100644 index 0000000..b368e8d --- /dev/null +++ b/content/publications/huntenburg-2017/index.md @@ -0,0 +1,20 @@ +--- +title: A Systematic Relationship Between Functional Connectivity and Intracortical + Myelin in the Human Cerebral Cortex +authors: +- Julia M. Huntenburg +- Pierre-Louis Bazin +- Alexandros Goulas +- Christine L. Tardif +- Arno Villringer +- Daniel S. Margulies +date: '2017-02-01' +publishDate: '2024-12-19T23:16:36.526513Z' +publication_types: +- article-journal +publication: '*Cerebral Cortex*' +doi: 10.1093/cercor/bhx030 +links: +- name: URL + url: http://dx.doi.org/10.1093/cercor/bhx030 +--- diff --git a/content/publications/ioanas-2024/cite.bib b/content/publications/ioanas-2024/cite.bib new file mode 100644 index 0000000..515cfed --- /dev/null +++ b/content/publications/ioanas-2024/cite.bib @@ -0,0 +1,14 @@ +@article{ioanas_2024, + author = {Ioanas, Horea-Ioan and Macdonald, Austin and Halchenko, +Yaroslav O.}, + doi = {10.3389/fninf.2024.1376022}, + issn = {1662-5196}, + journal = {Frontiers in Neuroinformatics}, + month = {July}, + publisher = {Frontiers Media SA}, + title = {Neuroimaging article reexecution and reproduction +assessment system}, + url = {http://dx.doi.org/10.3389/fninf.2024.1376022}, + volume = {18}, + year = {2024} +} diff --git a/content/publications/ioanas-2024/index.md b/content/publications/ioanas-2024/index.md new file mode 100644 index 0000000..e166ba1 --- /dev/null +++ b/content/publications/ioanas-2024/index.md @@ -0,0 +1,16 @@ +--- +title: Neuroimaging article reexecution and reproduction assessment system +authors: +- Horea-Ioan Ioanas +- Austin Macdonald +- Yaroslav O. Halchenko +date: '2024-07-01' +publishDate: '2024-12-19T23:16:36.530496Z' +publication_types: +- article-journal +publication: '*Frontiers in Neuroinformatics*' +doi: 10.3389/fninf.2024.1376022 +links: +- name: URL + url: http://dx.doi.org/10.3389/fninf.2024.1376022 +--- diff --git a/content/publications/irimia-2017/cite.bib b/content/publications/irimia-2017/cite.bib new file mode 100644 index 0000000..dbae393 --- /dev/null +++ b/content/publications/irimia-2017/cite.bib @@ -0,0 +1,16 @@ +@article{irimia_2017, + author = {Irimia, Andrei and Wei, Susan and Lu, Nanshu and Moore, +Constance M. and Kennedy, David N.}, + doi = {10.1007/s12021-017-9335-z}, + issn = {1559-0089}, + journal = {Neuroinformatics}, + month = {July}, + number = {3}, + pages = {227–230}, + publisher = {Springer Science and Business Media LLC}, + title = {Mobile Monitoring of Traumatic Brain Injury in Older +Adults: Challenges and Opportunities}, + url = {http://dx.doi.org/10.1007/s12021-017-9335-z}, + volume = {15}, + year = {2017} +} diff --git a/content/publications/irimia-2017/index.md b/content/publications/irimia-2017/index.md new file mode 100644 index 0000000..1e5111e --- /dev/null +++ b/content/publications/irimia-2017/index.md @@ -0,0 +1,19 @@ +--- +title: 'Mobile Monitoring of Traumatic Brain Injury in Older Adults: Challenges and + Opportunities' +authors: +- Andrei Irimia +- Susan Wei +- Nanshu Lu +- Constance M. Moore +- David N. Kennedy +date: '2017-07-01' +publishDate: '2024-12-19T23:16:36.534379Z' +publication_types: +- article-journal +publication: '*Neuroinformatics*' +doi: 10.1007/s12021-017-9335-z +links: +- name: URL + url: http://dx.doi.org/10.1007/s12021-017-9335-z +--- diff --git a/content/publications/james-2016/cite.bib b/content/publications/james-2016/cite.bib new file mode 100644 index 0000000..5946809 --- /dev/null +++ b/content/publications/james-2016/cite.bib @@ -0,0 +1,17 @@ +@article{james_2016, + author = {James, Eric G. and Leveille, Suzanne G. and Hausdorff, +Jeffrey M. and Travison, Thomas and Kennedy, David N. and +Tucker, Katherine L. and Al Snih, Soham and Markides, +Kyriakos S. and Bean, Jonathan F.}, + doi = {10.1093/gerona/glw236}, + issn = {1758-535X}, + journal = {The Journals of Gerontology Series A: Biological Sciences +and Medical Sciences}, + month = {December}, + pages = {glw236}, + publisher = {Oxford University Press (OUP)}, + title = {Rhythmic Interlimb Coordination Impairments and the Risk +for Developing Mobility Limitations}, + url = {http://dx.doi.org/10.1093/gerona/glw236}, + year = {2016} +} diff --git a/content/publications/james-2016/index.md b/content/publications/james-2016/index.md new file mode 100644 index 0000000..ebbc464 --- /dev/null +++ b/content/publications/james-2016/index.md @@ -0,0 +1,24 @@ +--- +title: Rhythmic Interlimb Coordination Impairments and the Risk for Developing Mobility + Limitations +authors: +- Eric G. James +- Suzanne G. Leveille +- Jeffrey M. Hausdorff +- Thomas Travison +- David N. Kennedy +- Katherine L. Tucker +- Soham Al Snih +- Kyriakos S. Markides +- Jonathan F. Bean +date: '2016-12-01' +publishDate: '2024-12-19T23:16:36.538363Z' +publication_types: +- article-journal +publication: '*The Journals of Gerontology Series A: Biological Sciences and Medical + Sciences*' +doi: 10.1093/gerona/glw236 +links: +- name: URL + url: http://dx.doi.org/10.1093/gerona/glw236 +--- diff --git a/content/publications/kennedy-2017/cite.bib b/content/publications/kennedy-2017/cite.bib new file mode 100644 index 0000000..12c4722 --- /dev/null +++ b/content/publications/kennedy-2017/cite.bib @@ -0,0 +1,14 @@ +@article{kennedy_2017, + author = {Kennedy, David N.}, + doi = {10.1007/s12021-017-9331-3}, + issn = {1559-0089}, + journal = {Neuroinformatics}, + month = {April}, + number = {2}, + pages = {113–114}, + publisher = {Springer Science and Business Media LLC}, + title = {The Information Sharing Statement Grows Some Teeth}, + url = {http://dx.doi.org/10.1007/s12021-017-9331-3}, + volume = {15}, + year = {2017} +} diff --git a/content/publications/kennedy-2017/index.md b/content/publications/kennedy-2017/index.md new file mode 100644 index 0000000..0bdc585 --- /dev/null +++ b/content/publications/kennedy-2017/index.md @@ -0,0 +1,14 @@ +--- +title: The Information Sharing Statement Grows Some Teeth +authors: +- David N. Kennedy +date: '2017-04-01' +publishDate: '2024-12-19T23:16:36.542340Z' +publication_types: +- article-journal +publication: '*Neuroinformatics*' +doi: 10.1007/s12021-017-9331-3 +links: +- name: URL + url: http://dx.doi.org/10.1007/s12021-017-9331-3 +--- diff --git a/content/publications/kennedy-2018/cite.bib b/content/publications/kennedy-2018/cite.bib new file mode 100644 index 0000000..64667e6 --- /dev/null +++ b/content/publications/kennedy-2018/cite.bib @@ -0,0 +1,15 @@ +@article{kennedy_2018, + author = {Kennedy, David N.}, + doi = {10.1007/s12021-018-9379-8}, + issn = {1559-0089}, + journal = {Neuroinformatics}, + month = {April}, + number = {2}, + pages = {149–150}, + publisher = {Springer Science and Business Media LLC}, + title = {Neuroimaging Neuroinformatics: Sample Size and Other +Evolutionary Topics}, + url = {http://dx.doi.org/10.1007/s12021-018-9379-8}, + volume = {16}, + year = {2018} +} diff --git a/content/publications/kennedy-2018/index.md b/content/publications/kennedy-2018/index.md new file mode 100644 index 0000000..ecb3a8e --- /dev/null +++ b/content/publications/kennedy-2018/index.md @@ -0,0 +1,14 @@ +--- +title: 'Neuroimaging Neuroinformatics: Sample Size and Other Evolutionary Topics' +authors: +- David N. Kennedy +date: '2018-04-01' +publishDate: '2024-12-19T23:16:36.546103Z' +publication_types: +- article-journal +publication: '*Neuroinformatics*' +doi: 10.1007/s12021-018-9379-8 +links: +- name: URL + url: http://dx.doi.org/10.1007/s12021-018-9379-8 +--- diff --git a/content/publications/kennedy-2019/cite.bib b/content/publications/kennedy-2019/cite.bib new file mode 100644 index 0000000..b104795 --- /dev/null +++ b/content/publications/kennedy-2019/cite.bib @@ -0,0 +1,21 @@ +@article{kennedy_2019, + author = {Kennedy, David N. and Abraham, Sanu A. and Bates, Julianna +F. and Crowley, Albert and Ghosh, Satrajit and Gillespie, +Tom and Goncalves, Mathias and Grethe, Jeffrey S. and +Halchenko, Yaroslav O. and Hanke, Michael and Haselgrove, +Christian and Hodge, Steven M. and Jarecka, Dorota and +Kaczmarzyk, Jakub and Keator, David B. and Meyer, Kyle and +Martone, Maryann E. and Padhy, Smruti and Poline, +Jean-Baptiste and Preuss, Nina and Sincomb, Troy and +Travers, Matt}, + doi = {10.3389/fninf.2019.00001}, + issn = {1662-5196}, + journal = {Frontiers in Neuroinformatics}, + month = {February}, + publisher = {Frontiers Media SA}, + title = {Everything Matters: The ReproNim Perspective on +Reproducible Neuroimaging}, + url = {http://dx.doi.org/10.3389/fninf.2019.00001}, + volume = {13}, + year = {2019} +} diff --git a/content/publications/kennedy-2019/index.md b/content/publications/kennedy-2019/index.md new file mode 100644 index 0000000..a29e771 --- /dev/null +++ b/content/publications/kennedy-2019/index.md @@ -0,0 +1,35 @@ +--- +title: 'Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging' +authors: +- David N. Kennedy +- Sanu A. Abraham +- Julianna F. Bates +- Albert Crowley +- Satrajit Ghosh +- Tom Gillespie +- Mathias Goncalves +- Jeffrey S. Grethe +- Yaroslav O. Halchenko +- Michael Hanke +- Christian Haselgrove +- Steven M. Hodge +- Dorota Jarecka +- Jakub Kaczmarzyk +- David B. Keator +- Kyle Meyer +- Maryann E. Martone +- Smruti Padhy +- Jean-Baptiste Poline +- Nina Preuss +- Troy Sincomb +- Matt Travers +date: '2019-02-01' +publishDate: '2024-12-19T23:16:36.549868Z' +publication_types: +- article-journal +publication: '*Frontiers in Neuroinformatics*' +doi: 10.3389/fninf.2019.00001 +links: +- name: URL + url: http://dx.doi.org/10.3389/fninf.2019.00001 +--- diff --git a/content/publications/keshavan-2019/cite.bib b/content/publications/keshavan-2019/cite.bib new file mode 100644 index 0000000..a136821 --- /dev/null +++ b/content/publications/keshavan-2019/cite.bib @@ -0,0 +1,13 @@ +@article{keshavan_2019, + author = {Keshavan, Anisha and Poline, Jean-Baptiste}, + doi = {10.3389/fninf.2019.00003}, + issn = {1662-5196}, + journal = {Frontiers in Neuroinformatics}, + month = {March}, + publisher = {Frontiers Media SA}, + title = {From the Wet Lab to the Web Lab: A Paradigm Shift in Brain +Imaging Research}, + url = {http://dx.doi.org/10.3389/fninf.2019.00003}, + volume = {13}, + year = {2019} +} diff --git a/content/publications/keshavan-2019/index.md b/content/publications/keshavan-2019/index.md new file mode 100644 index 0000000..590c5b4 --- /dev/null +++ b/content/publications/keshavan-2019/index.md @@ -0,0 +1,15 @@ +--- +title: 'From the Wet Lab to the Web Lab: A Paradigm Shift in Brain Imaging Research' +authors: +- Anisha Keshavan +- Jean-Baptiste Poline +date: '2019-03-01' +publishDate: '2024-12-19T23:16:36.554460Z' +publication_types: +- article-journal +publication: '*Frontiers in Neuroinformatics*' +doi: 10.3389/fninf.2019.00003 +links: +- name: URL + url: http://dx.doi.org/10.3389/fninf.2019.00003 +--- diff --git a/content/publications/kiar-2023/cite.bib b/content/publications/kiar-2023/cite.bib new file mode 100644 index 0000000..bdd5c90 --- /dev/null +++ b/content/publications/kiar-2023/cite.bib @@ -0,0 +1,19 @@ +@article{kiar_2023, + author = {Kiar, Gregory and Clucas, Jon and Feczko, Eric and +Goncalves, Mathias and Jarecka, Dorota and Markiewicz, +Christopher J. and Halchenko, Yaroslav O. and Hermosillo, +Robert and Li, Xinhui and Miranda-Dominguez, Oscar and +Ghosh, Satrajit and Poldrack, Russell A. and Satterthwaite, +Theodore D. and Milham, Michael P. and Fair, Damien}, + doi = {10.1038/s41562-023-01647-0}, + issn = {2397-3374}, + journal = {Nature Human Behaviour}, + month = {June}, + number = {7}, + pages = {1027–1028}, + publisher = {Springer Science and Business Media LLC}, + title = {Align with the NMIND consortium for better neuroimaging}, + url = {http://dx.doi.org/10.1038/s41562-023-01647-0}, + volume = {7}, + year = {2023} +} diff --git a/content/publications/kiar-2023/index.md b/content/publications/kiar-2023/index.md new file mode 100644 index 0000000..94185a7 --- /dev/null +++ b/content/publications/kiar-2023/index.md @@ -0,0 +1,28 @@ +--- +title: Align with the NMIND consortium for better neuroimaging +authors: +- Gregory Kiar +- Jon Clucas +- Eric Feczko +- Mathias Goncalves +- Dorota Jarecka +- Christopher J. Markiewicz +- Yaroslav O. Halchenko +- Robert Hermosillo +- Xinhui Li +- Oscar Miranda-Dominguez +- Satrajit Ghosh +- Russell A. Poldrack +- Theodore D. Satterthwaite +- Michael P. Milham +- Damien Fair +date: '2023-06-01' +publishDate: '2024-12-19T23:16:36.558307Z' +publication_types: +- article-journal +publication: '*Nature Human Behaviour*' +doi: 10.1038/s41562-023-01647-0 +links: +- name: URL + url: http://dx.doi.org/10.1038/s41562-023-01647-0 +--- diff --git a/content/publications/kim-2018/cite.bib b/content/publications/kim-2018/cite.bib new file mode 100644 index 0000000..0e9ac2c --- /dev/null +++ b/content/publications/kim-2018/cite.bib @@ -0,0 +1,15 @@ +@article{kim_2018, + author = {Kim, Yang-Min and Poline, Jean-Baptiste and Dumas, +Guillaume}, + doi = {10.1093/gigascience/giy077}, + issn = {2047-217X}, + journal = {GigaScience}, + month = {June}, + number = {7}, + publisher = {Oxford University Press (OUP)}, + title = {Experimenting with reproducibility: a case study of +robustness in bioinformatics}, + url = {http://dx.doi.org/10.1093/gigascience/giy077}, + volume = {7}, + year = {2018} +} diff --git a/content/publications/kim-2018/index.md b/content/publications/kim-2018/index.md new file mode 100644 index 0000000..5526b24 --- /dev/null +++ b/content/publications/kim-2018/index.md @@ -0,0 +1,16 @@ +--- +title: 'Experimenting with reproducibility: a case study of robustness in bioinformatics' +authors: +- Yang-Min Kim +- Jean-Baptiste Poline +- Guillaume Dumas +date: '2018-06-01' +publishDate: '2024-12-19T23:16:36.562428Z' +publication_types: +- article-journal +publication: '*GigaScience*' +doi: 10.1093/gigascience/giy077 +links: +- name: URL + url: http://dx.doi.org/10.1093/gigascience/giy077 +--- diff --git a/content/publications/klein-2017/cite.bib b/content/publications/klein-2017/cite.bib new file mode 100644 index 0000000..43b2dc3 --- /dev/null +++ b/content/publications/klein-2017/cite.bib @@ -0,0 +1,18 @@ +@article{klein_2017, + author = {Klein, Arno and Ghosh, Satrajit S. and Bao, Forrest S. and +Giard, Joachim and Häme, Yrjö and Stavsky, Eliezer and +Lee, Noah and Rossa, Brian and Reuter, Martin and Chaibub +Neto, Elias and Keshavan, Anisha}, + doi = {10.1371/journal.pcbi.1005350}, + editor = {Schneidman, Dina}, + issn = {1553-7358}, + journal = {PLOS Computational Biology}, + month = {February}, + number = {2}, + pages = {e1005350}, + publisher = {Public Library of Science (PLoS)}, + title = {Mindboggling morphometry of human brains}, + url = {http://dx.doi.org/10.1371/journal.pcbi.1005350}, + volume = {13}, + year = {2017} +} diff --git a/content/publications/klein-2017/index.md b/content/publications/klein-2017/index.md new file mode 100644 index 0000000..34b419c --- /dev/null +++ b/content/publications/klein-2017/index.md @@ -0,0 +1,24 @@ +--- +title: Mindboggling morphometry of human brains +authors: +- Arno Klein +- Satrajit S. Ghosh +- Forrest S. Bao +- Joachim Giard +- Yrjö Häme +- Eliezer Stavsky +- Noah Lee +- Brian Rossa +- Martin Reuter +- Elias Chaibub Neto +- Anisha Keshavan +date: '2017-02-01' +publishDate: '2024-12-19T23:16:36.566389Z' +publication_types: +- article-journal +publication: '*PLOS Computational Biology*' +doi: 10.1371/journal.pcbi.1005350 +links: +- name: URL + url: http://dx.doi.org/10.1371/journal.pcbi.1005350 +--- diff --git a/content/publications/klein-2021/cite.bib b/content/publications/klein-2021/cite.bib new file mode 100644 index 0000000..843737c --- /dev/null +++ b/content/publications/klein-2021/cite.bib @@ -0,0 +1,23 @@ +@article{klein_2021, + author = {Klein, Arno and Clucas, Jon and Krishnakumar, Anirudh and +Ghosh, Satrajit S and Van Auken, Wilhelm and Thonet, +Benjamin and Sabram, Ihor and Acuna, Nino and Keshavan, +Anisha and Rossiter, Henry and Xiao, Yao and Semenuta, +Sergey and Badioli, Alessandra and Konishcheva, Kseniia and +Abraham, Sanu Ann and Alexander, Lindsay M and Merikangas, +Kathleen R and Swendsen, Joel and Lindner, Ariel B and +Milham, Michael P}, + doi = {10.2196/22369}, + issn = {1438-8871}, + journal = {Journal of Medical Internet Research}, + month = {November}, + number = {11}, + pages = {e22369}, + publisher = {JMIR Publications Inc.}, + title = {Remote Digital Psychiatry for Mobile Mental Health +Assessment and Therapy: MindLogger Platform Development +Study}, + url = {http://dx.doi.org/10.2196/22369}, + volume = {23}, + year = {2021} +} diff --git a/content/publications/klein-2021/index.md b/content/publications/klein-2021/index.md new file mode 100644 index 0000000..b1cad1b --- /dev/null +++ b/content/publications/klein-2021/index.md @@ -0,0 +1,34 @@ +--- +title: 'Remote Digital Psychiatry for Mobile Mental Health Assessment and Therapy: + MindLogger Platform Development Study' +authors: +- Arno Klein +- Jon Clucas +- Anirudh Krishnakumar +- Satrajit S Ghosh +- Wilhelm Van Auken +- Benjamin Thonet +- Ihor Sabram +- Nino Acuna +- Anisha Keshavan +- Henry Rossiter +- Yao Xiao +- Sergey Semenuta +- Alessandra Badioli +- Kseniia Konishcheva +- Sanu Ann Abraham +- Lindsay M Alexander +- Kathleen R Merikangas +- Joel Swendsen +- Ariel B Lindner +- Michael P Milham +date: '2021-11-01' +publishDate: '2024-12-19T23:16:36.570480Z' +publication_types: +- article-journal +publication: '*Journal of Medical Internet Research*' +doi: 10.2196/22369 +links: +- name: URL + url: http://dx.doi.org/10.2196/22369 +--- diff --git a/content/publications/kumar-2022/cite.bib b/content/publications/kumar-2022/cite.bib new file mode 100644 index 0000000..a378919 --- /dev/null +++ b/content/publications/kumar-2022/cite.bib @@ -0,0 +1,17 @@ +@article{kumar_2022, + author = {Kumar, Ashmita and Crowley, Albert and Queder, Nazek and +Poline, JB and Ghosh, Satrajit S. and Kennedy, David and +Grethe, Jeffrey S. and Helmer, Karl G. and Keator, David +B.}, + doi = {10.12688/f1000research.108008.2}, + issn = {2046-1402}, + journal = {F1000Research}, + month = {July}, + pages = {228}, + publisher = {F1000 Research Ltd}, + title = {The Neuroimaging Data Model Linear Regression Tool +(nidm_linreg): PyNIDM Project}, + url = {http://dx.doi.org/10.12688/f1000research.108008.2}, + volume = {11}, + year = {2022} +} diff --git a/content/publications/kumar-2022/index.md b/content/publications/kumar-2022/index.md new file mode 100644 index 0000000..bd836e8 --- /dev/null +++ b/content/publications/kumar-2022/index.md @@ -0,0 +1,22 @@ +--- +title: 'The Neuroimaging Data Model Linear Regression Tool (nidm_linreg): PyNIDM Project' +authors: +- Ashmita Kumar +- Albert Crowley +- Nazek Queder +- JB Poline +- Satrajit S. Ghosh +- David Kennedy +- Jeffrey S. Grethe +- Karl G. Helmer +- David B. Keator +date: '2022-07-01' +publishDate: '2024-12-19T23:16:36.574733Z' +publication_types: +- article-journal +publication: '*F1000Research*' +doi: 10.12688/f1000research.108008.2 +links: +- name: URL + url: http://dx.doi.org/10.12688/f1000research.108008.2 +--- diff --git a/content/publications/larivi-re-2023/cite.bib b/content/publications/larivi-re-2023/cite.bib new file mode 100644 index 0000000..730682e --- /dev/null +++ b/content/publications/larivi-re-2023/cite.bib @@ -0,0 +1,18 @@ +@article{larivi_re_2023, + author = {Larivière, Sara and Bayrak, Şeyma and Vos de Wael, +Reinder and Benkarim, Oualid and Herholz, Peer and +Rodriguez-Cruces, Raul and Paquola, Casey and Hong, +Seok-Jun and Misic, Bratislav and Evans, Alan C. and Valk, +Sofie L. and Bernhardt, Boris C.}, + doi = {10.1016/j.neuroimage.2022.119807}, + issn = {1053-8119}, + journal = {NeuroImage}, + month = {February}, + pages = {119807}, + publisher = {Elsevier BV}, + title = {BrainStat: A toolbox for brain-wide statistics and +multimodal feature associations}, + url = {http://dx.doi.org/10.1016/j.neuroimage.2022.119807}, + volume = {266}, + year = {2023} +} diff --git a/content/publications/larivi-re-2023/index.md b/content/publications/larivi-re-2023/index.md new file mode 100644 index 0000000..385290c --- /dev/null +++ b/content/publications/larivi-re-2023/index.md @@ -0,0 +1,25 @@ +--- +title: 'BrainStat: A toolbox for brain-wide statistics and multimodal feature associations' +authors: +- Sara Larivière +- Şeyma Bayrak +- Reinder Vos de Wael +- Oualid Benkarim +- Peer Herholz +- Raul Rodriguez-Cruces +- Casey Paquola +- Seok-Jun Hong +- Bratislav Misic +- Alan C. Evans +- Sofie L. Valk +- Boris C. Bernhardt +date: '2023-02-01' +publishDate: '2024-12-19T23:16:36.578774Z' +publication_types: +- article-journal +publication: '*NeuroImage*' +doi: 10.1016/j.neuroimage.2022.119807 +links: +- name: URL + url: http://dx.doi.org/10.1016/j.neuroimage.2022.119807 +--- diff --git a/content/publications/lin-2020/cite.bib b/content/publications/lin-2020/cite.bib new file mode 100644 index 0000000..372c5e6 --- /dev/null +++ b/content/publications/lin-2020/cite.bib @@ -0,0 +1,19 @@ +@article{lin_2020, + author = {Lin, Dawei and Crabtree, Jonathan and Dillo, Ingrid and +Downs, Robert R. and Edmunds, Rorie and Giaretta, David and +De Giusti, Marisa and L’Hours, Hervé and Hugo, Wim and +Jenkyns, Reyna and Khodiyar, Varsha and Martone, Maryann E. +and Mokrane, Mustapha and Navale, Vivek and Petters, +Jonathan and Sierman, Barbara and Sokolova, Dina V. and +Stockhause, Martina and Westbrook, John}, + doi = {10.1038/s41597-020-0486-7}, + issn = {2052-4463}, + journal = {Scientific Data}, + month = {May}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {The TRUST Principles for digital repositories}, + url = {http://dx.doi.org/10.1038/s41597-020-0486-7}, + volume = {7}, + year = {2020} +} diff --git a/content/publications/lin-2020/index.md b/content/publications/lin-2020/index.md new file mode 100644 index 0000000..ffe5043 --- /dev/null +++ b/content/publications/lin-2020/index.md @@ -0,0 +1,32 @@ +--- +title: The TRUST Principles for digital repositories +authors: +- Dawei Lin +- Jonathan Crabtree +- Ingrid Dillo +- Robert R. Downs +- Rorie Edmunds +- David Giaretta +- Marisa De Giusti +- Hervé L’Hours +- Wim Hugo +- Reyna Jenkyns +- Varsha Khodiyar +- Maryann E. Martone +- Mustapha Mokrane +- Vivek Navale +- Jonathan Petters +- Barbara Sierman +- Dina V. Sokolova +- Martina Stockhause +- John Westbrook +date: '2020-05-01' +publishDate: '2024-12-19T23:16:36.582791Z' +publication_types: +- article-journal +publication: '*Scientific Data*' +doi: 10.1038/s41597-020-0486-7 +links: +- name: URL + url: http://dx.doi.org/10.1038/s41597-020-0486-7 +--- diff --git a/content/publications/lin-2024/cite.bib b/content/publications/lin-2024/cite.bib new file mode 100644 index 0000000..a5f9728 --- /dev/null +++ b/content/publications/lin-2024/cite.bib @@ -0,0 +1,16 @@ +@article{lin_2024, + author = {Lin, David J. and Backus, Deborah and Chakraborty, Stuti +and Liew, Sook-Lei and Valero-Cuevas, Francisco J. and +Patten, Carolynn and Cotton, R James}, + doi = {10.1186/s12984-024-01309-w}, + issn = {1743-0003}, + journal = {Journal of NeuroEngineering and Rehabilitation}, + month = {February}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {Transforming modeling in neurorehabilitation: clinical +insights for personalized rehabilitation}, + url = {http://dx.doi.org/10.1186/s12984-024-01309-w}, + volume = {21}, + year = {2024} +} diff --git a/content/publications/lin-2024/index.md b/content/publications/lin-2024/index.md new file mode 100644 index 0000000..c1d4894 --- /dev/null +++ b/content/publications/lin-2024/index.md @@ -0,0 +1,21 @@ +--- +title: 'Transforming modeling in neurorehabilitation: clinical insights for personalized + rehabilitation' +authors: +- David J. Lin +- Deborah Backus +- Stuti Chakraborty +- Sook-Lei Liew +- Francisco J. Valero-Cuevas +- Carolynn Patten +- R James Cotton +date: '2024-02-01' +publishDate: '2024-12-19T23:16:36.586976Z' +publication_types: +- article-journal +publication: '*Journal of NeuroEngineering and Rehabilitation*' +doi: 10.1186/s12984-024-01309-w +links: +- name: URL + url: http://dx.doi.org/10.1186/s12984-024-01309-w +--- diff --git a/content/publications/lo-2023/cite.bib b/content/publications/lo-2023/cite.bib new file mode 100644 index 0000000..1387e0b --- /dev/null +++ b/content/publications/lo-2023/cite.bib @@ -0,0 +1,14 @@ +@article{lo_2023, + author = {Lo, Bethany P. and Donnelly, Miranda R. and Barisano, +Giuseppe and Liew, Sook-Lei}, + doi = {10.3389/fnimg.2022.1098604}, + issn = {2813-1193}, + journal = {Frontiers in Neuroimaging}, + month = {January}, + publisher = {Frontiers Media SA}, + title = {A standardized protocol for manually segmenting stroke +lesions on high-resolution T1-weighted MR images}, + url = {http://dx.doi.org/10.3389/fnimg.2022.1098604}, + volume = {1}, + year = {2023} +} diff --git a/content/publications/lo-2023/index.md b/content/publications/lo-2023/index.md new file mode 100644 index 0000000..41cd1d7 --- /dev/null +++ b/content/publications/lo-2023/index.md @@ -0,0 +1,18 @@ +--- +title: A standardized protocol for manually segmenting stroke lesions on high-resolution + T1-weighted MR images +authors: +- Bethany P. Lo +- Miranda R. Donnelly +- Giuseppe Barisano +- Sook-Lei Liew +date: '2023-01-01' +publishDate: '2024-12-19T23:16:36.591137Z' +publication_types: +- article-journal +publication: '*Frontiers in Neuroimaging*' +doi: 10.3389/fnimg.2022.1098604 +links: +- name: URL + url: http://dx.doi.org/10.3389/fnimg.2022.1098604 +--- diff --git a/content/publications/low-2020/cite.bib b/content/publications/low-2020/cite.bib new file mode 100644 index 0000000..e8de50a --- /dev/null +++ b/content/publications/low-2020/cite.bib @@ -0,0 +1,12 @@ +@article{low_2020, + author = {Low, Daniel M. and Rao, Vishwanatha and Randolph, Gregory +and Song, Phillip C. and Ghosh, Satrajit S.}, + doi = {10.1101/2020.11.23.20235945}, + month = {November}, + publisher = {Cold Spring Harbor Laboratory}, + title = {Identifying bias in models that detect vocal fold +paralysis from audio recordings using explainable machine +learning and clinician ratings}, + url = {http://dx.doi.org/10.1101/2020.11.23.20235945}, + year = {2020} +} diff --git a/content/publications/low-2020/index.md b/content/publications/low-2020/index.md new file mode 100644 index 0000000..030f142 --- /dev/null +++ b/content/publications/low-2020/index.md @@ -0,0 +1,19 @@ +--- +title: Identifying bias in models that detect vocal fold paralysis from audio recordings + using explainable machine learning and clinician ratings +authors: +- Daniel M. Low +- Vishwanatha Rao +- Gregory Randolph +- Phillip C. Song +- Satrajit S. Ghosh +date: '2020-11-01' +publishDate: '2024-12-19T23:16:36.594994Z' +publication_types: +- article-journal +publication: '*Cold Spring Harbor Laboratory*' +doi: 10.1101/2020.11.23.20235945 +links: +- name: URL + url: http://dx.doi.org/10.1101/2020.11.23.20235945 +--- diff --git a/content/publications/low-2024/cite.bib b/content/publications/low-2024/cite.bib new file mode 100644 index 0000000..c24a85f --- /dev/null +++ b/content/publications/low-2024/cite.bib @@ -0,0 +1,18 @@ +@article{low_2024, + author = {Low, Daniel M. and Rao, Vishwanatha and Randolph, Gregory +and Song, Phillip C. and Ghosh, Satrajit S.}, + doi = {10.1371/journal.pdig.0000516}, + editor = {Li-Jessen, Nicole Yee-Key}, + issn = {2767-3170}, + journal = {PLOS Digital Health}, + month = {May}, + number = {5}, + pages = {e0000516}, + publisher = {Public Library of Science (PLoS)}, + title = {Identifying bias in models that detect vocal fold +paralysis from audio recordings using explainable machine +learning and clinician ratings}, + url = {http://dx.doi.org/10.1371/journal.pdig.0000516}, + volume = {3}, + year = {2024} +} diff --git a/content/publications/low-2024/index.md b/content/publications/low-2024/index.md new file mode 100644 index 0000000..babadd4 --- /dev/null +++ b/content/publications/low-2024/index.md @@ -0,0 +1,19 @@ +--- +title: Identifying bias in models that detect vocal fold paralysis from audio recordings + using explainable machine learning and clinician ratings +authors: +- Daniel M. Low +- Vishwanatha Rao +- Gregory Randolph +- Phillip C. Song +- Satrajit S. Ghosh +date: '2024-05-01' +publishDate: '2024-12-19T23:16:36.598985Z' +publication_types: +- article-journal +publication: '*PLOS Digital Health*' +doi: 10.1371/journal.pdig.0000516 +links: +- name: URL + url: http://dx.doi.org/10.1371/journal.pdig.0000516 +--- diff --git a/content/publications/makris-2023/cite.bib b/content/publications/makris-2023/cite.bib new file mode 100644 index 0000000..0c61a00 --- /dev/null +++ b/content/publications/makris-2023/cite.bib @@ -0,0 +1,20 @@ +@article{makris_2023, + author = {Makris, Nikos and Rushmore, Richard and Kaiser, Jonathan +and Albaugh, Matthew and Kubicki, Marek and Rathi, Yogesh +and Zhang, Fan and O’Donnell, Lauren J. and Yeterian, +Edward and Caviness, Verne S. and Kennedy, David N.}, + doi = {10.1159/000530358}, + issn = {1421-9859}, + journal = {Developmental Neuroscience}, + number = {4}, + pages = {161–180}, + publisher = {S. Karger AG}, + title = {A Proposed Human Structural Brain Connectivity Matrix in +the Center for Morphometric Analysis Harvard-Oxford Atlas +Framework: A Historical Perspective and Future Direction +for Enhancing the Precision of Human Structural +Connectivity with a Novel Neuroanatomical Typology}, + url = {http://dx.doi.org/10.1159/000530358}, + volume = {45}, + year = {2023} +} diff --git a/content/publications/makris-2023/index.md b/content/publications/makris-2023/index.md new file mode 100644 index 0000000..374e8ba --- /dev/null +++ b/content/publications/makris-2023/index.md @@ -0,0 +1,27 @@ +--- +title: 'A Proposed Human Structural Brain Connectivity Matrix in the Center for Morphometric + Analysis Harvard-Oxford Atlas Framework: A Historical Perspective and Future Direction + for Enhancing the Precision of Human Structural Connectivity with a Novel Neuroanatomical + Typology' +authors: +- Nikos Makris +- Richard Rushmore +- Jonathan Kaiser +- Matthew Albaugh +- Marek Kubicki +- Yogesh Rathi +- Fan Zhang +- Lauren J. O’Donnell +- Edward Yeterian +- Verne S. Caviness +- David N. Kennedy +date: '2023-01-01' +publishDate: '2024-12-19T23:16:36.602999Z' +publication_types: +- article-journal +publication: '*Developmental Neuroscience*' +doi: 10.1159/000530358 +links: +- name: URL + url: http://dx.doi.org/10.1159/000530358 +--- diff --git a/content/publications/manelis-2021/cite.bib b/content/publications/manelis-2021/cite.bib new file mode 100644 index 0000000..7b0c68f --- /dev/null +++ b/content/publications/manelis-2021/cite.bib @@ -0,0 +1,17 @@ +@article{manelis_2021, + author = {Manelis, Anna and Soehner, Adriane and Halchenko, Yaroslav +O. and Satz, Skye and Ragozzino, Rachel and Lucero, Mora +and Swartz, Holly A. and Phillips, Mary L. and Versace, +Amelia}, + doi = {10.1038/s41598-021-87069-2}, + issn = {2045-2322}, + journal = {Scientific Reports}, + month = {April}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {White matter abnormalities in adults with bipolar disorder +type-II and unipolar depression}, + url = {http://dx.doi.org/10.1038/s41598-021-87069-2}, + volume = {11}, + year = {2021} +} diff --git a/content/publications/manelis-2021/index.md b/content/publications/manelis-2021/index.md new file mode 100644 index 0000000..ad9ef3b --- /dev/null +++ b/content/publications/manelis-2021/index.md @@ -0,0 +1,23 @@ +--- +title: White matter abnormalities in adults with bipolar disorder type-II and unipolar + depression +authors: +- Anna Manelis +- Adriane Soehner +- Yaroslav O. Halchenko +- Skye Satz +- Rachel Ragozzino +- Mora Lucero +- Holly A. Swartz +- Mary L. Phillips +- Amelia Versace +date: '2021-04-01' +publishDate: '2024-12-19T23:16:36.607405Z' +publication_types: +- article-journal +publication: '*Scientific Reports*' +doi: 10.1038/s41598-021-87069-2 +links: +- name: URL + url: http://dx.doi.org/10.1038/s41598-021-87069-2 +--- diff --git a/content/publications/manelis-2022/cite.bib b/content/publications/manelis-2022/cite.bib new file mode 100644 index 0000000..7a01d2e --- /dev/null +++ b/content/publications/manelis-2022/cite.bib @@ -0,0 +1,17 @@ +@article{manelis_2022, + author = {Manelis, Anna and Halchenko, Yaroslav O. and Bonar, Lisa +and Stiffler, Richelle S. and Satz, Skye and Miceli, Rachel +and Ladouceur, Cecile D. and Bebko, Genna and Iyengar, +Satish and Swartz, Holly A. and Phillips, Mary L.}, + doi = {10.1038/s41398-022-02211-6}, + issn = {2158-3188}, + journal = {Translational Psychiatry}, + month = {October}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {Working memory updating in individuals with bipolar and +unipolar depression: fMRI study}, + url = {http://dx.doi.org/10.1038/s41398-022-02211-6}, + volume = {12}, + year = {2022} +} diff --git a/content/publications/manelis-2022/index.md b/content/publications/manelis-2022/index.md new file mode 100644 index 0000000..e65943c --- /dev/null +++ b/content/publications/manelis-2022/index.md @@ -0,0 +1,25 @@ +--- +title: 'Working memory updating in individuals with bipolar and unipolar depression: + fMRI study' +authors: +- Anna Manelis +- Yaroslav O. Halchenko +- Lisa Bonar +- Richelle S. Stiffler +- Skye Satz +- Rachel Miceli +- Cecile D. Ladouceur +- Genna Bebko +- Satish Iyengar +- Holly A. Swartz +- Mary L. Phillips +date: '2022-10-01' +publishDate: '2024-12-19T23:16:36.611558Z' +publication_types: +- article-journal +publication: '*Translational Psychiatry*' +doi: 10.1038/s41398-022-02211-6 +links: +- name: URL + url: http://dx.doi.org/10.1038/s41398-022-02211-6 +--- diff --git a/content/publications/margulies-2016/cite.bib b/content/publications/margulies-2016/cite.bib new file mode 100644 index 0000000..7e25af0 --- /dev/null +++ b/content/publications/margulies-2016/cite.bib @@ -0,0 +1,19 @@ +@article{margulies_2016, + author = {Margulies, Daniel S. and Ghosh, Satrajit S. and Goulas, +Alexandros and Falkiewicz, Marcel and Huntenburg, Julia M. +and Langs, Georg and Bezgin, Gleb and Eickhoff, Simon B. +and Castellanos, F. Xavier and Petrides, Michael and +Jefferies, Elizabeth and Smallwood, Jonathan}, + doi = {10.1073/pnas.1608282113}, + issn = {1091-6490}, + journal = {Proceedings of the National Academy of Sciences}, + month = {October}, + number = {44}, + pages = {12574–12579}, + publisher = {Proceedings of the National Academy of Sciences}, + title = {Situating the default-mode network along a principal +gradient of macroscale cortical organization}, + url = {http://dx.doi.org/10.1073/pnas.1608282113}, + volume = {113}, + year = {2016} +} diff --git a/content/publications/margulies-2016/index.md b/content/publications/margulies-2016/index.md new file mode 100644 index 0000000..03fd9f3 --- /dev/null +++ b/content/publications/margulies-2016/index.md @@ -0,0 +1,26 @@ +--- +title: Situating the default-mode network along a principal gradient of macroscale + cortical organization +authors: +- Daniel S. Margulies +- Satrajit S. Ghosh +- Alexandros Goulas +- Marcel Falkiewicz +- Julia M. Huntenburg +- Georg Langs +- Gleb Bezgin +- Simon B. Eickhoff +- F. Xavier Castellanos +- Michael Petrides +- Elizabeth Jefferies +- Jonathan Smallwood +date: '2016-10-01' +publishDate: '2024-12-19T23:16:36.615664Z' +publication_types: +- article-journal +publication: '*Proceedings of the National Academy of Sciences*' +doi: 10.1073/pnas.1608282113 +links: +- name: URL + url: http://dx.doi.org/10.1073/pnas.1608282113 +--- diff --git a/content/publications/markello-2021/cite.bib b/content/publications/markello-2021/cite.bib new file mode 100644 index 0000000..fa09288 --- /dev/null +++ b/content/publications/markello-2021/cite.bib @@ -0,0 +1,15 @@ +@article{markello_2021, + author = {Markello, Ross D and Arnatkeviciute, Aurina and Poline, +Jean-Baptiste and Fulcher, Ben D and Fornito, Alex and +Misic, Bratislav}, + doi = {10.7554/elife.72129}, + issn = {2050-084X}, + journal = {eLife}, + month = {November}, + publisher = {eLife Sciences Publications, Ltd}, + title = {Standardizing workflows in imaging transcriptomics with +the abagen toolbox}, + url = {http://dx.doi.org/10.7554/elife.72129}, + volume = {10}, + year = {2021} +} diff --git a/content/publications/markello-2021/index.md b/content/publications/markello-2021/index.md new file mode 100644 index 0000000..cb8c92e --- /dev/null +++ b/content/publications/markello-2021/index.md @@ -0,0 +1,19 @@ +--- +title: Standardizing workflows in imaging transcriptomics with the abagen toolbox +authors: +- Ross D Markello +- Aurina Arnatkeviciute +- Jean-Baptiste Poline +- Ben D Fulcher +- Alex Fornito +- Bratislav Misic +date: '2021-11-01' +publishDate: '2024-12-19T23:16:36.619789Z' +publication_types: +- article-journal +publication: '*eLife*' +doi: 10.7554/elife.72129 +links: +- name: URL + url: http://dx.doi.org/10.7554/elife.72129 +--- diff --git a/content/publications/markiewicz-2021/cite.bib b/content/publications/markiewicz-2021/cite.bib new file mode 100644 index 0000000..b045de8 --- /dev/null +++ b/content/publications/markiewicz-2021/cite.bib @@ -0,0 +1,16 @@ +@article{markiewicz_2021, + author = {Markiewicz, Christopher J and Gorgolewski, Krzysztof J and +Feingold, Franklin and Blair, Ross and Halchenko, Yaroslav +O and Miller, Eric and Hardcastle, Nell and Wexler, Joe and +Esteban, Oscar and Goncavles, Mathias and Jwa, Anita and +Poldrack, Russell}, + doi = {10.7554/elife.71774}, + issn = {2050-084X}, + journal = {eLife}, + month = {October}, + publisher = {eLife Sciences Publications, Ltd}, + title = {The OpenNeuro resource for sharing of neuroscience data}, + url = {http://dx.doi.org/10.7554/elife.71774}, + volume = {10}, + year = {2021} +} diff --git a/content/publications/markiewicz-2021/index.md b/content/publications/markiewicz-2021/index.md new file mode 100644 index 0000000..9bed3fb --- /dev/null +++ b/content/publications/markiewicz-2021/index.md @@ -0,0 +1,25 @@ +--- +title: The OpenNeuro resource for sharing of neuroscience data +authors: +- Christopher J Markiewicz +- Krzysztof J Gorgolewski +- Franklin Feingold +- Ross Blair +- Yaroslav O Halchenko +- Eric Miller +- Nell Hardcastle +- Joe Wexler +- Oscar Esteban +- Mathias Goncavles +- Anita Jwa +- Russell Poldrack +date: '2021-10-01' +publishDate: '2024-12-19T23:16:36.623769Z' +publication_types: +- article-journal +publication: '*eLife*' +doi: 10.7554/elife.71774 +links: +- name: URL + url: http://dx.doi.org/10.7554/elife.71774 +--- diff --git a/content/publications/maumet-2016/cite.bib b/content/publications/maumet-2016/cite.bib new file mode 100644 index 0000000..2be2ee2 --- /dev/null +++ b/content/publications/maumet-2016/cite.bib @@ -0,0 +1,20 @@ +@article{maumet_2016, + author = {Maumet, Camille and Auer, Tibor and Bowring, Alexander and +Chen, Gang and Das, Samir and Flandin, Guillaume and Ghosh, +Satrajit and Glatard, Tristan and Gorgolewski, Krzysztof J. +and Helmer, Karl G. and Jenkinson, Mark and Keator, David +B. and Nichols, B. Nolan and Poline, Jean-Baptiste and +Reynolds, Richard and Sochat, Vanessa and Turner, Jessica +and Nichols, Thomas E.}, + doi = {10.1038/sdata.2016.102}, + issn = {2052-4463}, + journal = {Scientific Data}, + month = {December}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {Sharing brain mapping statistical results with the +neuroimaging data model}, + url = {http://dx.doi.org/10.1038/sdata.2016.102}, + volume = {3}, + year = {2016} +} diff --git a/content/publications/maumet-2016/index.md b/content/publications/maumet-2016/index.md new file mode 100644 index 0000000..99638b1 --- /dev/null +++ b/content/publications/maumet-2016/index.md @@ -0,0 +1,31 @@ +--- +title: Sharing brain mapping statistical results with the neuroimaging data model +authors: +- Camille Maumet +- Tibor Auer +- Alexander Bowring +- Gang Chen +- Samir Das +- Guillaume Flandin +- Satrajit Ghosh +- Tristan Glatard +- Krzysztof J. Gorgolewski +- Karl G. Helmer +- Mark Jenkinson +- David B. Keator +- B. Nolan Nichols +- Jean-Baptiste Poline +- Richard Reynolds +- Vanessa Sochat +- Jessica Turner +- Thomas E. Nichols +date: '2016-12-01' +publishDate: '2024-12-19T23:16:36.628031Z' +publication_types: +- article-journal +publication: '*Scientific Data*' +doi: 10.1038/sdata.2016.102 +links: +- name: URL + url: http://dx.doi.org/10.1038/sdata.2016.102 +--- diff --git a/content/publications/mcavoy-2021/cite.bib b/content/publications/mcavoy-2021/cite.bib new file mode 100644 index 0000000..b515170 --- /dev/null +++ b/content/publications/mcavoy-2021/cite.bib @@ -0,0 +1,18 @@ +@article{mcavoy_2021, + author = {McAvoy, Malia and Prieto, Paola Calvachi and Kaczmarzyk, +Jakub R. and Fernández, Iván Sánchez and McNulty, Jack +and Smith, Timothy and Yu, Kun-Hsing and Gormley, William +B. and Arnaout, Omar}, + doi = {10.1038/s41598-021-94733-0}, + issn = {2045-2322}, + journal = {Scientific Reports}, + month = {July}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {Classification of glioblastoma versus primary central +nervous system lymphoma using convolutional neural +networks}, + url = {http://dx.doi.org/10.1038/s41598-021-94733-0}, + volume = {11}, + year = {2021} +} diff --git a/content/publications/mcavoy-2021/index.md b/content/publications/mcavoy-2021/index.md new file mode 100644 index 0000000..0456000 --- /dev/null +++ b/content/publications/mcavoy-2021/index.md @@ -0,0 +1,23 @@ +--- +title: Classification of glioblastoma versus primary central nervous system lymphoma + using convolutional neural networks +authors: +- Malia McAvoy +- Paola Calvachi Prieto +- Jakub R. Kaczmarzyk +- Iván Sánchez Fernández +- Jack McNulty +- Timothy Smith +- Kun-Hsing Yu +- William B. Gormley +- Omar Arnaout +date: '2021-07-01' +publishDate: '2024-12-19T23:16:36.632269Z' +publication_types: +- article-journal +publication: '*Scientific Reports*' +doi: 10.1038/s41598-021-94733-0 +links: +- name: URL + url: http://dx.doi.org/10.1038/s41598-021-94733-0 +--- diff --git a/content/publications/mcnaughton-2022/cite.bib b/content/publications/mcnaughton-2022/cite.bib new file mode 100644 index 0000000..260b118 --- /dev/null +++ b/content/publications/mcnaughton-2022/cite.bib @@ -0,0 +1,65 @@ +@article{mcnaughton_2022, + author = {McNaughton, Ryan and Pieper, Chris and Sakai, Osamu and +Rollins, Julie V. and Zhang, Xin and Kennedy, David N. and +Frazier, Jean A. and Douglass, Laurie and Heeren, Timothy +and Fry, Rebecca C. and O’Shea, T. Michael and Kuban, +Karl K. and Jara, Hernán and Rollins, Julie V. and Shah, +Bhavesh and Singh, Rachana and Vaidya, Ruben and Van +Marter, Linda and Martin, Camilla and Ware, Janice and +Rollins, Caitlin and Cole, Cynthia and Perrin, Ellen and +Sakai, Christina and Bednarek, Frank and Frazier, Jean and +Ehrenkranz, Richard and Benjamin, Jennifer and Montgomery, +Angela and O’Shea, T. Michael and Washburn, Lisa and +Gogcu, Semsa and Bose, Carl and Warner, Diane and O’Shea, +T. Michael and Engelke, Steve and Higginson, Amanda and +Higginson, Jason and Bear, Kelly and Poortenga, Mariel and +Pastyrnak, Steve and Karna, Padu and Paneth, Nigel and +Lenski, Madeleine and Schreiber, Michael and Hunter, Scott +and Msall, Michael and Batton, Danny and Klarr, Judith and +Lee, Young Ah and Obeid, Rawad and Christianson, Karen and +Klein, Deborah and Wagner, Katie and Pimental, Maureen and +Hallisey, Collen and Coster, Taryn and Dolins, Maddie and +Mittleman, Maggie and Haile, Hannah and Rohde, Julia and +Nylen, Ellen and Neger, Emily and Mattern, Kathryn and Ma, +Catherine and Toner, Deanna and Vitaro, Elizabeth and +Venuti, Lauren and Powers, Beth and Foley, Ann and Sacco, +Taylor and Williams, Joanne and Romano, Elaine and Henry, +Christine and Hiatt, Debbie and Peters, Nancy and Brown, +Patricia and Ansusinha, Emily and Smith, Jazmyne and Yang, +Nou and Bose, Gennie and Wereszczak, Janice and Bernhardt, +Janice and Adams, Joan and Wilson, Donna and Darden-Saad, +Nancy and Williams, Bree and Jones, Emily and Sutton, Dinah +and Rathbun, Julie and Fagerman, Stephanie and Boshoven, +William and Johnson, Jalen and James, Brandon and Miras, +Karen and Solomon, Carolyn and Weiland, Deborah and Yoon, +Grace and Ramoskaite, Rugile and Wiggins, Suzanne and +Washington, Krissy and Martin, Ryan and Prendergast, +Barbara and Lynch, Emma and Kring, Beth and Smith, Anne and +McQuiston, Susan and Butler, Samantha and Wilson, Rachel +and McGhee, Kirsten and Lee, Patricia and Asgarian, Aimee +and Sadhwani, Anjali and Henson, Brandi and Keller, Cecelia +and Walkowiak, Jenifer and Barron, Susan and Miller, Alice +and Dessureau, Brian and Wood, Molly and Damon-Minow, Jill +and Romano, Elaine and Mayes, Linda and Tsatsanis, Kathy +and Chawarska, Katarzyna and Kim, Sophy and Dieterich, +Susan and Bearrs, Karen and Waldrep, Ellen and Friedman, +Jackie and Hounshell, Gail and Allred, Debbie and Helms, +Rebecca and Whitley, Lynn and Stainback, Gary and Bostic, +Lisa and Jacobson, Amanda and McKeeman, Joni and Meyer, +Echo and Price, Joan and Lloyd, Megan and Plesha-Troyke, +Susan and Scott, Megan and Solomon, Katherine M. and +Brooklier, Kara and Vogt, Kelly}, + doi = {10.1148/radiol.210385}, + issn = {1527-1315}, + journal = {Radiology}, + month = {August}, + number = {2}, + pages = {419–428}, + publisher = {Radiological Society of North America (RSNA)}, + title = {Quantitative MRI Characterization of the Extremely Preterm +Brain at Adolescence: Atypical versus Neurotypical +Developmental Pathways}, + url = {http://dx.doi.org/10.1148/radiol.210385}, + volume = {304}, + year = {2022} +} diff --git a/content/publications/mcnaughton-2022/index.md b/content/publications/mcnaughton-2022/index.md new file mode 100644 index 0000000..c68c807 --- /dev/null +++ b/content/publications/mcnaughton-2022/index.md @@ -0,0 +1,160 @@ +--- +title: 'Quantitative MRI Characterization of the Extremely Preterm Brain at Adolescence: + Atypical versus Neurotypical Developmental Pathways' +authors: +- Ryan McNaughton +- Chris Pieper +- Osamu Sakai +- Julie V. Rollins +- Xin Zhang +- David N. Kennedy +- Jean A. Frazier +- Laurie Douglass +- Timothy Heeren +- Rebecca C. Fry +- T. Michael O’Shea +- Karl K. Kuban +- Hernán Jara +- Julie V. Rollins +- Bhavesh Shah +- Rachana Singh +- Ruben Vaidya +- Linda Van Marter +- Camilla Martin +- Janice Ware +- Caitlin Rollins +- Cynthia Cole +- Ellen Perrin +- Christina Sakai +- Frank Bednarek +- Jean Frazier +- Richard Ehrenkranz +- Jennifer Benjamin +- Angela Montgomery +- T. Michael O’Shea +- Lisa Washburn +- Semsa Gogcu +- Carl Bose +- Diane Warner +- T. Michael O’Shea +- Steve Engelke +- Amanda Higginson +- Jason Higginson +- Kelly Bear +- Mariel Poortenga +- Steve Pastyrnak +- Padu Karna +- Nigel Paneth +- Madeleine Lenski +- Michael Schreiber +- Scott Hunter +- Michael Msall +- Danny Batton +- Judith Klarr +- Young Ah Lee +- Rawad Obeid +- Karen Christianson +- Deborah Klein +- Katie Wagner +- Maureen Pimental +- Collen Hallisey +- Taryn Coster +- Maddie Dolins +- Maggie Mittleman +- Hannah Haile +- Julia Rohde +- Ellen Nylen +- Emily Neger +- Kathryn Mattern +- Catherine Ma +- Deanna Toner +- Elizabeth Vitaro +- Lauren Venuti +- Beth Powers +- Ann Foley +- Taylor Sacco +- Joanne Williams +- Elaine Romano +- Christine Henry +- Debbie Hiatt +- Nancy Peters +- Patricia Brown +- Emily Ansusinha +- Jazmyne Smith +- Nou Yang +- Gennie Bose +- Janice Wereszczak +- Janice Bernhardt +- Joan Adams +- Donna Wilson +- Nancy Darden-Saad +- Bree Williams +- Emily Jones +- Dinah Sutton +- Julie Rathbun +- Stephanie Fagerman +- William Boshoven +- Jalen Johnson +- Brandon James +- Karen Miras +- Carolyn Solomon +- Deborah Weiland +- Grace Yoon +- Rugile Ramoskaite +- Suzanne Wiggins +- Krissy Washington +- Ryan Martin +- Barbara Prendergast +- Emma Lynch +- Beth Kring +- Anne Smith +- Susan McQuiston +- Samantha Butler +- Rachel Wilson +- Kirsten McGhee +- Patricia Lee +- Aimee Asgarian +- Anjali Sadhwani +- Brandi Henson +- Cecelia Keller +- Jenifer Walkowiak +- Susan Barron +- Alice Miller +- Brian Dessureau +- Molly Wood +- Jill Damon-Minow +- Elaine Romano +- Linda Mayes +- Kathy Tsatsanis +- Katarzyna Chawarska +- Sophy Kim +- Susan Dieterich +- Karen Bearrs +- Ellen Waldrep +- Jackie Friedman +- Gail Hounshell +- Debbie Allred +- Rebecca Helms +- Lynn Whitley +- Gary Stainback +- Lisa Bostic +- Amanda Jacobson +- Joni McKeeman +- Echo Meyer +- Joan Price +- Megan Lloyd +- Susan Plesha-Troyke +- Megan Scott +- Katherine M. Solomon +- Kara Brooklier +- Kelly Vogt +date: '2022-08-01' +publishDate: '2024-12-19T23:16:36.636308Z' +publication_types: +- article-journal +publication: '*Radiology*' +doi: 10.1148/radiol.210385 +links: +- name: URL + url: http://dx.doi.org/10.1148/radiol.210385 +--- diff --git a/content/publications/millman-2018/cite.bib b/content/publications/millman-2018/cite.bib new file mode 100644 index 0000000..3f6f1e0 --- /dev/null +++ b/content/publications/millman-2018/cite.bib @@ -0,0 +1,13 @@ +@article{millman_2018, + author = {Millman, K. Jarrod and Brett, Matthew and Barnowski, Ross +and Poline, Jean-Baptiste}, + doi = {10.3389/fnins.2018.00727}, + issn = {1662-453X}, + journal = {Frontiers in Neuroscience}, + month = {October}, + publisher = {Frontiers Media SA}, + title = {Teaching Computational Reproducibility for Neuroimaging}, + url = {http://dx.doi.org/10.3389/fnins.2018.00727}, + volume = {12}, + year = {2018} +} diff --git a/content/publications/millman-2018/index.md b/content/publications/millman-2018/index.md new file mode 100644 index 0000000..132e1b4 --- /dev/null +++ b/content/publications/millman-2018/index.md @@ -0,0 +1,17 @@ +--- +title: Teaching Computational Reproducibility for Neuroimaging +authors: +- K. Jarrod Millman +- Matthew Brett +- Ross Barnowski +- Jean-Baptiste Poline +date: '2018-10-01' +publishDate: '2024-12-19T23:16:36.642797Z' +publication_types: +- article-journal +publication: '*Frontiers in Neuroscience*' +doi: 10.3389/fnins.2018.00727 +links: +- name: URL + url: http://dx.doi.org/10.3389/fnins.2018.00727 +--- diff --git a/content/publications/modarres-2021/cite.bib b/content/publications/modarres-2021/cite.bib new file mode 100644 index 0000000..ec019f4 --- /dev/null +++ b/content/publications/modarres-2021/cite.bib @@ -0,0 +1,18 @@ +@article{modarres_2021, + author = {Modarres, Mo and Cochran, David and Kennedy, David N. and +Schmidt, Richard and Fitzpatrick, Paula and Frazier, Jean +A.}, + doi = {10.1007/s12021-021-09517-8}, + issn = {1559-0089}, + journal = {Neuroinformatics}, + month = {March}, + number = {1}, + pages = {53–62}, + publisher = {Springer Science and Business Media LLC}, + title = {Biomarkers Based on Comprehensive Hierarchical EEG +Coherence Analysis: Example Application to Social +Competence in Autism (Preliminary Results)}, + url = {http://dx.doi.org/10.1007/s12021-021-09517-8}, + volume = {20}, + year = {2021} +} diff --git a/content/publications/modarres-2021/index.md b/content/publications/modarres-2021/index.md new file mode 100644 index 0000000..cfa8fa6 --- /dev/null +++ b/content/publications/modarres-2021/index.md @@ -0,0 +1,20 @@ +--- +title: 'Biomarkers Based on Comprehensive Hierarchical EEG Coherence Analysis: Example + Application to Social Competence in Autism (Preliminary Results)' +authors: +- Mo Modarres +- David Cochran +- David N. Kennedy +- Richard Schmidt +- Paula Fitzpatrick +- Jean A. Frazier +date: '2021-03-01' +publishDate: '2024-12-19T23:16:36.646851Z' +publication_types: +- article-journal +publication: '*Neuroinformatics*' +doi: 10.1007/s12021-021-09517-8 +links: +- name: URL + url: http://dx.doi.org/10.1007/s12021-021-09517-8 +--- diff --git a/content/publications/modarres-2023/cite.bib b/content/publications/modarres-2023/cite.bib new file mode 100644 index 0000000..e88a4e4 --- /dev/null +++ b/content/publications/modarres-2023/cite.bib @@ -0,0 +1,15 @@ +@article{modarres_2023, + author = {Modarres, Mo and Cochran, David and Kennedy, David N. and +Frazier, Jean A.}, + doi = {10.3389/fnhum.2023.1237651}, + issn = {1662-5161}, + journal = {Frontiers in Human Neuroscience}, + month = {November}, + publisher = {Frontiers Media SA}, + title = {Comparison of comprehensive quantitative EEG metrics +between typically developing boys and girls in resting +state eyes-open and eyes-closed conditions}, + url = {http://dx.doi.org/10.3389/fnhum.2023.1237651}, + volume = {17}, + year = {2023} +} diff --git a/content/publications/modarres-2023/index.md b/content/publications/modarres-2023/index.md new file mode 100644 index 0000000..76e63c7 --- /dev/null +++ b/content/publications/modarres-2023/index.md @@ -0,0 +1,18 @@ +--- +title: Comparison of comprehensive quantitative EEG metrics between typically developing + boys and girls in resting state eyes-open and eyes-closed conditions +authors: +- Mo Modarres +- David Cochran +- David N. Kennedy +- Jean A. Frazier +date: '2023-11-01' +publishDate: '2024-12-19T23:16:36.650846Z' +publication_types: +- article-journal +publication: '*Frontiers in Human Neuroscience*' +doi: 10.3389/fnhum.2023.1237651 +links: +- name: URL + url: http://dx.doi.org/10.3389/fnhum.2023.1237651 +--- diff --git a/content/publications/nastase-2021/cite.bib b/content/publications/nastase-2021/cite.bib new file mode 100644 index 0000000..9c38944 --- /dev/null +++ b/content/publications/nastase-2021/cite.bib @@ -0,0 +1,22 @@ +@article{nastase_2021, + author = {Nastase, Samuel A. and Liu, Yun-Fei and Hillman, Hanna and +Zadbood, Asieh and Hasenfratz, Liat and Keshavarzian, +Neggin and Chen, Janice and Honey, Christopher J. and +Yeshurun, Yaara and Regev, Mor and Nguyen, Mai and Chang, +Claire H. C. and Baldassano, Christopher and Lositsky, Olga +and Simony, Erez and Chow, Michael A. and Leong, Yuan Chang +and Brooks, Paula P. and Micciche, Emily and Choe, Gina and +Goldstein, Ariel and Vanderwal, Tamara and Halchenko, +Yaroslav O. and Norman, Kenneth A. and Hasson, Uri}, + doi = {10.1038/s41597-021-01033-3}, + issn = {2052-4463}, + journal = {Scientific Data}, + month = {September}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {The “Narratives” fMRI dataset for evaluating models of +naturalistic language comprehension}, + url = {http://dx.doi.org/10.1038/s41597-021-01033-3}, + volume = {8}, + year = {2021} +} diff --git a/content/publications/nastase-2021/index.md b/content/publications/nastase-2021/index.md new file mode 100644 index 0000000..f2a00c9 --- /dev/null +++ b/content/publications/nastase-2021/index.md @@ -0,0 +1,39 @@ +--- +title: The “Narratives” fMRI dataset for evaluating models of naturalistic language + comprehension +authors: +- Samuel A. Nastase +- Yun-Fei Liu +- Hanna Hillman +- Asieh Zadbood +- Liat Hasenfratz +- Neggin Keshavarzian +- Janice Chen +- Christopher J. Honey +- Yaara Yeshurun +- Mor Regev +- Mai Nguyen +- Claire H. C. Chang +- Christopher Baldassano +- Olga Lositsky +- Erez Simony +- Michael A. Chow +- Yuan Chang Leong +- Paula P. Brooks +- Emily Micciche +- Gina Choe +- Ariel Goldstein +- Tamara Vanderwal +- Yaroslav O. Halchenko +- Kenneth A. Norman +- Uri Hasson +date: '2021-09-01' +publishDate: '2024-12-19T23:16:36.654785Z' +publication_types: +- article-journal +publication: '*Scientific Data*' +doi: 10.1038/s41597-021-01033-3 +links: +- name: URL + url: http://dx.doi.org/10.1038/s41597-021-01033-3 +--- diff --git a/content/publications/nichols-2017/cite.bib b/content/publications/nichols-2017/cite.bib new file mode 100644 index 0000000..a8dc2d4 --- /dev/null +++ b/content/publications/nichols-2017/cite.bib @@ -0,0 +1,20 @@ +@article{nichols_2017, + author = {Nichols, Thomas E and Das, Samir and Eickhoff, Simon B and +Evans, Alan C and Glatard, Tristan and Hanke, Michael and +Kriegeskorte, Nikolaus and Milham, Michael P and Poldrack, +Russell A and Poline, Jean-Baptiste and Proal, Erika and +Thirion, Bertrand and Van Essen, David C and White, Tonya +and Yeo, B T Thomas}, + doi = {10.1038/nn.4500}, + issn = {1546-1726}, + journal = {Nature Neuroscience}, + month = {March}, + number = {3}, + pages = {299–303}, + publisher = {Springer Science and Business Media LLC}, + title = {Best practices in data analysis and sharing in +neuroimaging using MRI}, + url = {http://dx.doi.org/10.1038/nn.4500}, + volume = {20}, + year = {2017} +} diff --git a/content/publications/nichols-2017/index.md b/content/publications/nichols-2017/index.md new file mode 100644 index 0000000..56a33f5 --- /dev/null +++ b/content/publications/nichols-2017/index.md @@ -0,0 +1,28 @@ +--- +title: Best practices in data analysis and sharing in neuroimaging using MRI +authors: +- Thomas E Nichols +- Samir Das +- Simon B Eickhoff +- Alan C Evans +- Tristan Glatard +- Michael Hanke +- Nikolaus Kriegeskorte +- Michael P Milham +- Russell A Poldrack +- Jean-Baptiste Poline +- Erika Proal +- Bertrand Thirion +- David C Van Essen +- Tonya White +- B T Thomas Yeo +date: '2017-03-01' +publishDate: '2024-12-19T23:16:36.659132Z' +publication_types: +- article-journal +publication: '*Nature Neuroscience*' +doi: 10.1038/nn.4500 +links: +- name: URL + url: http://dx.doi.org/10.1038/nn.4500 +--- diff --git a/content/publications/niso-2022/cite.bib b/content/publications/niso-2022/cite.bib new file mode 100644 index 0000000..6196179 --- /dev/null +++ b/content/publications/niso-2022/cite.bib @@ -0,0 +1,22 @@ +@article{niso_2022, + author = {Niso, Guiomar and Botvinik-Nezer, Rotem and Appelhoff, +Stefan and De La Vega, Alejandro and Esteban, Oscar and +Etzel, Joset A. and Finc, Karolina and Ganz, Melanie and +Gau, Rémi and Halchenko, Yaroslav O. and Herholz, Peer and +Karakuzu, Agah and Keator, David B. and Markiewicz, +Christopher J. and Maumet, Camille and Pernet, Cyril R. and +Pestilli, Franco and Queder, Nazek and Schmitt, Tina and +Sójka, Weronika and Wagner, Adina S. and Whitaker, Kirstie +J. and Rieger, Jochem W.}, + doi = {10.1016/j.neuroimage.2022.119623}, + issn = {1053-8119}, + journal = {NeuroImage}, + month = {November}, + pages = {119623}, + publisher = {Elsevier BV}, + title = {Open and reproducible neuroimaging: From study inception +to publication}, + url = {http://dx.doi.org/10.1016/j.neuroimage.2022.119623}, + volume = {263}, + year = {2022} +} diff --git a/content/publications/niso-2022/index.md b/content/publications/niso-2022/index.md new file mode 100644 index 0000000..a8eb96f --- /dev/null +++ b/content/publications/niso-2022/index.md @@ -0,0 +1,36 @@ +--- +title: 'Open and reproducible neuroimaging: From study inception to publication' +authors: +- Guiomar Niso +- Rotem Botvinik-Nezer +- Stefan Appelhoff +- Alejandro De La Vega +- Oscar Esteban +- Joset A. Etzel +- Karolina Finc +- Melanie Ganz +- Rémi Gau +- Yaroslav O. Halchenko +- Peer Herholz +- Agah Karakuzu +- David B. Keator +- Christopher J. Markiewicz +- Camille Maumet +- Cyril R. Pernet +- Franco Pestilli +- Nazek Queder +- Tina Schmitt +- Weronika Sójka +- Adina S. Wagner +- Kirstie J. Whitaker +- Jochem W. Rieger +date: '2022-11-01' +publishDate: '2024-12-19T23:16:36.663301Z' +publication_types: +- article-journal +publication: '*NeuroImage*' +doi: 10.1016/j.neuroimage.2022.119623 +links: +- name: URL + url: http://dx.doi.org/10.1016/j.neuroimage.2022.119623 +--- diff --git a/content/publications/notter-2022/cite.bib b/content/publications/notter-2022/cite.bib new file mode 100644 index 0000000..308e737 --- /dev/null +++ b/content/publications/notter-2022/cite.bib @@ -0,0 +1,17 @@ +@article{notter_2022, + author = {Notter, Michael P. and Herholz, Peer and Da Costa, Sandra +and Gulban, Omer F. and Isik, Ayse Ilkay and Gaglianese, +Anna and Murray, Micah M.}, + doi = {10.1007/s10548-022-00935-8}, + issn = {1573-6792}, + journal = {Brain Topography}, + month = {December}, + number = {2}, + pages = {172–191}, + publisher = {Springer Science and Business Media LLC}, + title = {fMRIflows: A Consortium of Fully Automatic Univariate and +Multivariate fMRI Processing Pipelines}, + url = {http://dx.doi.org/10.1007/s10548-022-00935-8}, + volume = {36}, + year = {2022} +} diff --git a/content/publications/notter-2022/index.md b/content/publications/notter-2022/index.md new file mode 100644 index 0000000..7a8a839 --- /dev/null +++ b/content/publications/notter-2022/index.md @@ -0,0 +1,21 @@ +--- +title: 'fMRIflows: A Consortium of Fully Automatic Univariate and Multivariate fMRI + Processing Pipelines' +authors: +- Michael P. Notter +- Peer Herholz +- Sandra Da Costa +- Omer F. Gulban +- Ayse Ilkay Isik +- Anna Gaglianese +- Micah M. Murray +date: '2022-12-01' +publishDate: '2024-12-19T23:16:36.667849Z' +publication_types: +- article-journal +publication: '*Brain Topography*' +doi: 10.1007/s10548-022-00935-8 +links: +- name: URL + url: http://dx.doi.org/10.1007/s10548-022-00935-8 +--- diff --git a/content/publications/ozyurt-2018/cite.bib b/content/publications/ozyurt-2018/cite.bib new file mode 100644 index 0000000..07b7c18 --- /dev/null +++ b/content/publications/ozyurt-2018/cite.bib @@ -0,0 +1,13 @@ +@article{ozyurt_2018, + author = {Ozyurt, Ibrahim Burak and Grethe, Jeffrey S}, + doi = {10.1093/database/bay130}, + issn = {1758-0463}, + journal = {Database}, + month = {January}, + publisher = {Oxford University Press (OUP)}, + title = {Foundry: a message-oriented, horizontally scalable ETL +system for scientific data integration and enhancement}, + url = {http://dx.doi.org/10.1093/database/bay130}, + volume = {2018}, + year = {2018} +} diff --git a/content/publications/ozyurt-2018/index.md b/content/publications/ozyurt-2018/index.md new file mode 100644 index 0000000..4914d99 --- /dev/null +++ b/content/publications/ozyurt-2018/index.md @@ -0,0 +1,16 @@ +--- +title: 'Foundry: a message-oriented, horizontally scalable ETL system for scientific + data integration and enhancement' +authors: +- Ibrahim Burak Ozyurt +- Jeffrey S Grethe +date: '2018-01-01' +publishDate: '2024-12-19T23:16:36.671905Z' +publication_types: +- article-journal +publication: '*Database*' +doi: 10.1093/database/bay130 +links: +- name: URL + url: http://dx.doi.org/10.1093/database/bay130 +--- diff --git a/content/publications/peraza-2023/cite.bib b/content/publications/peraza-2023/cite.bib new file mode 100644 index 0000000..2cc0fc1 --- /dev/null +++ b/content/publications/peraza-2023/cite.bib @@ -0,0 +1,17 @@ +@article{peraza_2023, + author = {Peraza, Julio A. and Salo, Taylor and Riedel, Michael C. +and Bottenhorn, Katherine L. and Poline, Jean-Baptiste and +Dockès, Jérôme and Kent, James D. and Bartley, Jessica +E. and Flannery, Jessica S. and Hill-Bowen, Lauren D. and +Lobo, Rosario Pintos and Poudel, Ranjita and Ray, Kimberly +L. and Robinson, Jennifer L. and Laird, Robert W. and +Sutherland, Matthew T. and de la Vega, Alejandro and Laird, +Angela R.}, + doi = {10.1101/2023.08.01.551505}, + month = {August}, + publisher = {Cold Spring Harbor Laboratory}, + title = {Methods for decoding cortical gradients of functional +connectivity}, + url = {http://dx.doi.org/10.1101/2023.08.01.551505}, + year = {2023} +} diff --git a/content/publications/peraza-2023/index.md b/content/publications/peraza-2023/index.md new file mode 100644 index 0000000..2c14bee --- /dev/null +++ b/content/publications/peraza-2023/index.md @@ -0,0 +1,31 @@ +--- +title: Methods for decoding cortical gradients of functional connectivity +authors: +- Julio A. Peraza +- Taylor Salo +- Michael C. Riedel +- Katherine L. Bottenhorn +- Jean-Baptiste Poline +- Jérôme Dockès +- James D. Kent +- Jessica E. Bartley +- Jessica S. Flannery +- Lauren D. Hill-Bowen +- Rosario Pintos Lobo +- Ranjita Poudel +- Kimberly L. Ray +- Jennifer L. Robinson +- Robert W. Laird +- Matthew T. Sutherland +- Alejandro de la Vega +- Angela R. Laird +date: '2023-08-01' +publishDate: '2024-12-19T23:16:36.675826Z' +publication_types: +- article-journal +publication: '*Cold Spring Harbor Laboratory*' +doi: 10.1101/2023.08.01.551505 +links: +- name: URL + url: http://dx.doi.org/10.1101/2023.08.01.551505 +--- diff --git a/content/publications/perez-lebel-2022/cite.bib b/content/publications/perez-lebel-2022/cite.bib new file mode 100644 index 0000000..6d1ec87 --- /dev/null +++ b/content/publications/perez-lebel-2022/cite.bib @@ -0,0 +1,14 @@ +@article{perez_lebel_2022, + author = {Perez-Lebel, Alexandre and Varoquaux, Gaël and +Le Morvan, Marine and Josse, Julie and Poline, +Jean-Baptiste}, + doi = {10.1093/gigascience/giac013}, + issn = {2047-217X}, + journal = {GigaScience}, + publisher = {Oxford University Press (OUP)}, + title = {Benchmarking missing-values approaches for predictive +models on health databases}, + url = {http://dx.doi.org/10.1093/gigascience/giac013}, + volume = {11}, + year = {2022} +} diff --git a/content/publications/perez-lebel-2022/index.md b/content/publications/perez-lebel-2022/index.md new file mode 100644 index 0000000..9e58b90 --- /dev/null +++ b/content/publications/perez-lebel-2022/index.md @@ -0,0 +1,18 @@ +--- +title: Benchmarking missing-values approaches for predictive models on health databases +authors: +- Alexandre Perez-Lebel +- Gaël Varoquaux +- Marine Le Morvan +- Julie Josse +- Jean-Baptiste Poline +date: '2022-01-01' +publishDate: '2024-12-19T23:16:36.680066Z' +publication_types: +- article-journal +publication: '*GigaScience*' +doi: 10.1093/gigascience/giac013 +links: +- name: URL + url: http://dx.doi.org/10.1093/gigascience/giac013 +--- diff --git a/content/publications/poldrack-2017/cite.bib b/content/publications/poldrack-2017/cite.bib new file mode 100644 index 0000000..8fb4e25 --- /dev/null +++ b/content/publications/poldrack-2017/cite.bib @@ -0,0 +1,18 @@ +@article{poldrack_2017, + author = {Poldrack, Russell A. and Baker, Chris I. and Durnez, Joke +and Gorgolewski, Krzysztof J. and Matthews, Paul M. and +Munafò, Marcus R. and Nichols, Thomas E. and Poline, +Jean-Baptiste and Vul, Edward and Yarkoni, Tal}, + doi = {10.1038/nrn.2016.167}, + issn = {1471-0048}, + journal = {Nature Reviews Neuroscience}, + month = {January}, + number = {2}, + pages = {115–126}, + publisher = {Springer Science and Business Media LLC}, + title = {Scanning the horizon: towards transparent and reproducible +neuroimaging research}, + url = {http://dx.doi.org/10.1038/nrn.2016.167}, + volume = {18}, + year = {2017} +} diff --git a/content/publications/poldrack-2017/index.md b/content/publications/poldrack-2017/index.md new file mode 100644 index 0000000..828e2d3 --- /dev/null +++ b/content/publications/poldrack-2017/index.md @@ -0,0 +1,23 @@ +--- +title: 'Scanning the horizon: towards transparent and reproducible neuroimaging research' +authors: +- Russell A. Poldrack +- Chris I. Baker +- Joke Durnez +- Krzysztof J. Gorgolewski +- Paul M. Matthews +- Marcus R. Munafò +- Thomas E. Nichols +- Jean-Baptiste Poline +- Edward Vul +- Tal Yarkoni +date: '2017-01-01' +publishDate: '2024-12-19T23:16:36.683992Z' +publication_types: +- article-journal +publication: '*Nature Reviews Neuroscience*' +doi: 10.1038/nrn.2016.167 +links: +- name: URL + url: http://dx.doi.org/10.1038/nrn.2016.167 +--- diff --git a/content/publications/poldrack-2024/cite.bib b/content/publications/poldrack-2024/cite.bib new file mode 100644 index 0000000..04b8b35 --- /dev/null +++ b/content/publications/poldrack-2024/cite.bib @@ -0,0 +1,56 @@ +@article{poldrack_2024, + author = {Poldrack, Russell A. and Markiewicz, Christopher J. and +Appelhoff, Stefan and Ashar, Yoni K. and Auer, Tibor and +Baillet, Sylvain and Bansal, Shashank and Beltrachini, +Leandro and Benar, Christian G. and Bertazzoli, Giacomo and +Bhogawar, Suyash and Blair, Ross W. and Bortoletto, Marta +and Boudreau, Mathieu and Brooks, Teon L. and Calhoun, +Vince D. and Castelli, Filippo Maria and Clement, Patricia +and Cohen, Alexander L. and Cohen-Adad, Julien and +D’Ambrosio, Sasha and de Hollander, Gilles and de la +Iglesia-Vayá, María and de la Vega, Alejandro and +Delorme, Arnaud and Devinsky, Orrin and Draschkow, Dejan +and Duff, Eugene Paul and DuPre, Elizabeth and Earl, Eric +and Esteban, Oscar and Feingold, Franklin W. and Flandin, +Guillaume and Galassi, Anthony and Gallitto, Giuseppe and +Ganz, Melanie and Gau, Rémi and Gholam, James and Ghosh, +Satrajit S. and Giacomel, Alessio and Gillman, Ashley G. +and Gleeson, Padraig and Gramfort, Alexandre and Guay, +Samuel and Guidali, Giacomo and Halchenko, Yaroslav O. and +Handwerker, Daniel A. and Hardcastle, Nell and Herholz, +Peer and Hermes, Dora and Honey, Christopher J. and Innis, +Robert B. and Ioanas, Horea-Ioan and Jahn, Andrew and +Karakuzu, Agah and Keator, David B. and Kiar, Gregory and +Kincses, Balint and Laird, Angela R. and Lau, Jonathan C. +and Lazari, Alberto and Legarreta, Jon Haitz and Li, Adam +and Li, Xiangrui and Love, Bradley C. and Lu, Hanzhang and +Marcantoni, Eleonora and Maumet, Camille and Mazzamuto, +Giacomo and Meisler, Steven L. and Mikkelsen, Mark and +Mutsaerts, Henk and Nichols, Thomas E. and Nikolaidis, Aki +and Nilsonne, Gustav and Niso, Guiomar and Norgaard, Martin +and Okell, Thomas W. and Oostenveld, Robert and Ort, Eduard +and Park, Patrick J. and Pawlik, Mateusz and Pernet, Cyril +R. and Pestilli, Franco and Petr, Jan and Phillips, +Christophe and Poline, Jean-Baptiste and Pollonini, Luca +and Raamana, Pradeep Reddy and Ritter, Petra and Rizzo, +Gaia and Robbins, Kay A. and Rockhill, Alexander P. and +Rogers, Christine and Rokem, Ariel and Rorden, Chris and +Routier, Alexandre and Saborit-Torres, Jose Manuel and +Salo, Taylor and Schirner, Michael and Smith, Robert E. and +Spisak, Tamas and Sprenger, Julia and Swann, Nicole C. and +Szinte, Martin and Takerkart, Sylvain and Thirion, Bertrand +and Thomas, Adam G. and Torabian, Sajjad and Varoquaux, +Gael and Voytek, Bradley and Welzel, Julius and Wilson, +Martin and Yarkoni, Tal and Gorgolewski, Krzysztof J.}, + doi = {10.1162/imag_a_00103}, + issn = {2837-6056}, + journal = {Imaging Neuroscience}, + month = {March}, + pages = {1–19}, + publisher = {MIT Press}, + title = {The past, present, and future of the brain imaging data +structure (BIDS)}, + url = {http://dx.doi.org/10.1162/imag_a_00103}, + volume = {2}, + year = {2024} +} diff --git a/content/publications/poldrack-2024/index.md b/content/publications/poldrack-2024/index.md new file mode 100644 index 0000000..47c003d --- /dev/null +++ b/content/publications/poldrack-2024/index.md @@ -0,0 +1,128 @@ +--- +title: The past, present, and future of the brain imaging data structure (BIDS) +authors: +- Russell A. Poldrack +- Christopher J. Markiewicz +- Stefan Appelhoff +- Yoni K. Ashar +- Tibor Auer +- Sylvain Baillet +- Shashank Bansal +- Leandro Beltrachini +- Christian G. Benar +- Giacomo Bertazzoli +- Suyash Bhogawar +- Ross W. Blair +- Marta Bortoletto +- Mathieu Boudreau +- Teon L. Brooks +- Vince D. Calhoun +- Filippo Maria Castelli +- Patricia Clement +- Alexander L. Cohen +- Julien Cohen-Adad +- Sasha D’Ambrosio +- Gilles de Hollander +- María de la Iglesia-Vayá +- Alejandro de la Vega +- Arnaud Delorme +- Orrin Devinsky +- Dejan Draschkow +- Eugene Paul Duff +- Elizabeth DuPre +- Eric Earl +- Oscar Esteban +- Franklin W. Feingold +- Guillaume Flandin +- Anthony Galassi +- Giuseppe Gallitto +- Melanie Ganz +- Rémi Gau +- James Gholam +- Satrajit S. Ghosh +- Alessio Giacomel +- Ashley G. Gillman +- Padraig Gleeson +- Alexandre Gramfort +- Samuel Guay +- Giacomo Guidali +- Yaroslav O. Halchenko +- Daniel A. Handwerker +- Nell Hardcastle +- Peer Herholz +- Dora Hermes +- Christopher J. Honey +- Robert B. Innis +- Horea-Ioan Ioanas +- Andrew Jahn +- Agah Karakuzu +- David B. Keator +- Gregory Kiar +- Balint Kincses +- Angela R. Laird +- Jonathan C. Lau +- Alberto Lazari +- Jon Haitz Legarreta +- Adam Li +- Xiangrui Li +- Bradley C. Love +- Hanzhang Lu +- Eleonora Marcantoni +- Camille Maumet +- Giacomo Mazzamuto +- Steven L. Meisler +- Mark Mikkelsen +- Henk Mutsaerts +- Thomas E. Nichols +- Aki Nikolaidis +- Gustav Nilsonne +- Guiomar Niso +- Martin Norgaard +- Thomas W. Okell +- Robert Oostenveld +- Eduard Ort +- Patrick J. Park +- Mateusz Pawlik +- Cyril R. Pernet +- Franco Pestilli +- Jan Petr +- Christophe Phillips +- Jean-Baptiste Poline +- Luca Pollonini +- Pradeep Reddy Raamana +- Petra Ritter +- Gaia Rizzo +- Kay A. Robbins +- Alexander P. Rockhill +- Christine Rogers +- Ariel Rokem +- Chris Rorden +- Alexandre Routier +- Jose Manuel Saborit-Torres +- Taylor Salo +- Michael Schirner +- Robert E. Smith +- Tamas Spisak +- Julia Sprenger +- Nicole C. Swann +- Martin Szinte +- Sylvain Takerkart +- Bertrand Thirion +- Adam G. Thomas +- Sajjad Torabian +- Gael Varoquaux +- Bradley Voytek +- Julius Welzel +- Martin Wilson +- Tal Yarkoni +- Krzysztof J. Gorgolewski +date: '2024-03-01' +publishDate: '2024-12-19T23:16:36.688055Z' +publication_types: +- article-journal +publication: '*Imaging Neuroscience*' +doi: 10.1162/imag_a_00103 +links: +- name: URL + url: http://dx.doi.org/10.1162/imag_a_00103 +--- diff --git a/content/publications/poline-2019/cite.bib b/content/publications/poline-2019/cite.bib new file mode 100644 index 0000000..0203f7e --- /dev/null +++ b/content/publications/poline-2019/cite.bib @@ -0,0 +1,13 @@ +@article{poline_2019, + author = {Poline, Jean-Baptiste}, + doi = {10.12688/mniopenres.12772.2}, + issn = {2515-5059}, + journal = {MNI Open Research}, + month = {January}, + pages = {1}, + publisher = {F1000 Research Ltd}, + title = {From data sharing to data publishing}, + url = {http://dx.doi.org/10.12688/mniopenres.12772.2}, + volume = {2}, + year = {2019} +} diff --git a/content/publications/poline-2019/index.md b/content/publications/poline-2019/index.md new file mode 100644 index 0000000..c4582c7 --- /dev/null +++ b/content/publications/poline-2019/index.md @@ -0,0 +1,14 @@ +--- +title: From data sharing to data publishing +authors: +- Jean-Baptiste Poline +date: '2019-01-01' +publishDate: '2024-12-19T23:16:36.694105Z' +publication_types: +- article-journal +publication: '*MNI Open Research*' +doi: 10.12688/mniopenres.12772.2 +links: +- name: URL + url: http://dx.doi.org/10.12688/mniopenres.12772.2 +--- diff --git a/content/publications/poline-2022/cite.bib b/content/publications/poline-2022/cite.bib new file mode 100644 index 0000000..7b4f757 --- /dev/null +++ b/content/publications/poline-2022/cite.bib @@ -0,0 +1,21 @@ +@article{poline_2022, + author = {Poline, Jean-Baptiste and Kennedy, David N. and Sommer, +Friedrich T. and Ascoli, Giorgio A. and Van Essen, David C. +and Ferguson, Adam R. and Grethe, Jeffrey S. and Hawrylycz, +Michael J. and Thompson, Paul M. and Poldrack, Russell A. +and Ghosh, Satrajit S. and Keator, David B. and Athey, +Thomas L. and Vogelstein, Joshua T. and Mayberg, Helen S. +and Martone, Maryann E.}, + doi = {10.1007/s12021-021-09557-0}, + issn = {1559-0089}, + journal = {Neuroinformatics}, + month = {January}, + number = {2}, + pages = {507–512}, + publisher = {Springer Science and Business Media LLC}, + title = {Is Neuroscience FAIR? A Call for Collaborative +Standardisation of Neuroscience Data}, + url = {http://dx.doi.org/10.1007/s12021-021-09557-0}, + volume = {20}, + year = {2022} +} diff --git a/content/publications/poline-2022/index.md b/content/publications/poline-2022/index.md new file mode 100644 index 0000000..7123b03 --- /dev/null +++ b/content/publications/poline-2022/index.md @@ -0,0 +1,30 @@ +--- +title: Is Neuroscience FAIR? A Call for Collaborative Standardisation of Neuroscience + Data +authors: +- Jean-Baptiste Poline +- David N. Kennedy +- Friedrich T. Sommer +- Giorgio A. Ascoli +- David C. Van Essen +- Adam R. Ferguson +- Jeffrey S. Grethe +- Michael J. Hawrylycz +- Paul M. Thompson +- Russell A. Poldrack +- Satrajit S. Ghosh +- David B. Keator +- Thomas L. Athey +- Joshua T. Vogelstein +- Helen S. Mayberg +- Maryann E. Martone +date: '2022-01-01' +publishDate: '2024-12-19T23:16:36.697909Z' +publication_types: +- article-journal +publication: '*Neuroinformatics*' +doi: 10.1007/s12021-021-09557-0 +links: +- name: URL + url: http://dx.doi.org/10.1007/s12021-021-09557-0 +--- diff --git a/content/publications/poline-2023/cite.bib b/content/publications/poline-2023/cite.bib new file mode 100644 index 0000000..01571be --- /dev/null +++ b/content/publications/poline-2023/cite.bib @@ -0,0 +1,29 @@ +@article{poline_2023, + author = {Poline, Jean-Baptiste and Das, Samir and Glatard, Tristan +and Madjar, Cécile and Dickie, Erin W. and Lecours, Xavier +and Beaudry, Thomas and Beck, Natacha and Behan, Brendan +and Brown, Shawn T. and Bujold, David and Beauvais, Michael +and Caron, Bryan and Czech, Candice and Dharsee, Moyez and +Dugré, Mathieu and Evans, Ken and Gee, Tom and Ippoliti, +Giulia and Kiar, Gregory and Knoppers, Bartha Maria and +Kuehn, Tristan and Le, Diana and Lo, Derek and Mazaheri, +Mandana and MacFarlane, Dave and Muja, Naser and O’Brien, +Emmet A. and O’Callaghan, Liam and Paiva, Santiago and +Park, Patrick and Quesnel, Darcy and Rabelais, Henri and +Rioux, Pierre and Legault, Mélanie and Tremblay-Mercier, +Jennifer and Rotenberg, David and Stone, Jessica and +Strauss, Ted and Zaytseva, Ksenia and Zhou, Joey and +Duchesne, Simon and Khan, Ali R. and Hill, Sean and Evans, +Alan C.}, + doi = {10.1038/s41597-023-01946-1}, + issn = {2052-4463}, + journal = {Scientific Data}, + month = {April}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {Data and Tools Integration in the Canadian Open +Neuroscience Platform}, + url = {http://dx.doi.org/10.1038/s41597-023-01946-1}, + volume = {10}, + year = {2023} +} diff --git a/content/publications/poline-2023/index.md b/content/publications/poline-2023/index.md new file mode 100644 index 0000000..36e1514 --- /dev/null +++ b/content/publications/poline-2023/index.md @@ -0,0 +1,58 @@ +--- +title: Data and Tools Integration in the Canadian Open Neuroscience Platform +authors: +- Jean-Baptiste Poline +- Samir Das +- Tristan Glatard +- Cécile Madjar +- Erin W. Dickie +- Xavier Lecours +- Thomas Beaudry +- Natacha Beck +- Brendan Behan +- Shawn T. Brown +- David Bujold +- Michael Beauvais +- Bryan Caron +- Candice Czech +- Moyez Dharsee +- Mathieu Dugré +- Ken Evans +- Tom Gee +- Giulia Ippoliti +- Gregory Kiar +- Bartha Maria Knoppers +- Tristan Kuehn +- Diana Le +- Derek Lo +- Mandana Mazaheri +- Dave MacFarlane +- Naser Muja +- Emmet A. O’Brien +- Liam O’Callaghan +- Santiago Paiva +- Patrick Park +- Darcy Quesnel +- Henri Rabelais +- Pierre Rioux +- Mélanie Legault +- Jennifer Tremblay-Mercier +- David Rotenberg +- Jessica Stone +- Ted Strauss +- Ksenia Zaytseva +- Joey Zhou +- Simon Duchesne +- Ali R. Khan +- Sean Hill +- Alan C. Evans +date: '2023-04-01' +publishDate: '2024-12-19T23:16:36.702002Z' +publication_types: +- article-journal +publication: '*Scientific Data*' +doi: 10.1038/s41597-023-01946-1 +links: +- name: URL + url: http://dx.doi.org/10.1038/s41597-023-01946-1 +--- diff --git a/content/publications/publications.bib b/content/publications/publications.bib new file mode 100644 index 0000000..ad440ea --- /dev/null +++ b/content/publications/publications.bib @@ -0,0 +1,2265 @@ + +@Article{ abrams_2021, + title = {A Standards Organization for Open and FAIR Neuroscience: + the International Neuroinformatics Coordinating Facility}, + volume = {20}, + issn = {1559-0089}, + url = {http://dx.doi.org/10.1007/s12021-020-09509-0}, + doi = {10.1007/s12021-020-09509-0}, + number = {1}, + journal = {Neuroinformatics}, + publisher = {Springer Science and Business Media LLC}, + author = {Abrams, Mathew Birdsall and Bjaalie, Jan G. and Das, Samir + and Egan, Gary F. and Ghosh, Satrajit S. and Goscinski, + Wojtek J. and Grethe, Jeffrey S. and Kotaleski, Jeanette + Hellgren and Ho, Eric Tatt Wei and Kennedy, David N. and + Lanyon, Linda J. and Leergaard, Trygve B. and Mayberg, + Helen S. and Milanesi, Luciano and Mouček, Roman and + Poline, J. B. and Roy, Prasun K. and Strother, Stephen C. + and Tang, Tong Boon and Tiesinga, Paul and Wachtler, Thomas + and Wójcik, Daniel K. and Martone, Maryann E.}, + year = {2021}, + month = jan, + pages = {25–36} +} + +@Article{ abrams_2021, + title = {Correction to: A Standards Organization for Open and FAIR + Neuroscience: the International Neuroinformatics + Coordinating Facility}, + volume = {20}, + issn = {1559-0089}, + url = {http://dx.doi.org/10.1007/s12021-021-09522-x}, + doi = {10.1007/s12021-021-09522-x}, + number = {1}, + journal = {Neuroinformatics}, + publisher = {Springer Science and Business Media LLC}, + author = {Abrams, Mathew Birdsall and Bjaalie, Jan G. and Das, Samir + and Egan, Gary F. and Ghosh, Satrajit S. and Goscinski, + Wojtek J. and Grethe, Jeffrey S. and Kotaleski, Jeanette + Hellgren and Ho, Eric Tatt Wei and Kennedy, David N. and + Lanyon, Linda J. and Leergaard, Trygve B. and Mayberg, + Helen S. and Milanesi, Luciano and Mouček, Roman and + Poline, J. 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algorithm predicting + depressive disorders using the T1w/T2w ratio}, + volume = {8}, + issn = {2215-0161}, + url = {http://dx.doi.org/10.1016/j.mex.2021.101595}, + doi = {10.1016/j.mex.2021.101595}, + journal = {MethodsX}, + publisher = {Elsevier BV}, + author = {Baranger, David A.A. and Halchenko, Yaroslav O. and Satz, + Skye and Ragozzino, Rachel and Iyengar, Satish and Swartz, + Holly A. and Manelis, Anna}, + year = {2021}, + pages = {101595} +} + +@Article{ baranger_2021, + title = {Aberrant levels of cortical myelin distinguish individuals + with depressive disorders from healthy controls}, + volume = {32}, + issn = {2213-1582}, + url = {http://dx.doi.org/10.1016/j.nicl.2021.102790}, + doi = {10.1016/j.nicl.2021.102790}, + journal = {NeuroImage: Clinical}, + publisher = {Elsevier BV}, + author = {Baranger, David A.A. and Halchenko, Yaroslav O. and Satz, + Skye and Ragozzino, Rachel and Iyengar, Satish and Swartz, + Holly A. and Manelis, Anna}, + year = {2021}, + pages = {102790} +} + +@Article{ bazeille_2021, + title = {An empirical evaluation of functional alignment using + inter-subject decoding}, + volume = {245}, + issn = {1053-8119}, + url = {http://dx.doi.org/10.1016/j.neuroimage.2021.118683}, + doi = {10.1016/j.neuroimage.2021.118683}, + journal = {NeuroImage}, + publisher = {Elsevier BV}, + author = {Bazeille, Thomas and DuPre, Elizabeth and Richard, Hugo + and Poline, Jean-Baptiste and Thirion, Bertrand}, + year = {2021}, + month = dec, + pages = {118683} +} + +@Article{ bhagwat_2021, + title = {Understanding the impact of preprocessing pipelines on + neuroimaging cortical surface analyses}, + volume = {10}, + issn = {2047-217X}, + url = {http://dx.doi.org/10.1093/gigascience/giaa155}, + doi = {10.1093/gigascience/giaa155}, + number = {1}, + journal = {GigaScience}, + publisher = {Oxford University Press (OUP)}, + author = {Bhagwat, Nikhil and Barry, Amadou and Dickie, Erin W and + Brown, Shawn T and Devenyi, Gabriel A and Hatano, Koji and + DuPre, Elizabeth and Dagher, Alain and Chakravarty, Mallar + and Greenwood, Celia M T and Misic, Bratislav and Kennedy, + David N and Poline, Jean-Baptiste}, + year = {2021}, + month = jan +} + +@Article{ boaro_2022, + title = {Deep neural networks allow expert-level brain meningioma + segmentation and present potential for improvement of + clinical practice}, + volume = {12}, + issn = {2045-2322}, + url = {http://dx.doi.org/10.1038/s41598-022-19356-5}, + doi = {10.1038/s41598-022-19356-5}, + number = {1}, + journal = {Scientific Reports}, + publisher = {Springer Science and Business Media LLC}, + author = {Boaro, Alessandro and Kaczmarzyk, Jakub R. and Kavouridis, + Vasileios K. and Harary, Maya and Mammi, Marco and Dawood, + Hassan and Shea, Alice and Cho, Elise Y. and Juvekar, + Parikshit and Noh, Thomas and Rana, Aakanksha and Ghosh, + Satrajit and Arnaout, Omar}, + year = {2022}, + month = sep +} + +@Article{ bollmann_2023, + title = {Neurodesk: An accessible, flexible, and portable data + analysis environment for reproducible neuroimaging}, + url = {http://dx.doi.org/10.21203/rs.3.rs-2649734/v1}, + doi = {10.21203/rs.3.rs-2649734/v1}, + publisher = {Research Square Platform LLC}, + author = {Bollmann, Steffen and Renton, Angela and Dao, Thuy and + Johnstone, Tom and Civier, Oren and Sullivan, Ryan and + White, David and Lyons, Paris and Slade, Benjamin and + Abbott, David and Amos, Toluwani and Bollmann, Saskia and + Botting, Andy and Campbell, Megan and Chang, Jeryn and + Close, Thomas and Eckstein, Korbinian and Egan, Gary and + Evas, Stefanie and Flandin, Guillaume and Garner, Kelly and + Garrido, Marta and Ghosh, Satrajit and Grignard, Martin and + Hannan, Anthony and Huber, Laurentius (Renzo) and + Kaczmarzyk, Jakub and Kasper, Lars and Kuhlmann, Levin and + Lou, Kexin and Mantilla-Ramos, Yorguin-Jose and Mattingley, + Jason and Morris, Jo and Narayanan, Akshaiy and Pestilli, + Franco and Puce, Aina and Ribeiro, Fernanda and Rogasch, + Nigel and Rorden, Chris and Schira, Mark and Shaw, Thomas + and Sowman, Paul and Spitz, Gershon and Stewart, Ashley and + Ye, Xincheng and Zhu, Judy and Hughes, Matthew and + Narayanan, Aswin}, + year = {2023}, + month = mar +} + +@Article{ botvinik_nezer_2020, + title = {Variability in the analysis of a single neuroimaging + dataset by many teams}, + volume = {582}, + issn = {1476-4687}, + url = {http://dx.doi.org/10.1038/s41586-020-2314-9}, + doi = {10.1038/s41586-020-2314-9}, + number = {7810}, + journal = {Nature}, + publisher = {Springer Science and Business Media LLC}, + author = {Botvinik-Nezer, Rotem and Holzmeister, Felix and Camerer, + Colin F. and Dreber, Anna and Huber, Juergen and + Johannesson, Magnus and Kirchler, Michael and Iwanir, Roni + and Mumford, Jeanette A. and Adcock, R. Alison and Avesani, + Paolo and Baczkowski, Blazej M. and Bajracharya, Aahana and + Bakst, Leah and Ball, Sheryl and Barilari, Marco and Bault, + Nadège and Beaton, Derek and Beitner, Julia and Benoit, + Roland G. and Berkers, Ruud M. W. J. and Bhanji, Jamil P. + and Biswal, Bharat B. and Bobadilla-Suarez, Sebastian and + Bortolini, Tiago and Bottenhorn, Katherine L. and Bowring, + Alexander and Braem, Senne and Brooks, Hayley R. and + Brudner, Emily G. and Calderon, Cristian B. and Camilleri, + Julia A. and Castrellon, Jaime J. and Cecchetti, Luca and + Cieslik, Edna C. and Cole, Zachary J. and Collignon, + Olivier and Cox, Robert W. and Cunningham, William A. and + Czoschke, Stefan and Dadi, Kamalaker and Davis, Charles P. + and Luca, Alberto De and Delgado, Mauricio R. and + Demetriou, Lysia and Dennison, Jeffrey B. and Di, Xin and + Dickie, Erin W. and Dobryakova, Ekaterina and Donnat, + Claire L. and Dukart, Juergen and Duncan, Niall W. and + Durnez, Joke and Eed, Amr and Eickhoff, Simon B. and + Erhart, Andrew and Fontanesi, Laura and Fricke, G. Matthew + and Fu, Shiguang and Galván, Adriana and Gau, Remi and + Genon, Sarah and Glatard, Tristan and Glerean, Enrico and + Goeman, Jelle J. and Golowin, Sergej A. E. and + González-García, Carlos and Gorgolewski, Krzysztof J. and + Grady, Cheryl L. and Green, Mikella A. and Guassi Moreira, + João F. and Guest, Olivia and Hakimi, Shabnam and + Hamilton, J. Paul and Hancock, Roeland and Handjaras, + Giacomo and Harry, Bronson B. and Hawco, Colin and Herholz, + Peer and Herman, Gabrielle and Heunis, Stephan and + Hoffstaedter, Felix and Hogeveen, Jeremy and Holmes, Susan + and Hu, Chuan-Peng and Huettel, Scott A. and Hughes, + Matthew E. and Iacovella, Vittorio and Iordan, Alexandru D. + and Isager, Peder M. and Isik, Ayse I. and Jahn, Andrew and + Johnson, Matthew R. and Johnstone, Tom and Joseph, Michael + J. E. and Juliano, Anthony C. and Kable, Joseph W. and + Kassinopoulos, Michalis and Koba, Cemal and Kong, + Xiang-Zhen and Koscik, Timothy R. and Kucukboyaci, Nuri + Erkut and Kuhl, Brice A. and Kupek, Sebastian and Laird, + Angela R. and Lamm, Claus and Langner, Robert and + Lauharatanahirun, Nina and Lee, Hongmi and Lee, Sangil and + Leemans, Alexander and Leo, Andrea and Lesage, Elise and + Li, Flora and Li, Monica Y. 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Todd and Grant, Steven J. and Dowling, + Gayathri J. and Brown, Sandra A. and Jernigan, Terry L. and + Dale, Anders M.}, + year = {2019}, + month = nov, + pages = {116091} +} + +@Article{ halchenko_2021, + title = {DataLad: distributed system for joint management of code, + data, and their relationship}, + volume = {6}, + issn = {2475-9066}, + url = {http://dx.doi.org/10.21105/joss.03262}, + doi = {10.21105/joss.03262}, + number = {63}, + journal = {Journal of Open Source Software}, + publisher = {The Open Journal}, + author = {Halchenko, Yaroslav and Meyer, Kyle and Poldrack, Benjamin + and Solanky, Debanjum and Wagner, Adina and Gors, Jason and + MacFarlane, Dave and Pustina, Dorian and Sochat, Vanessa + and Ghosh, Satrajit and Mönch, Christian and Markiewicz, + Christopher and Waite, Laura and Shlyakhter, Ilya and de la + Vega, Alejandro and Hayashi, Soichi and Häusler, Christian + and Poline, Jean-Baptiste and Kadelka, Tobias and Skytén, + Kusti and Jarecka, Dorota and Kennedy, David and Strauss, + Ted and Cieslak, Matt and Vavra, Peter and Ioanas, + Horea-Ioan and Schneider, Robin and Pflüger, Mika and + Haxby, James and Eickhoff, Simon and Hanke, Michael}, + year = {2021}, + month = jul, + pages = {3262} +} + +@Article{ halchenko_2024, + title = {HeuDiConv — flexible DICOM conversion into structured + directory layouts}, + volume = {9}, + issn = {2475-9066}, + url = {http://dx.doi.org/10.21105/joss.05839}, + doi = {10.21105/joss.05839}, + number = {99}, + journal = {Journal of Open Source Software}, + publisher = {The Open Journal}, + author = {Halchenko, Yaroslav O. and Goncalves, Mathias and Ghosh, + Satrajit and Velasco, Pablo and Visconti di Oleggio + Castello, Matteo and Salo, Taylor and Wodder, John T. and + Hanke, Michael and Sadil, Patrick and Gorgolewski, + Krzysztof Jacek and Ioanas, Horea-Ioan and Rorden, Chris + and Hendrickson, Timothy J. and Dayan, Michael and + Houlihan, Sean Dae and Kent, James and Strauss, Ted and + Lee, John and To, Isaac and Markiewicz, Christopher J. and + Lukas, Darren and Butler, Ellyn R. and Thompson, Todd and + Termenon, Maite and Smith, David V. and Macdonald, Austin + and Kennedy, David N.}, + year = {2024}, + month = jul, + pages = {5839} +} + +@Article{ hanke_2021, + title = {In defense of decentralized research data management}, + volume = {0}, + issn = {0947-0875}, + url = {http://dx.doi.org/10.1515/nf-2020-0037}, + doi = {10.1515/nf-2020-0037}, + number = {0}, + journal = {Neuroforum}, + publisher = {Walter de Gruyter GmbH}, + author = {Hanke, Michael and Pestilli, Franco and Wagner, Adina S. + and Markiewicz, Christopher J. and Poline, Jean-Baptiste + and Halchenko, Yaroslav O.}, + year = {2021}, + month = jan +} + +@Article{ hodge_2021, + title = {An assessment of the autism neuroimaging literature for + the prospects of re-executability}, + volume = {9}, + issn = {2046-1402}, + url = {http://dx.doi.org/10.12688/f1000research.25306.2}, + doi = {10.12688/f1000research.25306.2}, + journal = {F1000Research}, + publisher = {F1000 Research Ltd}, + author = {Hodge, Steven M. and Haselgrove, Christian and Honor, Leah + and Kennedy, David N. and Frazier, Jean A.}, + year = {2021}, + month = mar, + pages = {1031} +} + +@Article{ honor_2016, + title = {Data Citation in Neuroimaging: Proposed Best Practices for + Data Identification and Attribution}, + volume = {10}, + issn = {1662-5196}, + url = {http://dx.doi.org/10.3389/fninf.2016.00034}, + doi = {10.3389/fninf.2016.00034}, + journal = {Frontiers in Neuroinformatics}, + publisher = {Frontiers Media SA}, + author = {Honor, Leah B. and Haselgrove, Christian and Frazier, Jean + A. and Kennedy, David N.}, + year = {2016}, + month = aug +} + +@Article{ hubbard_2020, + title = {Brain function and clinical characterization in the Boston + adolescent neuroimaging of depression and anxiety study}, + volume = {27}, + issn = {2213-1582}, + url = {http://dx.doi.org/10.1016/j.nicl.2020.102240}, + doi = {10.1016/j.nicl.2020.102240}, + journal = {NeuroImage: Clinical}, + publisher = {Elsevier BV}, + author = {Hubbard, N.A. and Siless, V. and Frosch, I.R. and + Goncalves, M. and Lo, N. and Wang, J. and Bauer, C.C.C. and + Conroy, K. and Cosby, E. and Hay, A. and Jones, R. and + Pinaire, M. and Vaz De Souza, F. and Vergara, G. and Ghosh, + S. and Henin, A. and Hirshfeld-Becker, D.R. and Hofmann, + S.G. and Rosso, I.M. and Auerbach, R.P. and Pizzagalli, + D.A. and Yendiki, A. and Gabrieli, J.D.E. and + Whitfield-Gabrieli, S.}, + year = {2020}, + pages = {102240} +} + +@Article{ hubbard_2024, + title = {The Human Connectome Project of adolescent anxiety and + depression dataset}, + volume = {11}, + issn = {2052-4463}, + url = {http://dx.doi.org/10.1038/s41597-024-03629-x}, + doi = {10.1038/s41597-024-03629-x}, + number = {1}, + journal = {Scientific Data}, + publisher = {Springer Science and Business Media LLC}, + author = {Hubbard, N. A. and Bauer, C. C. C. and Siless, V. and + Auerbach, R. P. and Elam, J. S. and Frosch, I. R. and + Henin, A. and Hofmann, S. G. and Hodge, M. R. and Jones, R. + and Lenzini, P. and Lo, N. and Park, A. T. and Pizzagalli, + D. A. and Vaz-DeSouza, F. and Gabrieli, J. D. E. and + Whitfield-Gabrieli, S. and Yendiki, A. and Ghosh, S. S.}, + year = {2024}, + month = aug +} + +@Article{ hung_2020, + title = {Cingulum-Callosal white-matter microstructure associated + with emotional dysregulation in children: A diffusion + tensor imaging study}, + volume = {27}, + issn = {2213-1582}, + url = {http://dx.doi.org/10.1016/j.nicl.2020.102266}, + doi = {10.1016/j.nicl.2020.102266}, + journal = {NeuroImage: Clinical}, + publisher = {Elsevier BV}, + author = {Hung, Yuwen and Uchida, Mai and Gaillard, Schuyler L. and + Woodworth, Hilary and Kelberman, Caroline and Capella, + James and Kadlec, Kelly and Goncalves, Mathias and Ghosh, + Satrajit and Yendiki, Anastasia and Chai, Xiaoqian J. and + Hirshfeld-Becker, Dina R. and Whitfield-Gabrieli, Susan and + Gabrieli, John D.E. and Biederman, Joseph}, + year = {2020}, + pages = {102266} +} + +@Article{ huntenburg_2017, + title = {A Systematic Relationship Between Functional Connectivity + and Intracortical Myelin in the Human Cerebral Cortex}, + volume = {27}, + issn = {1460-2199}, 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pages = {glw236} +} + +@Article{ kennedy_2017, + title = {The Information Sharing Statement Grows Some Teeth}, + volume = {15}, + issn = {1559-0089}, + url = {http://dx.doi.org/10.1007/s12021-017-9331-3}, + doi = {10.1007/s12021-017-9331-3}, + number = {2}, + journal = {Neuroinformatics}, + publisher = {Springer Science and Business Media LLC}, + author = {Kennedy, David N.}, + year = {2017}, + month = apr, + pages = {113–114} +} + +@Article{ kennedy_2018, + title = {Neuroimaging Neuroinformatics: Sample Size and Other + Evolutionary Topics}, + volume = {16}, + issn = {1559-0089}, + url = {http://dx.doi.org/10.1007/s12021-018-9379-8}, + doi = {10.1007/s12021-018-9379-8}, + number = {2}, + journal = {Neuroinformatics}, + publisher = {Springer Science and Business Media LLC}, + author = {Kennedy, David N.}, + year = {2018}, + month = apr, + pages = {149–150} +} + +@Article{ kennedy_2019, + title = {Everything Matters: The ReproNim Perspective on + Reproducible Neuroimaging}, + volume = {13}, + issn = {1662-5196}, + url = {http://dx.doi.org/10.3389/fninf.2019.00001}, + doi = {10.3389/fninf.2019.00001}, + journal = {Frontiers in Neuroinformatics}, + publisher = {Frontiers Media SA}, + author = {Kennedy, David N. and Abraham, Sanu A. and Bates, Julianna + F. and Crowley, Albert and Ghosh, Satrajit and Gillespie, + Tom and Goncalves, Mathias and Grethe, Jeffrey S. and + Halchenko, Yaroslav O. and Hanke, Michael and Haselgrove, + Christian and Hodge, Steven M. and Jarecka, Dorota and + Kaczmarzyk, Jakub and Keator, David B. and Meyer, Kyle and + Martone, Maryann E. and Padhy, Smruti and Poline, + Jean-Baptiste and Preuss, Nina and Sincomb, Troy and + Travers, Matt}, + year = {2019}, + month = feb +} + +@Article{ keshavan_2019, + title = {From the Wet Lab to the Web Lab: A Paradigm Shift in Brain + Imaging Research}, + volume = {13}, + issn = {1662-5196}, + url = {http://dx.doi.org/10.3389/fninf.2019.00003}, + doi = {10.3389/fninf.2019.00003}, + journal = {Frontiers in Neuroinformatics}, + publisher = {Frontiers Media SA}, + author = {Keshavan, Anisha and Poline, Jean-Baptiste}, + year = {2019}, + month = mar +} + +@Article{ kiar_2023, + title = {Align with the NMIND consortium for better neuroimaging}, + volume = {7}, + issn = {2397-3374}, + url = {http://dx.doi.org/10.1038/s41562-023-01647-0}, + doi = {10.1038/s41562-023-01647-0}, + number = {7}, + journal = {Nature Human Behaviour}, + publisher = {Springer Science and Business Media LLC}, + author = {Kiar, Gregory and Clucas, Jon and Feczko, Eric and + Goncalves, Mathias and Jarecka, Dorota and Markiewicz, + Christopher J. and Halchenko, Yaroslav O. and Hermosillo, + Robert and Li, Xinhui and Miranda-Dominguez, Oscar and + Ghosh, Satrajit and Poldrack, Russell A. and Satterthwaite, + Theodore D. and Milham, Michael P. and Fair, Damien}, + year = {2023}, + month = jun, + pages = {1027–1028} +} + +@Article{ kim_2018, + title = {Experimenting with reproducibility: a case study of + robustness in bioinformatics}, + volume = {7}, + issn = {2047-217X}, + url = {http://dx.doi.org/10.1093/gigascience/giy077}, + doi = {10.1093/gigascience/giy077}, + number = {7}, + journal = {GigaScience}, + publisher = {Oxford University Press (OUP)}, + author = {Kim, Yang-Min and Poline, Jean-Baptiste and Dumas, + Guillaume}, + year = {2018}, + month = jun +} + +@Article{ klein_2017, + title = {Mindboggling morphometry of human brains}, + volume = {13}, + issn = {1553-7358}, + url = {http://dx.doi.org/10.1371/journal.pcbi.1005350}, + doi = {10.1371/journal.pcbi.1005350}, + number = {2}, + journal = {PLOS Computational Biology}, + publisher = {Public Library of Science (PLoS)}, + author = {Klein, Arno and Ghosh, Satrajit S. and Bao, Forrest S. and + Giard, Joachim and Häme, Yrjö and Stavsky, Eliezer and + Lee, Noah and Rossa, Brian and Reuter, Martin and Chaibub + Neto, Elias and Keshavan, Anisha}, + editor = {Schneidman, Dina}, + year = {2017}, + month = feb, + pages = {e1005350} +} + +@Article{ klein_2021, + title = {Remote Digital Psychiatry for Mobile Mental Health + Assessment and Therapy: MindLogger Platform Development + Study}, + volume = {23}, + issn = {1438-8871}, + url = {http://dx.doi.org/10.2196/22369}, + doi = {10.2196/22369}, + number = {11}, + journal = {Journal of Medical Internet Research}, + publisher = {JMIR Publications Inc.}, + author = {Klein, Arno and Clucas, Jon and Krishnakumar, Anirudh and + Ghosh, Satrajit S and Van Auken, Wilhelm and Thonet, + Benjamin and Sabram, Ihor and Acuna, Nino and Keshavan, + Anisha and Rossiter, Henry and Xiao, Yao and Semenuta, + Sergey and Badioli, Alessandra and Konishcheva, Kseniia and + Abraham, Sanu Ann and Alexander, Lindsay M and Merikangas, + Kathleen R and Swendsen, Joel and Lindner, Ariel B and + Milham, Michael P}, + year = {2021}, + month = nov, + pages = {e22369} +} + +@Article{ kumar_2022, + title = {The Neuroimaging Data Model Linear Regression Tool + (nidm_linreg): PyNIDM Project}, + volume = {11}, + issn = {2046-1402}, + url = {http://dx.doi.org/10.12688/f1000research.108008.2}, + doi = {10.12688/f1000research.108008.2}, + journal = {F1000Research}, + publisher = {F1000 Research Ltd}, + author = {Kumar, Ashmita and Crowley, Albert and Queder, Nazek and + Poline, JB and Ghosh, Satrajit S. and Kennedy, David and + Grethe, Jeffrey S. and Helmer, Karl G. and Keator, David + B.}, + year = {2022}, + month = jul, + pages = {228} +} + +@Article{ larivi_re_2023, + title = {BrainStat: A toolbox for brain-wide statistics and + multimodal feature associations}, + volume = {266}, + issn = {1053-8119}, + url = {http://dx.doi.org/10.1016/j.neuroimage.2022.119807}, + doi = {10.1016/j.neuroimage.2022.119807}, + journal = {NeuroImage}, + publisher = {Elsevier BV}, + author = {Larivière, Sara and Bayrak, Şeyma and Vos de Wael, + Reinder and Benkarim, Oualid and Herholz, Peer and + Rodriguez-Cruces, Raul and Paquola, Casey and Hong, + Seok-Jun and Misic, Bratislav and Evans, Alan C. and Valk, + Sofie L. and Bernhardt, Boris C.}, + year = {2023}, + month = feb, + pages = {119807} +} + +@Article{ lin_2020, + title = {The TRUST Principles for digital repositories}, + volume = {7}, + issn = {2052-4463}, + url = {http://dx.doi.org/10.1038/s41597-020-0486-7}, + doi = {10.1038/s41597-020-0486-7}, + number = {1}, + journal = {Scientific Data}, + publisher = {Springer Science and Business Media LLC}, + author = {Lin, Dawei and Crabtree, Jonathan and Dillo, Ingrid and + Downs, Robert R. and Edmunds, Rorie and Giaretta, David and + De Giusti, Marisa and L’Hours, Hervé and Hugo, Wim and + Jenkyns, Reyna and Khodiyar, Varsha and Martone, Maryann E. + and Mokrane, Mustapha and Navale, Vivek and Petters, + Jonathan and Sierman, Barbara and Sokolova, Dina V. and + Stockhause, Martina and Westbrook, John}, + year = {2020}, + month = may +} + +@Article{ lin_2024, + title = {Transforming modeling in neurorehabilitation: clinical + insights for personalized rehabilitation}, + volume = {21}, + issn = {1743-0003}, + url = {http://dx.doi.org/10.1186/s12984-024-01309-w}, + doi = {10.1186/s12984-024-01309-w}, + number = {1}, + journal = {Journal of NeuroEngineering and Rehabilitation}, + publisher = {Springer Science and Business Media LLC}, + author = {Lin, David J. and Backus, Deborah and Chakraborty, Stuti + and Liew, Sook-Lei and Valero-Cuevas, Francisco J. and + Patten, Carolynn and Cotton, R James}, + year = {2024}, + month = feb +} + +@Article{ lo_2023, + title = {A standardized protocol for manually segmenting stroke + lesions on high-resolution T1-weighted MR images}, + volume = {1}, + issn = {2813-1193}, + url = {http://dx.doi.org/10.3389/fnimg.2022.1098604}, + doi = {10.3389/fnimg.2022.1098604}, + journal = {Frontiers in Neuroimaging}, + publisher = {Frontiers Media SA}, + author = {Lo, Bethany P. and Donnelly, Miranda R. and Barisano, + Giuseppe and Liew, Sook-Lei}, + year = {2023}, + month = jan +} + +@Article{ low_2020, + title = {Identifying bias in models that detect vocal fold + paralysis from audio recordings using explainable machine + learning and clinician ratings}, + url = {http://dx.doi.org/10.1101/2020.11.23.20235945}, + doi = {10.1101/2020.11.23.20235945}, + publisher = {Cold Spring Harbor Laboratory}, + author = {Low, Daniel M. and Rao, Vishwanatha and Randolph, Gregory + and Song, Phillip C. and Ghosh, Satrajit S.}, + year = {2020}, + month = nov +} + +@Article{ low_2020, + title = {Automated assessment of psychiatric disorders using + speech: A systematic review}, + volume = {5}, + issn = {2378-8038}, + url = {http://dx.doi.org/10.1002/lio2.354}, + doi = {10.1002/lio2.354}, + number = {1}, + journal = {Laryngoscope Investigative Otolaryngology}, + publisher = {Wiley}, + author = {Low, Daniel M. and Bentley, Kate H. and Ghosh, Satrajit + S.}, + year = {2020}, + month = jan, + pages = {96–116} +} + +@Article{ low_2024, + title = {Identifying bias in models that detect vocal fold + paralysis from audio recordings using explainable machine + learning and clinician ratings}, + volume = {3}, + issn = {2767-3170}, + url = {http://dx.doi.org/10.1371/journal.pdig.0000516}, + doi = {10.1371/journal.pdig.0000516}, + number = {5}, + journal = {PLOS Digital Health}, + publisher = {Public Library of Science (PLoS)}, + author = {Low, Daniel M. and Rao, Vishwanatha and Randolph, Gregory + and Song, Phillip C. and Ghosh, Satrajit S.}, + editor = {Li-Jessen, Nicole Yee-Key}, + year = {2024}, + month = may, + pages = {e0000516} +} + +@Article{ makris_2023, + title = {A Proposed Human Structural Brain Connectivity Matrix in + the Center for Morphometric Analysis Harvard-Oxford Atlas + Framework: A Historical Perspective and Future Direction + for Enhancing the Precision of Human Structural + Connectivity with a Novel Neuroanatomical Typology}, + volume = {45}, + issn = {1421-9859}, + url = {http://dx.doi.org/10.1159/000530358}, + doi = {10.1159/000530358}, + number = {4}, + journal = {Developmental Neuroscience}, + publisher = {S. Karger AG}, + author = {Makris, Nikos and Rushmore, Richard and Kaiser, Jonathan + and Albaugh, Matthew and Kubicki, Marek and Rathi, Yogesh + and Zhang, Fan and O’Donnell, Lauren J. and Yeterian, + Edward and Caviness, Verne S. and Kennedy, David N.}, + year = {2023}, + pages = {161–180} +} + +@Article{ manelis_2021, + title = {White matter abnormalities in adults with bipolar disorder + type-II and unipolar depression}, + volume = {11}, + issn = {2045-2322}, + url = {http://dx.doi.org/10.1038/s41598-021-87069-2}, + doi = {10.1038/s41598-021-87069-2}, + number = {1}, + journal = {Scientific Reports}, + publisher = {Springer Science and Business Media LLC}, + author = {Manelis, Anna and Soehner, Adriane and Halchenko, Yaroslav + O. and Satz, Skye and Ragozzino, Rachel and Lucero, Mora + and Swartz, Holly A. and Phillips, Mary L. and Versace, + Amelia}, + year = {2021}, + month = apr +} + +@Article{ manelis_2022, + title = {Working memory updating in individuals with bipolar and + unipolar depression: fMRI study}, + volume = {12}, + issn = {2158-3188}, + url = {http://dx.doi.org/10.1038/s41398-022-02211-6}, + doi = {10.1038/s41398-022-02211-6}, + number = {1}, + journal = {Translational Psychiatry}, + publisher = {Springer Science and Business Media LLC}, + author = {Manelis, Anna and Halchenko, Yaroslav O. and Bonar, Lisa + and Stiffler, Richelle S. and Satz, Skye and Miceli, Rachel + and Ladouceur, Cecile D. and Bebko, Genna and Iyengar, + Satish and Swartz, Holly A. and Phillips, Mary L.}, + year = {2022}, + month = oct +} + +@Article{ margulies_2016, + title = {Situating the default-mode network along a principal + gradient of macroscale cortical organization}, + volume = {113}, + issn = {1091-6490}, + url = {http://dx.doi.org/10.1073/pnas.1608282113}, + doi = {10.1073/pnas.1608282113}, + number = {44}, + journal = {Proceedings of the National Academy of Sciences}, + publisher = {Proceedings of the National Academy of Sciences}, + author = {Margulies, Daniel S. and Ghosh, Satrajit S. and Goulas, + Alexandros and Falkiewicz, Marcel and Huntenburg, Julia M. + and Langs, Georg and Bezgin, Gleb and Eickhoff, Simon B. + and Castellanos, F. Xavier and Petrides, Michael and + Jefferies, Elizabeth and Smallwood, Jonathan}, + year = {2016}, + month = oct, + pages = {12574–12579} +} + +@Article{ markello_2021, + title = {Standardizing workflows in imaging transcriptomics with + the abagen toolbox}, + volume = {10}, + issn = {2050-084X}, + url = {http://dx.doi.org/10.7554/elife.72129}, + doi = {10.7554/elife.72129}, + journal = {eLife}, + publisher = {eLife Sciences Publications, Ltd}, + author = {Markello, Ross D and Arnatkeviciute, Aurina and Poline, + Jean-Baptiste and Fulcher, Ben D and Fornito, Alex and + Misic, Bratislav}, + year = {2021}, + month = nov +} + +@Article{ markiewicz_2021, + title = {The OpenNeuro resource for sharing of neuroscience data}, + volume = {10}, + issn = {2050-084X}, + url = {http://dx.doi.org/10.7554/elife.71774}, + doi = {10.7554/elife.71774}, + journal = {eLife}, + publisher = {eLife Sciences Publications, Ltd}, + author = {Markiewicz, Christopher J and Gorgolewski, Krzysztof J and + Feingold, Franklin and Blair, Ross and Halchenko, Yaroslav + O and Miller, Eric and Hardcastle, Nell and Wexler, Joe and + Esteban, Oscar and Goncavles, Mathias and Jwa, Anita and + Poldrack, Russell}, + year = {2021}, + month = oct +} + +@Article{ maumet_2016, + title = {Sharing brain mapping statistical results with the + neuroimaging data model}, + volume = {3}, + issn = {2052-4463}, + url = {http://dx.doi.org/10.1038/sdata.2016.102}, + doi = {10.1038/sdata.2016.102}, + number = {1}, + journal = {Scientific Data}, + publisher = {Springer Science and Business Media LLC}, + author = {Maumet, Camille and Auer, Tibor and Bowring, Alexander and + Chen, Gang and Das, Samir and Flandin, Guillaume and Ghosh, + Satrajit and Glatard, Tristan and Gorgolewski, Krzysztof J. + and Helmer, Karl G. and Jenkinson, Mark and Keator, David + B. and Nichols, B. Nolan and Poline, Jean-Baptiste and + Reynolds, Richard and Sochat, Vanessa and Turner, Jessica + and Nichols, Thomas E.}, + year = {2016}, + month = dec +} + +@Article{ mcavoy_2021, + title = {Classification of glioblastoma versus primary central + nervous system lymphoma using convolutional neural + networks}, + volume = {11}, + issn = {2045-2322}, + url = {http://dx.doi.org/10.1038/s41598-021-94733-0}, + doi = {10.1038/s41598-021-94733-0}, + number = {1}, + journal = {Scientific Reports}, + publisher = {Springer Science and Business Media LLC}, + author = {McAvoy, Malia and Prieto, Paola Calvachi and Kaczmarzyk, + Jakub R. and Fernández, Iván Sánchez and McNulty, Jack + and Smith, Timothy and Yu, Kun-Hsing and Gormley, William + B. and Arnaout, Omar}, + year = {2021}, + month = jul +} + +@Article{ mcnaughton_2022, + title = {Quantitative MRI Characterization of the Extremely Preterm + Brain at Adolescence: Atypical versus Neurotypical + Developmental Pathways}, + volume = {304}, + issn = {1527-1315}, + url = {http://dx.doi.org/10.1148/radiol.210385}, + doi = {10.1148/radiol.210385}, + number = {2}, + journal = {Radiology}, + publisher = {Radiological Society of North America (RSNA)}, + author = {McNaughton, Ryan and Pieper, Chris and Sakai, Osamu and + Rollins, Julie V. and Zhang, Xin and Kennedy, David N. and + Frazier, Jean A. and Douglass, Laurie and Heeren, Timothy + and Fry, Rebecca C. and O’Shea, T. Michael and Kuban, + Karl K. and Jara, Hernán and Rollins, Julie V. and Shah, + Bhavesh and Singh, Rachana and Vaidya, Ruben and Van + Marter, Linda and Martin, Camilla and Ware, Janice and + Rollins, Caitlin and Cole, Cynthia and Perrin, Ellen and + Sakai, Christina and Bednarek, Frank and Frazier, Jean and + Ehrenkranz, Richard and Benjamin, Jennifer and Montgomery, + Angela and O’Shea, T. Michael and Washburn, Lisa and + Gogcu, Semsa and Bose, Carl and Warner, Diane and O’Shea, + T. Michael and Engelke, Steve and Higginson, Amanda and + Higginson, Jason and Bear, Kelly and Poortenga, Mariel and + Pastyrnak, Steve and Karna, Padu and Paneth, Nigel and + Lenski, Madeleine and Schreiber, Michael and Hunter, Scott + and Msall, Michael and Batton, Danny and Klarr, Judith and + Lee, Young Ah and Obeid, Rawad and Christianson, Karen and + Klein, Deborah and Wagner, Katie and Pimental, Maureen and + Hallisey, Collen and Coster, Taryn and Dolins, Maddie and + Mittleman, Maggie and Haile, Hannah and Rohde, Julia and + Nylen, Ellen and Neger, Emily and Mattern, Kathryn and Ma, + Catherine and Toner, Deanna and Vitaro, Elizabeth and + Venuti, Lauren and Powers, Beth and Foley, Ann and Sacco, + Taylor and Williams, Joanne and Romano, Elaine and Henry, + Christine and Hiatt, Debbie and Peters, Nancy and Brown, + Patricia and Ansusinha, Emily and Smith, Jazmyne and Yang, + Nou and Bose, Gennie and Wereszczak, Janice and Bernhardt, + Janice and Adams, Joan and Wilson, Donna and Darden-Saad, + Nancy and Williams, Bree and Jones, Emily and Sutton, Dinah + and Rathbun, Julie and Fagerman, Stephanie and Boshoven, + William and Johnson, Jalen and James, Brandon and Miras, + Karen and Solomon, Carolyn and Weiland, Deborah and Yoon, + Grace and Ramoskaite, Rugile and Wiggins, Suzanne and + Washington, Krissy and Martin, Ryan and Prendergast, + Barbara and Lynch, Emma and Kring, Beth and Smith, Anne and + McQuiston, Susan and Butler, Samantha and Wilson, Rachel + and McGhee, Kirsten and Lee, Patricia and Asgarian, Aimee + and Sadhwani, Anjali and Henson, Brandi and Keller, Cecelia + and Walkowiak, Jenifer and Barron, Susan and Miller, Alice + and Dessureau, Brian and Wood, Molly and Damon-Minow, Jill + and Romano, Elaine and Mayes, Linda and Tsatsanis, Kathy + and Chawarska, Katarzyna and Kim, Sophy and Dieterich, + Susan and Bearrs, Karen and Waldrep, Ellen and Friedman, + Jackie and Hounshell, Gail and Allred, Debbie and Helms, + Rebecca and Whitley, Lynn and Stainback, Gary and Bostic, + Lisa and Jacobson, Amanda and McKeeman, Joni and Meyer, + Echo and Price, Joan and Lloyd, Megan and Plesha-Troyke, + Susan and Scott, Megan and Solomon, Katherine M. and + Brooklier, Kara and Vogt, Kelly}, + year = {2022}, + month = aug, + pages = {419–428} +} + +@Article{ millman_2018, + title = {Teaching Computational Reproducibility for Neuroimaging}, + volume = {12}, + issn = {1662-453X}, + url = {http://dx.doi.org/10.3389/fnins.2018.00727}, + doi = {10.3389/fnins.2018.00727}, + journal = {Frontiers in Neuroscience}, + publisher = {Frontiers Media SA}, + author = {Millman, K. Jarrod and Brett, Matthew and Barnowski, Ross + and Poline, Jean-Baptiste}, + year = {2018}, + month = oct +} + +@Article{ modarres_2021, + title = {Biomarkers Based on Comprehensive Hierarchical EEG + Coherence Analysis: Example Application to Social + Competence in Autism (Preliminary Results)}, + volume = {20}, + issn = {1559-0089}, + url = {http://dx.doi.org/10.1007/s12021-021-09517-8}, + doi = {10.1007/s12021-021-09517-8}, + number = {1}, + journal = {Neuroinformatics}, + publisher = {Springer Science and Business Media LLC}, + author = {Modarres, Mo and Cochran, David and Kennedy, David N. and + Schmidt, Richard and Fitzpatrick, Paula and Frazier, Jean + A.}, + year = {2021}, + month = mar, + pages = {53–62} +} + +@Article{ modarres_2023, + title = {Comparison of comprehensive quantitative EEG metrics + between typically developing boys and girls in resting + state eyes-open and eyes-closed conditions}, + volume = {17}, + issn = {1662-5161}, + url = {http://dx.doi.org/10.3389/fnhum.2023.1237651}, + doi = {10.3389/fnhum.2023.1237651}, + journal = {Frontiers in Human Neuroscience}, + publisher = {Frontiers Media SA}, + author = {Modarres, Mo and Cochran, David and Kennedy, David N. and + Frazier, Jean A.}, + year = {2023}, + month = nov +} + +@Article{ nastase_2021, + title = {The “Narratives” fMRI dataset for evaluating models of + naturalistic language comprehension}, + volume = {8}, + issn = {2052-4463}, + url = {http://dx.doi.org/10.1038/s41597-021-01033-3}, + doi = {10.1038/s41597-021-01033-3}, + number = {1}, + journal = {Scientific Data}, + publisher = {Springer Science and Business Media LLC}, + author = {Nastase, Samuel A. and Liu, Yun-Fei and Hillman, Hanna and + Zadbood, Asieh and Hasenfratz, Liat and Keshavarzian, + Neggin and Chen, Janice and Honey, Christopher J. and + Yeshurun, Yaara and Regev, Mor and Nguyen, Mai and Chang, + Claire H. C. and Baldassano, Christopher and Lositsky, Olga + and Simony, Erez and Chow, Michael A. and Leong, Yuan Chang + and Brooks, Paula P. and Micciche, Emily and Choe, Gina and + Goldstein, Ariel and Vanderwal, Tamara and Halchenko, + Yaroslav O. and Norman, Kenneth A. and Hasson, Uri}, + year = {2021}, + month = sep +} + +@Article{ nichols_2017, + title = {Best practices in data analysis and sharing in + neuroimaging using MRI}, + volume = {20}, + issn = {1546-1726}, + url = {http://dx.doi.org/10.1038/nn.4500}, + doi = {10.1038/nn.4500}, + number = {3}, + journal = {Nature Neuroscience}, + publisher = {Springer Science and Business Media LLC}, + author = {Nichols, Thomas E and Das, Samir and Eickhoff, Simon B and + Evans, Alan C and Glatard, Tristan and Hanke, Michael and + Kriegeskorte, Nikolaus and Milham, Michael P and Poldrack, + Russell A and Poline, Jean-Baptiste and Proal, Erika and + Thirion, Bertrand and Van Essen, David C and White, Tonya + and Yeo, B T Thomas}, + year = {2017}, + month = mar, + pages = {299–303} +} + +@Article{ niso_2022, + title = {Open and reproducible neuroimaging: From study inception + to publication}, + volume = {263}, + issn = {1053-8119}, + url = {http://dx.doi.org/10.1016/j.neuroimage.2022.119623}, + doi = {10.1016/j.neuroimage.2022.119623}, + journal = {NeuroImage}, + publisher = {Elsevier BV}, + author = {Niso, Guiomar and Botvinik-Nezer, Rotem and Appelhoff, + Stefan and De La Vega, Alejandro and Esteban, Oscar and + Etzel, Joset A. and Finc, Karolina and Ganz, Melanie and + Gau, Rémi and Halchenko, Yaroslav O. and Herholz, Peer and + Karakuzu, Agah and Keator, David B. and Markiewicz, + Christopher J. and Maumet, Camille and Pernet, Cyril R. and + Pestilli, Franco and Queder, Nazek and Schmitt, Tina and + Sójka, Weronika and Wagner, Adina S. and Whitaker, Kirstie + J. and Rieger, Jochem W.}, + year = {2022}, + month = nov, + pages = {119623} +} + +@Article{ notter_2022, + title = {fMRIflows: A Consortium of Fully Automatic Univariate and + Multivariate fMRI Processing Pipelines}, + volume = {36}, + issn = {1573-6792}, + url = {http://dx.doi.org/10.1007/s10548-022-00935-8}, + doi = {10.1007/s10548-022-00935-8}, + number = {2}, + journal = {Brain Topography}, + publisher = {Springer Science and Business Media LLC}, + author = {Notter, Michael P. and Herholz, Peer and Da Costa, Sandra + and Gulban, Omer F. and Isik, Ayse Ilkay and Gaglianese, + Anna and Murray, Micah M.}, + year = {2022}, + month = dec, + pages = {172–191} +} + +@Article{ ozyurt_2018, + title = {Foundry: a message-oriented, horizontally scalable ETL + system for scientific data integration and enhancement}, + volume = {2018}, + issn = {1758-0463}, + url = {http://dx.doi.org/10.1093/database/bay130}, + doi = {10.1093/database/bay130}, + journal = {Database}, + publisher = {Oxford University Press (OUP)}, + author = {Ozyurt, Ibrahim Burak and Grethe, Jeffrey S}, + year = {2018}, + month = jan +} + +@Article{ peraza_2023, + title = {Methods for decoding cortical gradients of functional + connectivity}, + url = {http://dx.doi.org/10.1101/2023.08.01.551505}, + doi = {10.1101/2023.08.01.551505}, + publisher = {Cold Spring Harbor Laboratory}, + author = {Peraza, Julio A. and Salo, Taylor and Riedel, Michael C. + and Bottenhorn, Katherine L. and Poline, Jean-Baptiste and + Dockès, Jérôme and Kent, James D. and Bartley, Jessica + E. and Flannery, Jessica S. and Hill-Bowen, Lauren D. and + Lobo, Rosario Pintos and Poudel, Ranjita and Ray, Kimberly + L. and Robinson, Jennifer L. and Laird, Robert W. and + Sutherland, Matthew T. and de la Vega, Alejandro and Laird, + Angela R.}, + year = {2023}, + month = aug +} + +@Article{ perez_lebel_2022, + title = {Benchmarking missing-values approaches for predictive + models on health databases}, + volume = {11}, + issn = {2047-217X}, + url = {http://dx.doi.org/10.1093/gigascience/giac013}, + doi = {10.1093/gigascience/giac013}, + journal = {GigaScience}, + publisher = {Oxford University Press (OUP)}, + author = {Perez-Lebel, Alexandre and Varoquaux, Gaël and + Le Morvan, Marine and Josse, Julie and Poline, + Jean-Baptiste}, + year = {2022} +} + +@Article{ poldrack_2017, + title = {Scanning the horizon: towards transparent and reproducible + neuroimaging research}, + volume = {18}, + issn = {1471-0048}, + url = {http://dx.doi.org/10.1038/nrn.2016.167}, + doi = {10.1038/nrn.2016.167}, + number = {2}, + journal = {Nature Reviews Neuroscience}, + publisher = {Springer Science and Business Media LLC}, + author = {Poldrack, Russell A. and Baker, Chris I. and Durnez, Joke + and Gorgolewski, Krzysztof J. and Matthews, Paul M. and + Munafò, Marcus R. and Nichols, Thomas E. and Poline, + Jean-Baptiste and Vul, Edward and Yarkoni, Tal}, + year = {2017}, + month = jan, + pages = {115–126} +} + +@Article{ poldrack_2024, + title = {The past, present, and future of the brain imaging data + structure (BIDS)}, + volume = {2}, + issn = {2837-6056}, + url = {http://dx.doi.org/10.1162/imag_a_00103}, + doi = {10.1162/imag_a_00103}, + journal = {Imaging Neuroscience}, + publisher = {MIT Press}, + author = {Poldrack, Russell A. and Markiewicz, Christopher J. and + Appelhoff, Stefan and Ashar, Yoni K. and Auer, Tibor and + Baillet, Sylvain and Bansal, Shashank and Beltrachini, + Leandro and Benar, Christian G. and Bertazzoli, Giacomo and + Bhogawar, Suyash and Blair, Ross W. and Bortoletto, Marta + and Boudreau, Mathieu and Brooks, Teon L. and Calhoun, + Vince D. and Castelli, Filippo Maria and Clement, Patricia + and Cohen, Alexander L. and Cohen-Adad, Julien and + D’Ambrosio, Sasha and de Hollander, Gilles and de la + Iglesia-Vayá, María and de la Vega, Alejandro and + Delorme, Arnaud and Devinsky, Orrin and Draschkow, Dejan + and Duff, Eugene Paul and DuPre, Elizabeth and Earl, Eric + and Esteban, Oscar and Feingold, Franklin W. and Flandin, + Guillaume and Galassi, Anthony and Gallitto, Giuseppe and + Ganz, Melanie and Gau, Rémi and Gholam, James and Ghosh, + Satrajit S. and Giacomel, Alessio and Gillman, Ashley G. + and Gleeson, Padraig and Gramfort, Alexandre and Guay, + Samuel and Guidali, Giacomo and Halchenko, Yaroslav O. and + Handwerker, Daniel A. and Hardcastle, Nell and Herholz, + Peer and Hermes, Dora and Honey, Christopher J. and Innis, + Robert B. and Ioanas, Horea-Ioan and Jahn, Andrew and + Karakuzu, Agah and Keator, David B. and Kiar, Gregory and + Kincses, Balint and Laird, Angela R. and Lau, Jonathan C. + and Lazari, Alberto and Legarreta, Jon Haitz and Li, Adam + and Li, Xiangrui and Love, Bradley C. and Lu, Hanzhang and + Marcantoni, Eleonora and Maumet, Camille and Mazzamuto, + Giacomo and Meisler, Steven L. and Mikkelsen, Mark and + Mutsaerts, Henk and Nichols, Thomas E. and Nikolaidis, Aki + and Nilsonne, Gustav and Niso, Guiomar and Norgaard, Martin + and Okell, Thomas W. and Oostenveld, Robert and Ort, Eduard + and Park, Patrick J. and Pawlik, Mateusz and Pernet, Cyril + R. and Pestilli, Franco and Petr, Jan and Phillips, + Christophe and Poline, Jean-Baptiste and Pollonini, Luca + and Raamana, Pradeep Reddy and Ritter, Petra and Rizzo, + Gaia and Robbins, Kay A. and Rockhill, Alexander P. and + Rogers, Christine and Rokem, Ariel and Rorden, Chris and + Routier, Alexandre and Saborit-Torres, Jose Manuel and + Salo, Taylor and Schirner, Michael and Smith, Robert E. and + Spisak, Tamas and Sprenger, Julia and Swann, Nicole C. and + Szinte, Martin and Takerkart, Sylvain and Thirion, Bertrand + and Thomas, Adam G. and Torabian, Sajjad and Varoquaux, + Gael and Voytek, Bradley and Welzel, Julius and Wilson, + Martin and Yarkoni, Tal and Gorgolewski, Krzysztof J.}, + year = {2024}, + month = mar, + pages = {1–19} +} + +@Article{ poline_2019, + title = {From data sharing to data publishing}, + volume = {2}, + issn = {2515-5059}, + url = {http://dx.doi.org/10.12688/mniopenres.12772.2}, + doi = {10.12688/mniopenres.12772.2}, + journal = {MNI Open Research}, + publisher = {F1000 Research Ltd}, + author = {Poline, Jean-Baptiste}, + year = {2019}, + month = jan, + pages = {1} +} + +@Article{ poline_2022, + title = {Is Neuroscience FAIR? A Call for Collaborative + Standardisation of Neuroscience Data}, + volume = {20}, + issn = {1559-0089}, + url = {http://dx.doi.org/10.1007/s12021-021-09557-0}, + doi = {10.1007/s12021-021-09557-0}, + number = {2}, + journal = {Neuroinformatics}, + publisher = {Springer Science and Business Media LLC}, + author = {Poline, Jean-Baptiste and Kennedy, David N. and Sommer, + Friedrich T. and Ascoli, Giorgio A. and Van Essen, David C. + and Ferguson, Adam R. and Grethe, Jeffrey S. and Hawrylycz, + Michael J. and Thompson, Paul M. and Poldrack, Russell A. + and Ghosh, Satrajit S. and Keator, David B. and Athey, + Thomas L. and Vogelstein, Joshua T. and Mayberg, Helen S. + and Martone, Maryann E.}, + year = {2022}, + month = jan, + pages = {507–512} +} + +@Article{ poline_2023, + title = {Data and Tools Integration in the Canadian Open + Neuroscience Platform}, + volume = {10}, + issn = {2052-4463}, + url = {http://dx.doi.org/10.1038/s41597-023-01946-1}, + doi = {10.1038/s41597-023-01946-1}, + number = {1}, + journal = {Scientific Data}, + publisher = {Springer Science and Business Media LLC}, + author = {Poline, Jean-Baptiste and Das, Samir and Glatard, Tristan + and Madjar, Cécile and Dickie, Erin W. and Lecours, Xavier + and Beaudry, Thomas and Beck, Natacha and Behan, Brendan + and Brown, Shawn T. and Bujold, David and Beauvais, Michael + and Caron, Bryan and Czech, Candice and Dharsee, Moyez and + Dugré, Mathieu and Evans, Ken and Gee, Tom and Ippoliti, + Giulia and Kiar, Gregory and Knoppers, Bartha Maria and + Kuehn, Tristan and Le, Diana and Lo, Derek and Mazaheri, + Mandana and MacFarlane, Dave and Muja, Naser and O’Brien, + Emmet A. and O’Callaghan, Liam and Paiva, Santiago and + Park, Patrick and Quesnel, Darcy and Rabelais, Henri and + Rioux, Pierre and Legault, Mélanie and Tremblay-Mercier, + Jennifer and Rotenberg, David and Stone, Jessica and + Strauss, Ted and Zaytseva, Ksenia and Zhou, Joey and + Duchesne, Simon and Khan, Ali R. and Hill, Sean and Evans, + Alan C.}, + year = {2023}, + month = apr +} + +@Article{ queder_2023, + title = {NIDM-Terms: community-based terminology management for + improved neuroimaging dataset descriptions and query}, + volume = {17}, + issn = {1662-5196}, + url = {http://dx.doi.org/10.3389/fninf.2023.1174156}, + doi = {10.3389/fninf.2023.1174156}, + journal = {Frontiers in Neuroinformatics}, + publisher = {Frontiers Media SA}, + author = {Queder, Nazek and Tien, Vivian B. and Abraham, Sanu Ann + and Urchs, Sebastian Georg Wenzel and Helmer, Karl G. and + Chaplin, Derek and van Erp, Theo G. M. and Kennedy, David + N. and Poline, Jean-Baptiste and Grethe, Jeffrey S. and + Ghosh, Satrajit S. and Keator, David B.}, + year = {2023}, + month = jul +} + +@Article{ renton_2024, + title = {Neurodesk: an accessible, flexible and portable data + analysis environment for reproducible neuroimaging}, + volume = {21}, + issn = {1548-7105}, + url = {http://dx.doi.org/10.1038/s41592-023-02145-x}, + doi = {10.1038/s41592-023-02145-x}, + number = {5}, + journal = {Nature Methods}, + publisher = {Springer Science and Business Media LLC}, + author = {Renton, Angela I. and Dao, Thuy T. and Johnstone, Tom and + Civier, Oren and Sullivan, Ryan P. and White, David J. and + Lyons, Paris and Slade, Benjamin M. and Abbott, David F. + and Amos, Toluwani J. and Bollmann, Saskia and Botting, + Andy and Campbell, Megan E. J. and Chang, Jeryn and Close, + Thomas G. and Dörig, Monika and Eckstein, Korbinian and + Egan, Gary F. and Evas, Stefanie and Flandin, Guillaume and + Garner, Kelly G. and Garrido, Marta I. and Ghosh, Satrajit + S. and Grignard, Martin and Halchenko, Yaroslav O. and + Hannan, Anthony J. and Heinsfeld, Anibal S. and Huber, + Laurentius and Hughes, Matthew E. and Kaczmarzyk, Jakub R. + and Kasper, Lars and Kuhlmann, Levin and Lou, Kexin and + Mantilla-Ramos, Yorguin-Jose and Mattingley, Jason B. and + Meier, Michael L. and Morris, Jo and Narayanan, Akshaiy and + Pestilli, Franco and Puce, Aina and Ribeiro, Fernanda L. + and Rogasch, Nigel C. and Rorden, Chris and Schira, Mark M. + and Shaw, Thomas B. and Sowman, Paul F. and Spitz, Gershon + and Stewart, Ashley W. and Ye, Xincheng and Zhu, Judy D. + and Narayanan, Aswin and Bollmann, Steffen}, + year = {2024}, + month = jan, + pages = {804–808} +} + +@Article{ royer_2022, + title = {An Open MRI Dataset For Multiscale Neuroscience}, + volume = {9}, + issn = {2052-4463}, + url = {http://dx.doi.org/10.1038/s41597-022-01682-y}, + doi = {10.1038/s41597-022-01682-y}, + number = {1}, + journal = {Scientific Data}, + publisher = {Springer Science and Business Media LLC}, + author = {Royer, Jessica and Rodríguez-Cruces, Raúl and Tavakol, + Shahin and Larivière, Sara and Herholz, Peer and Li, + Qiongling and Vos de Wael, Reinder and Paquola, Casey and + Benkarim, Oualid and Park, Bo-yong and Lowe, Alexander J. + and Margulies, Daniel and Smallwood, Jonathan and + Bernasconi, Andrea and Bernasconi, Neda and Frauscher, + Birgit and Bernhardt, Boris C.}, + year = {2022}, + month = sep +} + +@Article{ sansone_2017, + title = {DATS, the data tag suite to enable discoverability of + datasets}, + volume = {4}, + issn = {2052-4463}, + url = {http://dx.doi.org/10.1038/sdata.2017.59}, + doi = {10.1038/sdata.2017.59}, + number = {1}, + journal = {Scientific Data}, + publisher = {Springer Science and Business Media LLC}, + author = {Sansone, Susanna-Assunta and Gonzalez-Beltran, Alejandra + and Rocca-Serra, Philippe and Alter, George and Grethe, + Jeffrey S. and Xu, Hua and Fore, Ian M. and Lyle, Jared and + Gururaj, Anupama E. and Chen, Xiaoling and Kim, Hyeon-eui + and Zong, Nansu and Li, Yueling and Liu, Ruiling and + Ozyurt, I. Burak and Ohno-Machado, Lucila}, + year = {2017}, + month = jun +} + +@Article{ satz_2022, + title = {The Relationship Between Default Mode and Dorsal Attention + Networks Is Associated With Depressive Disorder Diagnosis + and the Strength of Memory Representations Acquired Prior + to the Resting State Scan}, + volume = {16}, + issn = {1662-5161}, + url = {http://dx.doi.org/10.3389/fnhum.2022.749767}, + doi = {10.3389/fnhum.2022.749767}, + journal = {Frontiers in Human Neuroscience}, + publisher = {Frontiers Media SA}, + author = {Satz, Skye and Halchenko, Yaroslav O. and Ragozzino, + Rachel and Lucero, Mora M. and Phillips, Mary L. and + Swartz, Holly A. and Manelis, Anna}, + year = {2022}, + month = feb +} + +@Article{ siless_2020, + title = {Image acquisition and quality assurance in the Boston + Adolescent Neuroimaging of Depression and Anxiety study}, + volume = {26}, + issn = {2213-1582}, + url = {http://dx.doi.org/10.1016/j.nicl.2020.102242}, + doi = {10.1016/j.nicl.2020.102242}, + journal = {NeuroImage: Clinical}, + publisher = {Elsevier BV}, + author = {Siless, Viviana and Hubbard, Nicholas A. and Jones, Robert + and Wang, Jonathan and Lo, Nicole and Bauer, Clemens C.C. + and Goncalves, Mathias and Frosch, Isabelle and Norton, + Daniel and Vergara, Genesis and Conroy, Kristina and De + Souza, Flavia Vaz and Rosso, Isabelle M. and Wickham, + Aleena Hay and Cosby, Elizabeth Ann and Pinaire, Megan and + Hirshfeld-Becker, Dina and Pizzagalli, Diego A. and Henin, + Aude and Hofmann, Stefan G. and Auerbach, Randy P. and + Ghosh, Satrajit and Gabrieli, John and Whitfield-Gabrieli, + Susan and Yendiki, Anastasia}, + year = {2020}, + pages = {102242} +} + +@Article{ sitek_2019, + title = {Mapping the human subcortical auditory system using + histology, postmortem MRI and in vivo MRI at 7T}, + volume = {8}, + issn = {2050-084X}, + url = {http://dx.doi.org/10.7554/elife.48932}, + doi = {10.7554/elife.48932}, + journal = {eLife}, + publisher = {eLife Sciences Publications, Ltd}, + author = {Sitek, Kevin R and Gulban, Omer Faruk and Calabrese, Evan + and Johnson, G Allan and Lage-Castellanos, Agustin and + Moerel, Michelle and Ghosh, Satrajit S and De Martino, + Federico}, + year = {2019}, + month = aug +} + +@Article{ soko_owski_2024, + title = {Longitudinal brain structure changes in Parkinson’s + disease: A replication study}, + volume = {19}, + issn = {1932-6203}, + url = {http://dx.doi.org/10.1371/journal.pone.0295069}, + doi = {10.1371/journal.pone.0295069}, + number = {1}, + journal = {PLOS ONE}, + publisher = {Public Library of Science (PLoS)}, + author = {Sokołowski, Andrzej and Bhagwat, Nikhil and Chatelain, + Yohan and Dugré, Mathieu and Hanganu, Alexandru and + Monchi, Oury and McPherson, Brent and Wang, Michelle and + Poline, Jean-Baptiste and Sharp, Madeleine and Glatard, + Tristan}, + editor = {Bergsland, Niels}, + year = {2024}, + month = jan, + pages = {e0295069} +} + +@Article{ solo_2018, + title = {Connectivity in fMRI: Blind Spots and Breakthroughs}, + volume = {37}, + issn = {1558-254X}, + url = {http://dx.doi.org/10.1109/tmi.2018.2831261}, + doi = {10.1109/tmi.2018.2831261}, + number = {7}, + journal = {IEEE Transactions on Medical Imaging}, + publisher = {Institute of Electrical and Electronics Engineers (IEEE)}, + author = {Solo, Victor and Poline, Jean-Baptiste and Lindquist, + Martin A. and Simpson, Sean L. and Bowman, F. DuBois and + Chung, Moo K. and Cassidy, Ben}, + year = {2018}, + month = jul, + pages = {1537–1550} +} + +@Article{ szczepanik_2024, + title = {Teaching Research Data Management with DataLad: A + Multi-year, Multi-domain Effort}, + volume = {22}, + issn = {1559-0089}, + url = {http://dx.doi.org/10.1007/s12021-024-09665-7}, + doi = {10.1007/s12021-024-09665-7}, + number = {4}, + journal = {Neuroinformatics}, + publisher = {Springer Science and Business Media LLC}, + author = {Szczepanik, Michał and Wagner, Adina S. and Heunis, + Stephan and Waite, Laura K. and Eickhoff, Simon B. and + Hanke, Michael}, + year = {2024}, + month = may, + pages = {635–645} +} + +@Article{ torabi_2024, + title = {On the variability of dynamic functional connectivity + assessment methods}, + volume = {13}, + issn = {2047-217X}, + url = {http://dx.doi.org/10.1093/gigascience/giae009}, + doi = {10.1093/gigascience/giae009}, + journal = {GigaScience}, + publisher = {Oxford University Press (OUP)}, + author = {Torabi, Mohammad and Mitsis, Georgios D and Poline, + Jean-Baptiste}, + year = {2024} +} + +@Article{ torabian_2023, + title = {The PyMVPA BIDS-App: a robust multivariate pattern + analysis pipeline for fMRI data}, + volume = {17}, + issn = {1662-453X}, + url = {http://dx.doi.org/10.3389/fnins.2023.1233416}, + doi = {10.3389/fnins.2023.1233416}, + journal = {Frontiers in Neuroscience}, + publisher = {Frontiers Media SA}, + author = {Torabian, Sajjad and Vélez, Natalia and Sochat, Vanessa + and Halchenko, Yaroslav O. and Grossman, Emily D.}, + year = {2023}, + month = aug +} + +@Article{ torres_esp_n_2021, + title = {Promoting FAIR Data Through Community-driven Agile Design: + the Open Data Commons for Spinal Cord Injury + (odc-sci.org)}, + volume = {20}, + issn = {1559-0089}, + url = {http://dx.doi.org/10.1007/s12021-021-09533-8}, + doi = {10.1007/s12021-021-09533-8}, + number = {1}, + journal = {Neuroinformatics}, + publisher = {Springer Science and Business Media LLC}, + author = {Torres-Espín, Abel and Almeida, Carlos A. and Chou, + Austin and Huie, J. Russell and Chiu, Michael and Vavrek, + Romana and Sacramento, Jeff and Orr, Michael B. and Gensel, + John C. and Grethe, Jeffery S. and Martone, Maryann E. and + Fouad, Karim and Ferguson, Adam R. and Alilain, Warren and + Bacon, Mark and Batty, Nicholas and Beattie, Michael and + Bresnahan, Jacqueline and Burnside, Emily and Busch, Sarah + and Carpenter, Randall and Quijorna, Isaac Francos and Guo, + Xiaohui and Haggerty, Agnes and Haroon, Sarah and Harris, + Jack and Jakeman, Lyn and Jones, Linda and Kleitman, Naomi + and Kopper, Timothy and Lane, Michael and Magana, Francisco + and Magnuson, David and Maldonado, Ines and May, Verena and + McFarlane, Katelyn and Morioka, Kazuhito and Oudega, Martin + and Pascual, Philip Leo and Poline, Jean-Baptiste and + Rosenzweig, Ephron and Schmidt, Emma and Tetzlaff, Wolfram + and Zholudeva, Lana}, + year = {2021}, + month = aug, + pages = {203–219} +} + +@Article{ wang_2023, + title = {Reproducibility of cerebellar involvement as quantified by + consensus structural MRI biomarkers in advanced essential + tremor}, + volume = {13}, + issn = {2045-2322}, + url = {http://dx.doi.org/10.1038/s41598-022-25306-y}, + doi = {10.1038/s41598-022-25306-y}, + number = {1}, + journal = {Scientific Reports}, + publisher = {Springer Science and Business Media LLC}, + author = {Wang, Qing and Aljassar, Meshal and Bhagwat, Nikhil and + Zeighami, Yashar and Evans, Alan C. and Dagher, Alain and + Pike, G. Bruce and Sadikot, Abbas F. and Poline, + Jean-Baptiste}, + year = {2023}, + month = jan +} + +@Article{ wimalaratne_2018, + title = {Uniform resolution of compact identifiers for biomedical + data}, + volume = {5}, + issn = {2052-4463}, + url = {http://dx.doi.org/10.1038/sdata.2018.29}, + doi = {10.1038/sdata.2018.29}, + number = {1}, + journal = {Scientific Data}, + publisher = {Springer Science and Business Media LLC}, + author = {Wimalaratne, Sarala M. and Juty, Nick and Kunze, John and + Janée, Greg and McMurry, Julie A. and Beard, Niall and + Jimenez, Rafael and Grethe, Jeffrey S. and Hermjakob, + Henning and Martone, Maryann E. and Clark, Tim}, + year = {2018}, + month = may +} + +@Article{ yarkoni_2019, + title = {PyBIDS: Python tools for BIDS datasets}, + volume = {4}, + issn = {2475-9066}, + url = {http://dx.doi.org/10.21105/joss.01294}, + doi = {10.21105/joss.01294}, + number = {40}, + journal = {Journal of Open Source Software}, + publisher = {The Open Journal}, + author = {Yarkoni, Tal and Markiewicz, Christopher and de la Vega, + Alejandro and Gorgolewski, Krzysztof and Salo, Taylor and + Halchenko, Yaroslav and McNamara, Quinten and DeStasio, + Krista and Poline, Jean-Baptiste and Petrov, Dmitry and + Hayot-Sasson, Valérie and Nielson, Dylan and Carlin, Johan + and Kiar, Gregory and Whitaker, Kirstie and DuPre, + Elizabeth and Wagner, Adina and Tirrell, Lee and Jas, + Mainak and Hanke, Michael and Poldrack, Russell and + Esteban, Oscar and Appelhoff, Stefan and Holdgraf, Chris + and Staden, Isla and Thirion, Bertrand and Kleinschmidt, + Dave and Lee, John and di Castello, Matteo and Notter, + Michael and Blair, Ross}, + year = {2019}, + month = aug, + pages = {1294} +} + +@Article{ zhao_2023, + title = {A reproducible and generalizable software workflow for + analysis of large-scale neuroimaging data collections using + BIDS Apps}, + url = {http://dx.doi.org/10.1101/2023.08.16.552472}, + doi = {10.1101/2023.08.16.552472}, + publisher = {Cold Spring Harbor Laboratory}, + author = {Zhao, Chenying and Jarecka, Dorota and Covitz, Sydney and + Chen, Yibei and Eickhoff, Simon B. and Fair, Damien A. and + Franco, Alexandre R. and Halchenko, Yaroslav O. and + Hendrickson, Timothy J. and Hoffstaedter, Felix and + Houghton, Audrey and Kiar, Gregory and Macdonald, Austin + and Mehta, Kahini and Milham, Michael P. and Salo, Taylor + and Hanke, Michael and Ghosh, Satrajit S. and Cieslak, + Matthew and Satterthwaite, Theodore D.}, + year = {2023}, + month = aug +} diff --git a/content/publications/queder-2023/cite.bib b/content/publications/queder-2023/cite.bib new file mode 100644 index 0000000..c6a0e5c --- /dev/null +++ b/content/publications/queder-2023/cite.bib @@ -0,0 +1,17 @@ +@article{queder_2023, + author = {Queder, Nazek and Tien, Vivian B. and Abraham, Sanu Ann +and Urchs, Sebastian Georg Wenzel and Helmer, Karl G. and +Chaplin, Derek and van Erp, Theo G. M. and Kennedy, David +N. and Poline, Jean-Baptiste and Grethe, Jeffrey S. and +Ghosh, Satrajit S. and Keator, David B.}, + doi = {10.3389/fninf.2023.1174156}, + issn = {1662-5196}, + journal = {Frontiers in Neuroinformatics}, + month = {July}, + publisher = {Frontiers Media SA}, + title = {NIDM-Terms: community-based terminology management for +improved neuroimaging dataset descriptions and query}, + url = {http://dx.doi.org/10.3389/fninf.2023.1174156}, + volume = {17}, + year = {2023} +} diff --git a/content/publications/queder-2023/index.md b/content/publications/queder-2023/index.md new file mode 100644 index 0000000..2b63fd1 --- /dev/null +++ b/content/publications/queder-2023/index.md @@ -0,0 +1,26 @@ +--- +title: 'NIDM-Terms: community-based terminology management for improved neuroimaging + dataset descriptions and query' +authors: +- Nazek Queder +- Vivian B. Tien +- Sanu Ann Abraham +- Sebastian Georg Wenzel Urchs +- Karl G. Helmer +- Derek Chaplin +- Theo G. M. van Erp +- David N. Kennedy +- Jean-Baptiste Poline +- Jeffrey S. Grethe +- Satrajit S. Ghosh +- David B. Keator +date: '2023-07-01' +publishDate: '2024-12-19T23:16:36.706771Z' +publication_types: +- article-journal +publication: '*Frontiers in Neuroinformatics*' +doi: 10.3389/fninf.2023.1174156 +links: +- name: URL + url: http://dx.doi.org/10.3389/fninf.2023.1174156 +--- diff --git a/content/publications/renton-2024/cite.bib b/content/publications/renton-2024/cite.bib new file mode 100644 index 0000000..65b23e2 --- /dev/null +++ b/content/publications/renton-2024/cite.bib @@ -0,0 +1,33 @@ +@article{renton_2024, + author = {Renton, Angela I. and Dao, Thuy T. and Johnstone, Tom and +Civier, Oren and Sullivan, Ryan P. and White, David J. and +Lyons, Paris and Slade, Benjamin M. and Abbott, David F. +and Amos, Toluwani J. and Bollmann, Saskia and Botting, +Andy and Campbell, Megan E. J. and Chang, Jeryn and Close, +Thomas G. and Dörig, Monika and Eckstein, Korbinian and +Egan, Gary F. and Evas, Stefanie and Flandin, Guillaume and +Garner, Kelly G. and Garrido, Marta I. and Ghosh, Satrajit +S. and Grignard, Martin and Halchenko, Yaroslav O. and +Hannan, Anthony J. and Heinsfeld, Anibal S. and Huber, +Laurentius and Hughes, Matthew E. and Kaczmarzyk, Jakub R. +and Kasper, Lars and Kuhlmann, Levin and Lou, Kexin and +Mantilla-Ramos, Yorguin-Jose and Mattingley, Jason B. and +Meier, Michael L. and Morris, Jo and Narayanan, Akshaiy and +Pestilli, Franco and Puce, Aina and Ribeiro, Fernanda L. +and Rogasch, Nigel C. and Rorden, Chris and Schira, Mark M. +and Shaw, Thomas B. and Sowman, Paul F. and Spitz, Gershon +and Stewart, Ashley W. and Ye, Xincheng and Zhu, Judy D. +and Narayanan, Aswin and Bollmann, Steffen}, + doi = {10.1038/s41592-023-02145-x}, + issn = {1548-7105}, + journal = {Nature Methods}, + month = {January}, + number = {5}, + pages = {804–808}, + publisher = {Springer Science and Business Media LLC}, + title = {Neurodesk: an accessible, flexible and portable data +analysis environment for reproducible neuroimaging}, + url = {http://dx.doi.org/10.1038/s41592-023-02145-x}, + volume = {21}, + year = {2024} +} diff --git a/content/publications/renton-2024/index.md b/content/publications/renton-2024/index.md new file mode 100644 index 0000000..204e2f8 --- /dev/null +++ b/content/publications/renton-2024/index.md @@ -0,0 +1,66 @@ +--- +title: 'Neurodesk: an accessible, flexible and portable data analysis environment + for reproducible neuroimaging' +authors: +- Angela I. Renton +- Thuy T. Dao +- Tom Johnstone +- Oren Civier +- Ryan P. Sullivan +- David J. White +- Paris Lyons +- Benjamin M. Slade +- David F. Abbott +- Toluwani J. Amos +- Saskia Bollmann +- Andy Botting +- Megan E. J. Campbell +- Jeryn Chang +- Thomas G. Close +- Monika Dörig +- Korbinian Eckstein +- Gary F. Egan +- Stefanie Evas +- Guillaume Flandin +- Kelly G. Garner +- Marta I. Garrido +- Satrajit S. Ghosh +- Martin Grignard +- Yaroslav O. Halchenko +- Anthony J. Hannan +- Anibal S. Heinsfeld +- Laurentius Huber +- Matthew E. Hughes +- Jakub R. Kaczmarzyk +- Lars Kasper +- Levin Kuhlmann +- Kexin Lou +- Yorguin-Jose Mantilla-Ramos +- Jason B. Mattingley +- Michael L. Meier +- Jo Morris +- Akshaiy Narayanan +- Franco Pestilli +- Aina Puce +- Fernanda L. Ribeiro +- Nigel C. Rogasch +- Chris Rorden +- Mark M. Schira +- Thomas B. Shaw +- Paul F. Sowman +- Gershon Spitz +- Ashley W. Stewart +- Xincheng Ye +- Judy D. Zhu +- Aswin Narayanan +- Steffen Bollmann +date: '2024-01-01' +publishDate: '2024-12-19T23:16:36.710906Z' +publication_types: +- article-journal +publication: '*Nature Methods*' +doi: 10.1038/s41592-023-02145-x +links: +- name: URL + url: http://dx.doi.org/10.1038/s41592-023-02145-x +--- diff --git a/content/publications/royer-2022/cite.bib b/content/publications/royer-2022/cite.bib new file mode 100644 index 0000000..5baccaf --- /dev/null +++ b/content/publications/royer-2022/cite.bib @@ -0,0 +1,19 @@ +@article{royer_2022, + author = {Royer, Jessica and Rodríguez-Cruces, Raúl and Tavakol, +Shahin and Larivière, Sara and Herholz, Peer and Li, +Qiongling and Vos de Wael, Reinder and Paquola, Casey and +Benkarim, Oualid and Park, Bo-yong and Lowe, Alexander J. +and Margulies, Daniel and Smallwood, Jonathan and +Bernasconi, Andrea and Bernasconi, Neda and Frauscher, +Birgit and Bernhardt, Boris C.}, + doi = {10.1038/s41597-022-01682-y}, + issn = {2052-4463}, + journal = {Scientific Data}, + month = {September}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {An Open MRI Dataset For Multiscale Neuroscience}, + url = {http://dx.doi.org/10.1038/s41597-022-01682-y}, + volume = {9}, + year = {2022} +} diff --git a/content/publications/royer-2022/index.md b/content/publications/royer-2022/index.md new file mode 100644 index 0000000..5234a9f --- /dev/null +++ b/content/publications/royer-2022/index.md @@ -0,0 +1,30 @@ +--- +title: An Open MRI Dataset For Multiscale Neuroscience +authors: +- Jessica Royer +- Raúl Rodríguez-Cruces +- Shahin Tavakol +- Sara Larivière +- Peer Herholz +- Qiongling Li +- Reinder Vos de Wael +- Casey Paquola +- Oualid Benkarim +- Bo-yong Park +- Alexander J. Lowe +- Daniel Margulies +- Jonathan Smallwood +- Andrea Bernasconi +- Neda Bernasconi +- Birgit Frauscher +- Boris C. Bernhardt +date: '2022-09-01' +publishDate: '2024-12-19T23:16:36.715798Z' +publication_types: +- article-journal +publication: '*Scientific Data*' +doi: 10.1038/s41597-022-01682-y +links: +- name: URL + url: http://dx.doi.org/10.1038/s41597-022-01682-y +--- diff --git a/content/publications/sansone-2017/cite.bib b/content/publications/sansone-2017/cite.bib new file mode 100644 index 0000000..f836d5e --- /dev/null +++ b/content/publications/sansone-2017/cite.bib @@ -0,0 +1,19 @@ +@article{sansone_2017, + author = {Sansone, Susanna-Assunta and Gonzalez-Beltran, Alejandra +and Rocca-Serra, Philippe and Alter, George and Grethe, +Jeffrey S. and Xu, Hua and Fore, Ian M. and Lyle, Jared and +Gururaj, Anupama E. and Chen, Xiaoling and Kim, Hyeon-eui +and Zong, Nansu and Li, Yueling and Liu, Ruiling and +Ozyurt, I. Burak and Ohno-Machado, Lucila}, + doi = {10.1038/sdata.2017.59}, + issn = {2052-4463}, + journal = {Scientific Data}, + month = {June}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {DATS, the data tag suite to enable discoverability of +datasets}, + url = {http://dx.doi.org/10.1038/sdata.2017.59}, + volume = {4}, + year = {2017} +} diff --git a/content/publications/sansone-2017/index.md b/content/publications/sansone-2017/index.md new file mode 100644 index 0000000..f4d4a99 --- /dev/null +++ b/content/publications/sansone-2017/index.md @@ -0,0 +1,29 @@ +--- +title: DATS, the data tag suite to enable discoverability of datasets +authors: +- Susanna-Assunta Sansone +- Alejandra Gonzalez-Beltran +- Philippe Rocca-Serra +- George Alter +- Jeffrey S. Grethe +- Hua Xu +- Ian M. Fore +- Jared Lyle +- Anupama E. Gururaj +- Xiaoling Chen +- Hyeon-eui Kim +- Nansu Zong +- Yueling Li +- Ruiling Liu +- I. Burak Ozyurt +- Lucila Ohno-Machado +date: '2017-06-01' +publishDate: '2024-12-19T23:16:36.719994Z' +publication_types: +- article-journal +publication: '*Scientific Data*' +doi: 10.1038/sdata.2017.59 +links: +- name: URL + url: http://dx.doi.org/10.1038/sdata.2017.59 +--- diff --git a/content/publications/satz-2022/cite.bib b/content/publications/satz-2022/cite.bib new file mode 100644 index 0000000..975111f --- /dev/null +++ b/content/publications/satz-2022/cite.bib @@ -0,0 +1,17 @@ +@article{satz_2022, + author = {Satz, Skye and Halchenko, Yaroslav O. and Ragozzino, +Rachel and Lucero, Mora M. and Phillips, Mary L. and +Swartz, Holly A. and Manelis, Anna}, + doi = {10.3389/fnhum.2022.749767}, + issn = {1662-5161}, + journal = {Frontiers in Human Neuroscience}, + month = {February}, + publisher = {Frontiers Media SA}, + title = {The Relationship Between Default Mode and Dorsal Attention +Networks Is Associated With Depressive Disorder Diagnosis +and the Strength of Memory Representations Acquired Prior +to the Resting State Scan}, + url = {http://dx.doi.org/10.3389/fnhum.2022.749767}, + volume = {16}, + year = {2022} +} diff --git a/content/publications/satz-2022/index.md b/content/publications/satz-2022/index.md new file mode 100644 index 0000000..2ceee25 --- /dev/null +++ b/content/publications/satz-2022/index.md @@ -0,0 +1,22 @@ +--- +title: The Relationship Between Default Mode and Dorsal Attention Networks Is Associated + With Depressive Disorder Diagnosis and the Strength of Memory Representations Acquired + Prior to the Resting State Scan +authors: +- Skye Satz +- Yaroslav O. Halchenko +- Rachel Ragozzino +- Mora M. Lucero +- Mary L. Phillips +- Holly A. Swartz +- Anna Manelis +date: '2022-02-01' +publishDate: '2024-12-19T23:16:36.724149Z' +publication_types: +- article-journal +publication: '*Frontiers in Human Neuroscience*' +doi: 10.3389/fnhum.2022.749767 +links: +- name: URL + url: http://dx.doi.org/10.3389/fnhum.2022.749767 +--- diff --git a/content/publications/siless-2020/cite.bib b/content/publications/siless-2020/cite.bib new file mode 100644 index 0000000..e4171f6 --- /dev/null +++ b/content/publications/siless-2020/cite.bib @@ -0,0 +1,22 @@ +@article{siless_2020, + author = {Siless, Viviana and Hubbard, Nicholas A. and Jones, Robert +and Wang, Jonathan and Lo, Nicole and Bauer, Clemens C.C. +and Goncalves, Mathias and Frosch, Isabelle and Norton, +Daniel and Vergara, Genesis and Conroy, Kristina and De +Souza, Flavia Vaz and Rosso, Isabelle M. and Wickham, +Aleena Hay and Cosby, Elizabeth Ann and Pinaire, Megan and +Hirshfeld-Becker, Dina and Pizzagalli, Diego A. and Henin, +Aude and Hofmann, Stefan G. and Auerbach, Randy P. and +Ghosh, Satrajit and Gabrieli, John and Whitfield-Gabrieli, +Susan and Yendiki, Anastasia}, + doi = {10.1016/j.nicl.2020.102242}, + issn = {2213-1582}, + journal = {NeuroImage: Clinical}, + pages = {102242}, + publisher = {Elsevier BV}, + title = {Image acquisition and quality assurance in the Boston +Adolescent Neuroimaging of Depression and Anxiety study}, + url = {http://dx.doi.org/10.1016/j.nicl.2020.102242}, + volume = {26}, + year = {2020} +} diff --git a/content/publications/siless-2020/index.md b/content/publications/siless-2020/index.md new file mode 100644 index 0000000..02e17da --- /dev/null +++ b/content/publications/siless-2020/index.md @@ -0,0 +1,39 @@ +--- +title: Image acquisition and quality assurance in the Boston Adolescent Neuroimaging + of Depression and Anxiety study +authors: +- Viviana Siless +- Nicholas A. Hubbard +- Robert Jones +- Jonathan Wang +- Nicole Lo +- Clemens C.C. Bauer +- Mathias Goncalves +- Isabelle Frosch +- Daniel Norton +- Genesis Vergara +- Kristina Conroy +- Flavia Vaz De Souza +- Isabelle M. Rosso +- Aleena Hay Wickham +- Elizabeth Ann Cosby +- Megan Pinaire +- Dina Hirshfeld-Becker +- Diego A. Pizzagalli +- Aude Henin +- Stefan G. Hofmann +- Randy P. Auerbach +- Satrajit Ghosh +- John Gabrieli +- Susan Whitfield-Gabrieli +- Anastasia Yendiki +date: '2020-01-01' +publishDate: '2024-12-19T23:16:36.728104Z' +publication_types: +- article-journal +publication: '*NeuroImage: Clinical*' +doi: 10.1016/j.nicl.2020.102242 +links: +- name: URL + url: http://dx.doi.org/10.1016/j.nicl.2020.102242 +--- diff --git a/content/publications/sitek-2019/cite.bib b/content/publications/sitek-2019/cite.bib new file mode 100644 index 0000000..aa38d58 --- /dev/null +++ b/content/publications/sitek-2019/cite.bib @@ -0,0 +1,16 @@ +@article{sitek_2019, + author = {Sitek, Kevin R and Gulban, Omer Faruk and Calabrese, Evan +and Johnson, G Allan and Lage-Castellanos, Agustin and +Moerel, Michelle and Ghosh, Satrajit S and De Martino, +Federico}, + doi = {10.7554/elife.48932}, + issn = {2050-084X}, + journal = {eLife}, + month = {August}, + publisher = {eLife Sciences Publications, Ltd}, + title = {Mapping the human subcortical auditory system using +histology, postmortem MRI and in vivo MRI at 7T}, + url = {http://dx.doi.org/10.7554/elife.48932}, + volume = {8}, + year = {2019} +} diff --git a/content/publications/sitek-2019/index.md b/content/publications/sitek-2019/index.md new file mode 100644 index 0000000..0b0cdc3 --- /dev/null +++ b/content/publications/sitek-2019/index.md @@ -0,0 +1,22 @@ +--- +title: Mapping the human subcortical auditory system using histology, postmortem MRI + and in vivo MRI at 7T +authors: +- Kevin R Sitek +- Omer Faruk Gulban +- Evan Calabrese +- G Allan Johnson +- Agustin Lage-Castellanos +- Michelle Moerel +- Satrajit S Ghosh +- Federico De Martino +date: '2019-08-01' +publishDate: '2024-12-19T23:16:36.732376Z' +publication_types: +- article-journal +publication: '*eLife*' +doi: 10.7554/elife.48932 +links: +- name: URL + url: http://dx.doi.org/10.7554/elife.48932 +--- diff --git a/content/publications/soko-owski-2024/cite.bib b/content/publications/soko-owski-2024/cite.bib new file mode 100644 index 0000000..b87c0fb --- /dev/null +++ b/content/publications/soko-owski-2024/cite.bib @@ -0,0 +1,20 @@ +@article{soko_owski_2024, + author = {Sokołowski, Andrzej and Bhagwat, Nikhil and Chatelain, +Yohan and Dugré, Mathieu and Hanganu, Alexandru and +Monchi, Oury and McPherson, Brent and Wang, Michelle and +Poline, Jean-Baptiste and Sharp, Madeleine and Glatard, +Tristan}, + doi = {10.1371/journal.pone.0295069}, + editor = {Bergsland, Niels}, + issn = {1932-6203}, + journal = {PLOS ONE}, + month = {January}, + number = {1}, + pages = {e0295069}, + publisher = {Public Library of Science (PLoS)}, + title = {Longitudinal brain structure changes in Parkinson’s +disease: A replication study}, + url = {http://dx.doi.org/10.1371/journal.pone.0295069}, + volume = {19}, + year = {2024} +} diff --git a/content/publications/soko-owski-2024/index.md b/content/publications/soko-owski-2024/index.md new file mode 100644 index 0000000..194becb --- /dev/null +++ b/content/publications/soko-owski-2024/index.md @@ -0,0 +1,25 @@ +--- +title: 'Longitudinal brain structure changes in Parkinson’s disease: A replication + study' +authors: +- Andrzej Sokołowski +- Nikhil Bhagwat +- Yohan Chatelain +- Mathieu Dugré +- Alexandru Hanganu +- Oury Monchi +- Brent McPherson +- Michelle Wang +- Jean-Baptiste Poline +- Madeleine Sharp +- Tristan Glatard +date: '2024-01-01' +publishDate: '2024-12-19T23:16:36.736403Z' +publication_types: +- article-journal +publication: '*PLOS ONE*' +doi: 10.1371/journal.pone.0295069 +links: +- name: URL + url: http://dx.doi.org/10.1371/journal.pone.0295069 +--- diff --git a/content/publications/solo-2018/cite.bib b/content/publications/solo-2018/cite.bib new file mode 100644 index 0000000..9e163ba --- /dev/null +++ b/content/publications/solo-2018/cite.bib @@ -0,0 +1,16 @@ +@article{solo_2018, + author = {Solo, Victor and Poline, Jean-Baptiste and Lindquist, +Martin A. and Simpson, Sean L. and Bowman, F. DuBois and +Chung, Moo K. and Cassidy, Ben}, + doi = {10.1109/tmi.2018.2831261}, + issn = {1558-254X}, + journal = {IEEE Transactions on Medical Imaging}, + month = {July}, + number = {7}, + pages = {1537–1550}, + publisher = {Institute of Electrical and Electronics Engineers (IEEE)}, + title = {Connectivity in fMRI: Blind Spots and Breakthroughs}, + url = {http://dx.doi.org/10.1109/tmi.2018.2831261}, + volume = {37}, + year = {2018} +} diff --git a/content/publications/solo-2018/index.md b/content/publications/solo-2018/index.md new file mode 100644 index 0000000..5e10b7e --- /dev/null +++ b/content/publications/solo-2018/index.md @@ -0,0 +1,20 @@ +--- +title: 'Connectivity in fMRI: Blind Spots and Breakthroughs' +authors: +- Victor Solo +- Jean-Baptiste Poline +- Martin A. Lindquist +- Sean L. Simpson +- F. DuBois Bowman +- Moo K. Chung +- Ben Cassidy +date: '2018-07-01' +publishDate: '2024-12-19T23:16:36.740512Z' +publication_types: +- article-journal +publication: '*IEEE Transactions on Medical Imaging*' +doi: 10.1109/tmi.2018.2831261 +links: +- name: URL + url: http://dx.doi.org/10.1109/tmi.2018.2831261 +--- diff --git a/content/publications/szczepanik-2024/cite.bib b/content/publications/szczepanik-2024/cite.bib new file mode 100644 index 0000000..fde8d6e --- /dev/null +++ b/content/publications/szczepanik-2024/cite.bib @@ -0,0 +1,17 @@ +@article{szczepanik_2024, + author = {Szczepanik, Michał and Wagner, Adina S. and Heunis, +Stephan and Waite, Laura K. and Eickhoff, Simon B. and +Hanke, Michael}, + doi = {10.1007/s12021-024-09665-7}, + issn = {1559-0089}, + journal = {Neuroinformatics}, + month = {May}, + number = {4}, + pages = {635–645}, + publisher = {Springer Science and Business Media LLC}, + title = {Teaching Research Data Management with DataLad: A +Multi-year, Multi-domain Effort}, + url = {http://dx.doi.org/10.1007/s12021-024-09665-7}, + volume = {22}, + year = {2024} +} diff --git a/content/publications/szczepanik-2024/index.md b/content/publications/szczepanik-2024/index.md new file mode 100644 index 0000000..e250481 --- /dev/null +++ b/content/publications/szczepanik-2024/index.md @@ -0,0 +1,20 @@ +--- +title: 'Teaching Research Data Management with DataLad: A Multi-year, Multi-domain + Effort' +authors: +- Michał Szczepanik +- Adina S. Wagner +- Stephan Heunis +- Laura K. Waite +- Simon B. Eickhoff +- Michael Hanke +date: '2024-05-01' +publishDate: '2024-12-19T23:16:36.744635Z' +publication_types: +- article-journal +publication: '*Neuroinformatics*' +doi: 10.1007/s12021-024-09665-7 +links: +- name: URL + url: http://dx.doi.org/10.1007/s12021-024-09665-7 +--- diff --git a/content/publications/torabi-2024/cite.bib b/content/publications/torabi-2024/cite.bib new file mode 100644 index 0000000..c2c9c3b --- /dev/null +++ b/content/publications/torabi-2024/cite.bib @@ -0,0 +1,13 @@ +@article{torabi_2024, + author = {Torabi, Mohammad and Mitsis, Georgios D and Poline, +Jean-Baptiste}, + doi = {10.1093/gigascience/giae009}, + issn = {2047-217X}, + journal = {GigaScience}, + publisher = {Oxford University Press (OUP)}, + title = {On the variability of dynamic functional connectivity +assessment methods}, + url = {http://dx.doi.org/10.1093/gigascience/giae009}, + volume = {13}, + year = {2024} +} diff --git a/content/publications/torabi-2024/index.md b/content/publications/torabi-2024/index.md new file mode 100644 index 0000000..3b8189f --- /dev/null +++ b/content/publications/torabi-2024/index.md @@ -0,0 +1,16 @@ +--- +title: On the variability of dynamic functional connectivity assessment methods +authors: +- Mohammad Torabi +- Georgios D Mitsis +- Jean-Baptiste Poline +date: '2024-01-01' +publishDate: '2024-12-19T23:16:36.748621Z' +publication_types: +- article-journal +publication: '*GigaScience*' +doi: 10.1093/gigascience/giae009 +links: +- name: URL + url: http://dx.doi.org/10.1093/gigascience/giae009 +--- diff --git a/content/publications/torabian-2023/cite.bib b/content/publications/torabian-2023/cite.bib new file mode 100644 index 0000000..5984c75 --- /dev/null +++ b/content/publications/torabian-2023/cite.bib @@ -0,0 +1,14 @@ +@article{torabian_2023, + author = {Torabian, Sajjad and Vélez, Natalia and Sochat, Vanessa +and Halchenko, Yaroslav O. and Grossman, Emily D.}, + doi = {10.3389/fnins.2023.1233416}, + issn = {1662-453X}, + journal = {Frontiers in Neuroscience}, + month = {August}, + publisher = {Frontiers Media SA}, + title = {The PyMVPA BIDS-App: a robust multivariate pattern +analysis pipeline for fMRI data}, + url = {http://dx.doi.org/10.3389/fnins.2023.1233416}, + volume = {17}, + year = {2023} +} diff --git a/content/publications/torabian-2023/index.md b/content/publications/torabian-2023/index.md new file mode 100644 index 0000000..842bd52 --- /dev/null +++ b/content/publications/torabian-2023/index.md @@ -0,0 +1,19 @@ +--- +title: 'The PyMVPA BIDS-App: a robust multivariate pattern analysis pipeline for fMRI + data' +authors: +- Sajjad Torabian +- Natalia Vélez +- Vanessa Sochat +- Yaroslav O. Halchenko +- Emily D. Grossman +date: '2023-08-01' +publishDate: '2024-12-19T23:16:36.752491Z' +publication_types: +- article-journal +publication: '*Frontiers in Neuroscience*' +doi: 10.3389/fnins.2023.1233416 +links: +- name: URL + url: http://dx.doi.org/10.3389/fnins.2023.1233416 +--- diff --git a/content/publications/torres-esp-n-2021/cite.bib b/content/publications/torres-esp-n-2021/cite.bib new file mode 100644 index 0000000..85eb93f --- /dev/null +++ b/content/publications/torres-esp-n-2021/cite.bib @@ -0,0 +1,31 @@ +@article{torres_esp_n_2021, + author = {Torres-Espín, Abel and Almeida, Carlos A. and Chou, +Austin and Huie, J. Russell and Chiu, Michael and Vavrek, +Romana and Sacramento, Jeff and Orr, Michael B. and Gensel, +John C. and Grethe, Jeffery S. and Martone, Maryann E. and +Fouad, Karim and Ferguson, Adam R. and Alilain, Warren and +Bacon, Mark and Batty, Nicholas and Beattie, Michael and +Bresnahan, Jacqueline and Burnside, Emily and Busch, Sarah +and Carpenter, Randall and Quijorna, Isaac Francos and Guo, +Xiaohui and Haggerty, Agnes and Haroon, Sarah and Harris, +Jack and Jakeman, Lyn and Jones, Linda and Kleitman, Naomi +and Kopper, Timothy and Lane, Michael and Magana, Francisco +and Magnuson, David and Maldonado, Ines and May, Verena and +McFarlane, Katelyn and Morioka, Kazuhito and Oudega, Martin +and Pascual, Philip Leo and Poline, Jean-Baptiste and +Rosenzweig, Ephron and Schmidt, Emma and Tetzlaff, Wolfram +and Zholudeva, Lana}, + doi = {10.1007/s12021-021-09533-8}, + issn = {1559-0089}, + journal = {Neuroinformatics}, + month = {August}, + number = {1}, + pages = {203–219}, + publisher = {Springer Science and Business Media LLC}, + title = {Promoting FAIR Data Through Community-driven Agile Design: +the Open Data Commons for Spinal Cord Injury +(odc-sci.org)}, + url = {http://dx.doi.org/10.1007/s12021-021-09533-8}, + volume = {20}, + year = {2021} +} diff --git a/content/publications/torres-esp-n-2021/index.md b/content/publications/torres-esp-n-2021/index.md new file mode 100644 index 0000000..44ca024 --- /dev/null +++ b/content/publications/torres-esp-n-2021/index.md @@ -0,0 +1,58 @@ +--- +title: 'Promoting FAIR Data Through Community-driven Agile Design: the Open Data Commons + for Spinal Cord Injury (odc-sci.org)' +authors: +- Abel Torres-Espín +- Carlos A. Almeida +- Austin Chou +- J. Russell Huie +- Michael Chiu +- Romana Vavrek +- Jeff Sacramento +- Michael B. Orr +- John C. Gensel +- Jeffery S. Grethe +- Maryann E. Martone +- Karim Fouad +- Adam R. Ferguson +- Warren Alilain +- Mark Bacon +- Nicholas Batty +- Michael Beattie +- Jacqueline Bresnahan +- Emily Burnside +- Sarah Busch +- Randall Carpenter +- Isaac Francos Quijorna +- Xiaohui Guo +- Agnes Haggerty +- Sarah Haroon +- Jack Harris +- Lyn Jakeman +- Linda Jones +- Naomi Kleitman +- Timothy Kopper +- Michael Lane +- Francisco Magana +- David Magnuson +- Ines Maldonado +- Verena May +- Katelyn McFarlane +- Kazuhito Morioka +- Martin Oudega +- Philip Leo Pascual +- Jean-Baptiste Poline +- Ephron Rosenzweig +- Emma Schmidt +- Wolfram Tetzlaff +- Lana Zholudeva +date: '2021-08-01' +publishDate: '2024-12-19T23:16:36.756484Z' +publication_types: +- article-journal +publication: '*Neuroinformatics*' +doi: 10.1007/s12021-021-09533-8 +links: +- name: URL + url: http://dx.doi.org/10.1007/s12021-021-09533-8 +--- diff --git a/content/publications/wang-2023/cite.bib b/content/publications/wang-2023/cite.bib new file mode 100644 index 0000000..c065bf8 --- /dev/null +++ b/content/publications/wang-2023/cite.bib @@ -0,0 +1,18 @@ +@article{wang_2023, + author = {Wang, Qing and Aljassar, Meshal and Bhagwat, Nikhil and +Zeighami, Yashar and Evans, Alan C. and Dagher, Alain and +Pike, G. Bruce and Sadikot, Abbas F. and Poline, +Jean-Baptiste}, + doi = {10.1038/s41598-022-25306-y}, + issn = {2045-2322}, + journal = {Scientific Reports}, + month = {January}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {Reproducibility of cerebellar involvement as quantified by +consensus structural MRI biomarkers in advanced essential +tremor}, + url = {http://dx.doi.org/10.1038/s41598-022-25306-y}, + volume = {13}, + year = {2023} +} diff --git a/content/publications/wang-2023/index.md b/content/publications/wang-2023/index.md new file mode 100644 index 0000000..23a51c5 --- /dev/null +++ b/content/publications/wang-2023/index.md @@ -0,0 +1,23 @@ +--- +title: Reproducibility of cerebellar involvement as quantified by consensus structural + MRI biomarkers in advanced essential tremor +authors: +- Qing Wang +- Meshal Aljassar +- Nikhil Bhagwat +- Yashar Zeighami +- Alan C. Evans +- Alain Dagher +- G. Bruce Pike +- Abbas F. Sadikot +- Jean-Baptiste Poline +date: '2023-01-01' +publishDate: '2024-12-19T23:16:36.761207Z' +publication_types: +- article-journal +publication: '*Scientific Reports*' +doi: 10.1038/s41598-022-25306-y +links: +- name: URL + url: http://dx.doi.org/10.1038/s41598-022-25306-y +--- diff --git a/content/publications/wimalaratne-2018/cite.bib b/content/publications/wimalaratne-2018/cite.bib new file mode 100644 index 0000000..cd6d51b --- /dev/null +++ b/content/publications/wimalaratne-2018/cite.bib @@ -0,0 +1,17 @@ +@article{wimalaratne_2018, + author = {Wimalaratne, Sarala M. and Juty, Nick and Kunze, John and +Janée, Greg and McMurry, Julie A. and Beard, Niall and +Jimenez, Rafael and Grethe, Jeffrey S. and Hermjakob, +Henning and Martone, Maryann E. and Clark, Tim}, + doi = {10.1038/sdata.2018.29}, + issn = {2052-4463}, + journal = {Scientific Data}, + month = {May}, + number = {1}, + publisher = {Springer Science and Business Media LLC}, + title = {Uniform resolution of compact identifiers for biomedical +data}, + url = {http://dx.doi.org/10.1038/sdata.2018.29}, + volume = {5}, + year = {2018} +} diff --git a/content/publications/wimalaratne-2018/index.md b/content/publications/wimalaratne-2018/index.md new file mode 100644 index 0000000..49a7000 --- /dev/null +++ b/content/publications/wimalaratne-2018/index.md @@ -0,0 +1,24 @@ +--- +title: Uniform resolution of compact identifiers for biomedical data +authors: +- Sarala M. Wimalaratne +- Nick Juty +- John Kunze +- Greg Janée +- Julie A. McMurry +- Niall Beard +- Rafael Jimenez +- Jeffrey S. Grethe +- Henning Hermjakob +- Maryann E. Martone +- Tim Clark +date: '2018-05-01' +publishDate: '2024-12-19T23:16:36.765210Z' +publication_types: +- article-journal +publication: '*Scientific Data*' +doi: 10.1038/sdata.2018.29 +links: +- name: URL + url: http://dx.doi.org/10.1038/sdata.2018.29 +--- diff --git a/content/publications/yarkoni-2019/cite.bib b/content/publications/yarkoni-2019/cite.bib new file mode 100644 index 0000000..31bc4ae --- /dev/null +++ b/content/publications/yarkoni-2019/cite.bib @@ -0,0 +1,25 @@ +@article{yarkoni_2019, + author = {Yarkoni, Tal and Markiewicz, Christopher and de la Vega, +Alejandro and Gorgolewski, Krzysztof and Salo, Taylor and +Halchenko, Yaroslav and McNamara, Quinten and DeStasio, +Krista and Poline, Jean-Baptiste and Petrov, Dmitry and +Hayot-Sasson, Valérie and Nielson, Dylan and Carlin, Johan +and Kiar, Gregory and Whitaker, Kirstie and DuPre, +Elizabeth and Wagner, Adina and Tirrell, Lee and Jas, +Mainak and Hanke, Michael and Poldrack, Russell and +Esteban, Oscar and Appelhoff, Stefan and Holdgraf, Chris +and Staden, Isla and Thirion, Bertrand and Kleinschmidt, +Dave and Lee, John and di Castello, Matteo and Notter, +Michael and Blair, Ross}, + doi = {10.21105/joss.01294}, + issn = {2475-9066}, + journal = {Journal of Open Source Software}, + month = {August}, + number = {40}, + pages = {1294}, + publisher = {The Open Journal}, + title = {PyBIDS: Python tools for BIDS datasets}, + url = {http://dx.doi.org/10.21105/joss.01294}, + volume = {4}, + year = {2019} +} diff --git a/content/publications/yarkoni-2019/index.md b/content/publications/yarkoni-2019/index.md new file mode 100644 index 0000000..6b94a33 --- /dev/null +++ b/content/publications/yarkoni-2019/index.md @@ -0,0 +1,44 @@ +--- +title: 'PyBIDS: Python tools for BIDS datasets' +authors: +- Tal Yarkoni +- Christopher Markiewicz +- Alejandro de la Vega +- Krzysztof Gorgolewski +- Taylor Salo +- Yaroslav Halchenko +- Quinten McNamara +- Krista DeStasio +- Jean-Baptiste Poline +- Dmitry Petrov +- Valérie Hayot-Sasson +- Dylan Nielson +- Johan Carlin +- Gregory Kiar +- Kirstie Whitaker +- Elizabeth DuPre +- Adina Wagner +- Lee Tirrell +- Mainak Jas +- Michael Hanke +- Russell Poldrack +- Oscar Esteban +- Stefan Appelhoff +- Chris Holdgraf +- Isla Staden +- Bertrand Thirion +- Dave Kleinschmidt +- John Lee +- Matteo di Castello +- Michael Notter +- Ross Blair +date: '2019-08-01' +publishDate: '2024-12-19T23:16:36.769287Z' +publication_types: +- article-journal +publication: '*Journal of Open Source Software*' +doi: 10.21105/joss.01294 +links: +- name: URL + url: http://dx.doi.org/10.21105/joss.01294 +--- diff --git a/content/publications/zhao-2023/cite.bib b/content/publications/zhao-2023/cite.bib new file mode 100644 index 0000000..3b51f93 --- /dev/null +++ b/content/publications/zhao-2023/cite.bib @@ -0,0 +1,18 @@ +@article{zhao_2023, + author = {Zhao, Chenying and Jarecka, Dorota and Covitz, Sydney and +Chen, Yibei and Eickhoff, Simon B. and Fair, Damien A. and +Franco, Alexandre R. and Halchenko, Yaroslav O. and +Hendrickson, Timothy J. and Hoffstaedter, Felix and +Houghton, Audrey and Kiar, Gregory and Macdonald, Austin +and Mehta, Kahini and Milham, Michael P. and Salo, Taylor +and Hanke, Michael and Ghosh, Satrajit S. and Cieslak, +Matthew and Satterthwaite, Theodore D.}, + doi = {10.1101/2023.08.16.552472}, + month = {August}, + publisher = {Cold Spring Harbor Laboratory}, + title = {A reproducible and generalizable software workflow for +analysis of large-scale neuroimaging data collections using +BIDS Apps}, + url = {http://dx.doi.org/10.1101/2023.08.16.552472}, + year = {2023} +} diff --git a/content/publications/zhao-2023/index.md b/content/publications/zhao-2023/index.md new file mode 100644 index 0000000..28775d1 --- /dev/null +++ b/content/publications/zhao-2023/index.md @@ -0,0 +1,34 @@ +--- +title: A reproducible and generalizable software workflow for analysis of large-scale + neuroimaging data collections using BIDS Apps +authors: +- Chenying Zhao +- Dorota Jarecka +- Sydney Covitz +- Yibei Chen +- Simon B. Eickhoff +- Damien A. Fair +- Alexandre R. Franco +- Yaroslav O. Halchenko +- Timothy J. Hendrickson +- Felix Hoffstaedter +- Audrey Houghton +- Gregory Kiar +- Austin Macdonald +- Kahini Mehta +- Michael P. Milham +- Taylor Salo +- Michael Hanke +- Satrajit S. Ghosh +- Matthew Cieslak +- Theodore D. Satterthwaite +date: '2023-08-01' +publishDate: '2024-12-19T23:16:36.773770Z' +publication_types: +- article-journal +publication: '*Cold Spring Harbor Laboratory*' +doi: 10.1101/2023.08.16.552472 +links: +- name: URL + url: http://dx.doi.org/10.1101/2023.08.16.552472 +---