A consensus protocol for functional connectivity analysis in the rat brain

Joanes Grandjean; Gabriel Desrosiers-Gregoire; Cynthia Anckaerts; Diego Angeles-Valdez; Fadi Ayad; David A. Barrière; Ines Blockx; Aleksandra Bortel; Margaret Broadwater; Beatriz M. Cardoso; Marina Célestine; Jorge E. Chavez-Negrete; Sangcheon Choi; Emma Christiaen; Perrin Clavijo; Luis Colon-Perez; Samuel Cramer; Tolomeo Daniele; Elaine Dempsey; Yujian Diao; Arno Doelemeyer; David Dopfel; Lenka Dvořáková; Claudia Falfán-Melgoza; Francisca F. Fernandes; Caitlin F. Fowler; Antonio Fuentes-Ibañez; Clément Garin; Eveline Gelderman; Carla E. M. Golden; Chao C. G. Guo; Marloes J. A. G. Henckens; Lauren A. Hennessy; Peter Herman; Nita Hofwijks; Corey Horien; Tudor M. Ionescu; Jolyon Jones; Johannes Kaesser; Eugene Kim; Henriette Lambers; Alberto Lazari; Sung-Ho Lee; Amanda Lillywhite; Yikang Liu; Yanyan Y. Liu; Alejandra López -Castro; Xavier López-Gil; Zilu Ma; Eilidh MacNicol; Dan Madularu; Francesca Mandino; Sabina Marciano; Matthew J. McAuslan; Patrick McCunn; Alison McIntosh; Xianzong Meng; Lisa Meyer-Baese; Stephan Missault; Federico Moro; Daphne M. P. Naessens; Laura J. Nava-Gomez; Hiroi Nonaka; Juan J. Ortiz; Jaakko Paasonen; Lore M. Peeters; Mickaël Pereira; Pablo D. Perez; Marjory Pompilus; Malcolm Prior; Rustam Rakhmatullin; Henning M. Reimann; Jonathan Reinwald; Rodrigo Triana del Rio; Alejandro Rivera-Olvera; Daniel Ruiz-Pérez; Gabriele Russo; Tobias J. Rutten; Rie Ryoke; Markus Sack; Piergiorgio Salvan; Basavaraju G. Sanganahalli; Aileen Schroeter; Bhedita J. Seewoo; Erwan Selingue; Aline Seuwen; Bowen Shi; Nikoloz Sirmpilatze; Joanna A. B. Smith; Corrie Smith; Filip Sobczak; Petteri J. Stenroos; Milou Straathof; Sandra Strobelt; Akira Sumiyoshi; Kengo Takahashi; Maria E. Torres-García; Raul Tudela; Monica van den Berg; Kajo van der Marel; Aran T. B. van Hout; Roberta Vertullo; Benjamin Vidal; Roël M. Vrooman; Victora X. Wang; Isabel Wank; David J. G. Watson; Ting Yin; Yongzhi Zhang; Stefan Zurbruegg; Sophie Achard; Sarael Alcauter; Dorothee P. Auer; Emmanuel L. Barbier; J. rgen Baudewig; Christian F. Beckmann; Nicolau Beckmann; Guillaume J. P. C. Becq; Erwin L. A. Blezer; Radu Bolbos; Susann Boretius; Sandrine Bouvard; Eike Budinger; Joseph D. Buxbaum; Diana Cash; Victoria Chapman; Kai-Hsiang Chuang; Luisa Ciobanu; Bram F. Coolen; Jeffrey W. Dalley; Marc Dhenain; Rick M. Dijkhuizen; Oscar Esteban; Cornelius Faber; Marcelo Febo; Kirk W. Feindel; Gianluigi Forloni; J. rémie Fouquet; Eduardo A. Garza-Villarreal; Natalia Gass; Jeffrey C. Glennon; Alessandro Gozzi; Olli Gröhn; Andrew Harkin; Arend Heerschap; Xavier Helluy; Kristina Herfert; Arnd Heuser; Judith R. Homberg; Danielle J. Houwing; Fahmeed Hyder; Giovanna Diletta Ielacqua; Ileana O. Jelescu; Heidi Johansen-Berg; Gen Kaneko; Ryuta Kawashima; Shella D. Keilholz; Georgios A. Keliris; Clare Kelly; Christian Kerskens; Jibran Y. Khokhar; Peter C. Kind; Jean-Baptiste Langlois; Jason P. Lerch; Monica A. López-Hidalgo; Denise Manahan-Vaughan; Fabien Marchand; Rogier B. Mars; Gerardo Marsella; Edoardo Micotti; Emma Muñoz-Moreno; Jamie Near; Thoralf Niendorf; Willem M. Otte; Patricia Pais-Roldán; Wen-Ju Pan; Roberto A. Prado-Alcalá; Gina L. Quirarte; Jennifer Rodger; Tim Rosenow; Cassandra Sampaio-Baptista; Alexander Sartorius; Stephen J. Sawiak; Tom W. J. Scheenen; Noam Shemesh; Yen-Yu Ian Shih; Amir Shmuel; Guadalupe Soria; Ron Stoop; Garth J. Thompson; Sally M. Till; Nick Todd; Annemie van der Linden; Annette van der Toorn; Geralda A. F. van Tilborg; Christian Vanhove; Andor Veltien; Marleen Verhoye; Lydia Wachsmuth; Wolfgang Weber-Fahr; Patricia Wenk; Xin Yu; Valerio Zerbi; Nanyin Zhang; Baogui B. Zhang; Luc Zimmer; Gabriel A. Devenyi; M. Mallar Chakravarty; Andreas Hess

doi:https://doi.org/10.1038/s41593-023-01286-8

A consensus protocol for functional connectivity analysis in the rat brain

Joanes Grandjean, Gabriel Desrosiers-Gregoire, Cynthia Anckaerts, Diego Angeles-Valdez, Fadi Ayad, David A. Barrière, Ines Blockx, Aleksandra Bortel, Margaret Broadwater, Beatriz M. Cardoso, Marina Célestine, Jorge E. Chavez-Negrete, Sangcheon Choi, Emma Christiaen, Perrin Clavijo, Luis Colon-Perez, Samuel Cramer, Tolomeo Daniele, Elaine Dempsey, Yujian DiaoArno Doelemeyer, David Dopfel, Lenka Dvořáková, Claudia Falfán-Melgoza, Francisca F. Fernandes, Caitlin F. Fowler, Antonio Fuentes-Ibañez, Clément Garin, Eveline Gelderman, Carla E. M. Golden, Chao C. G. Guo, Marloes J. A. G. Henckens, Lauren A. Hennessy, Peter Herman, Nita Hofwijks, Corey Horien, Tudor M. Ionescu, Jolyon Jones, Johannes Kaesser, Eugene Kim, Henriette Lambers, Alberto Lazari, Sung-Ho Lee, Amanda Lillywhite, Yikang Liu, Yanyan Y. Liu, Alejandra López -Castro, Xavier López-Gil, Zilu Ma, Eilidh MacNicol, Dan Madularu, Francesca Mandino, Sabina Marciano, Matthew J. McAuslan, Patrick McCunn, Alison McIntosh, Xianzong Meng, Lisa Meyer-Baese, Stephan Missault, Federico Moro, Daphne M. P. Naessens, Laura J. Nava-Gomez, Hiroi Nonaka, Juan J. Ortiz, Jaakko Paasonen, Lore M. Peeters, Mickaël Pereira, Pablo D. Perez, Marjory Pompilus, Malcolm Prior, Rustam Rakhmatullin, Henning M. Reimann, Jonathan Reinwald, Rodrigo Triana del Rio, Alejandro Rivera-Olvera, Daniel Ruiz-Pérez, Gabriele Russo, Tobias J. Rutten, Rie Ryoke, Markus Sack, Piergiorgio Salvan, Basavaraju G. Sanganahalli, Aileen Schroeter, Bhedita J. Seewoo, Erwan Selingue, Aline Seuwen, Bowen Shi, Nikoloz Sirmpilatze, Joanna A. B. Smith, Corrie Smith, Filip Sobczak, Petteri J. Stenroos, Milou Straathof, Sandra Strobelt, Akira Sumiyoshi, Kengo Takahashi, Maria E. Torres-García, Raul Tudela, Monica van den Berg, Kajo van der Marel, Aran T. B. van Hout, Roberta Vertullo, Benjamin Vidal, Roël M. Vrooman, Victora X. Wang, Isabel Wank, David J. G. Watson, Ting Yin, Yongzhi Zhang, Stefan Zurbruegg, Sophie Achard, Sarael Alcauter, Dorothee P. Auer, Emmanuel L. Barbier, J. rgen Baudewig, Christian F. Beckmann, Nicolau Beckmann, Guillaume J. P. C. Becq, Erwin L. A. Blezer, Radu Bolbos, Susann Boretius, Sandrine Bouvard, Eike Budinger, Joseph D. Buxbaum, Diana Cash, Victoria Chapman, Kai-Hsiang Chuang, Luisa Ciobanu, Bram F. Coolen, Jeffrey W. Dalley, Marc Dhenain, Rick M. Dijkhuizen, Oscar Esteban, Cornelius Faber, Marcelo Febo, Kirk W. Feindel, Gianluigi Forloni, J. rémie Fouquet, Eduardo A. Garza-Villarreal, Natalia Gass, Jeffrey C. Glennon, Alessandro Gozzi, Olli Gröhn, Andrew Harkin, Arend Heerschap, Xavier Helluy, Kristina Herfert, Arnd Heuser, Judith R. Homberg, Danielle J. Houwing, Fahmeed Hyder, Giovanna Diletta Ielacqua, Ileana O. Jelescu, Heidi Johansen-Berg, Gen Kaneko, Ryuta Kawashima, Shella D. Keilholz, Georgios A. Keliris, Clare Kelly, Christian Kerskens, Jibran Y. Khokhar, Peter C. Kind, Jean-Baptiste Langlois, Jason P. Lerch, Monica A. López-Hidalgo, Denise Manahan-Vaughan, Fabien Marchand, Rogier B. Mars, Gerardo Marsella, Edoardo Micotti, Emma Muñoz-Moreno, Jamie Near, Thoralf Niendorf, Willem M. Otte, Patricia Pais-Roldán, Wen-Ju Pan, Roberto A. Prado-Alcalá, Gina L. Quirarte, Jennifer Rodger, Tim Rosenow, Cassandra Sampaio-Baptista, Alexander Sartorius, Stephen J. Sawiak, Tom W. J. Scheenen, Noam Shemesh, Yen-Yu Ian Shih, Amir Shmuel, Guadalupe Soria, Ron Stoop, Garth J. Thompson, Sally M. Till, Nick Todd, Annemie van der Linden, Annette van der Toorn, Geralda A. F. van Tilborg, Christian Vanhove, Andor Veltien, Marleen Verhoye, Lydia Wachsmuth, Wolfgang Weber-Fahr, Patricia Wenk, Xin Yu, Valerio Zerbi, Nanyin Zhang, Baogui B. Zhang, Luc Zimmer, Gabriel A. Devenyi, M. Mallar Chakravarty, Andreas Hess

Research output: Contribution to journal › Article › Academic › peer-review

17 Citations (Scopus)

Abstract

Task-free functional connectivity in animal models provides an experimental framework to examine connectivity phenomena under controlled conditions and allows for comparisons with data modalities collected under invasive or terminal procedures. Currently, animal acquisitions are performed with varying protocols and analyses that hamper result comparison and integration. Here we introduce StandardRat, a consensus rat functional magnetic resonance imaging acquisition protocol tested across 20 centers. To develop this protocol with optimized acquisition and processing parameters, we initially aggregated 65 functional imaging datasets acquired from rats across 46 centers. We developed a reproducible pipeline for analyzing rat data acquired with diverse protocols and determined experimental and processing parameters associated with the robust detection of functional connectivity across centers. We show that the standardized protocol enhances biologically plausible functional connectivity patterns relative to previous acquisitions. The protocol and processing pipeline described here is openly shared with the neuroimaging community to promote interoperability and cooperation toward tackling the most important challenges in neuroscience.

Original language	English
Pages (from-to)	673-681
Number of pages	9
Journal	Nature neuroscience
Volume	26
Issue number	4
Early online date	2023
DOIs	https://doi.org/10.1038/s41593-023-01286-8
Publication status	Published - Apr 2023

Access to Document

https://doi.org/10.1038/s41593-023-01286-8

Cite this

Grandjean, J., Desrosiers-Gregoire, G., Anckaerts, C., Angeles-Valdez, D., Ayad, F., Barrière, D. A., Blockx, I., Bortel, A., Broadwater, M., Cardoso, B. M., Célestine, M., Chavez-Negrete, J. E., Choi, S., Christiaen, E., Clavijo, P., Colon-Perez, L., Cramer, S., Daniele, T., Dempsey, E., ... Hess, A. (2023). A consensus protocol for functional connectivity analysis in the rat brain. Nature neuroscience, 26(4), 673-681. https://doi.org/10.1038/s41593-023-01286-8

@article{297a28ea5bac496c830110152066bdfc,

title = "A consensus protocol for functional connectivity analysis in the rat brain",

abstract = "Task-free functional connectivity in animal models provides an experimental framework to examine connectivity phenomena under controlled conditions and allows for comparisons with data modalities collected under invasive or terminal procedures. Currently, animal acquisitions are performed with varying protocols and analyses that hamper result comparison and integration. Here we introduce StandardRat, a consensus rat functional magnetic resonance imaging acquisition protocol tested across 20 centers. To develop this protocol with optimized acquisition and processing parameters, we initially aggregated 65 functional imaging datasets acquired from rats across 46 centers. We developed a reproducible pipeline for analyzing rat data acquired with diverse protocols and determined experimental and processing parameters associated with the robust detection of functional connectivity across centers. We show that the standardized protocol enhances biologically plausible functional connectivity patterns relative to previous acquisitions. The protocol and processing pipeline described here is openly shared with the neuroimaging community to promote interoperability and cooperation toward tackling the most important challenges in neuroscience.",

author = "Joanes Grandjean and Gabriel Desrosiers-Gregoire and Cynthia Anckaerts and Diego Angeles-Valdez and Fadi Ayad and Barri{\`e}re, {David A.} and Ines Blockx and Aleksandra Bortel and Margaret Broadwater and Cardoso, {Beatriz M.} and Marina C{\'e}lestine and Chavez-Negrete, {Jorge E.} and Sangcheon Choi and Emma Christiaen and Perrin Clavijo and Luis Colon-Perez and Samuel Cramer and Tolomeo Daniele and Elaine Dempsey and Yujian Diao and Arno Doelemeyer and David Dopfel and Lenka Dvo{\v r}{\'a}kov{\'a} and Claudia Falf{\'a}n-Melgoza and Fernandes, {Francisca F.} and Fowler, {Caitlin F.} and Antonio Fuentes-Iba{\~n}ez and Cl{\'e}ment Garin and Eveline Gelderman and Golden, {Carla E. M.} and Guo, {Chao C. G.} and Henckens, {Marloes J. A. G.} and Hennessy, {Lauren A.} and Peter Herman and Nita Hofwijks and Corey Horien and Ionescu, {Tudor M.} and Jolyon Jones and Johannes Kaesser and Eugene Kim and Henriette Lambers and Alberto Lazari and Sung-Ho Lee and Amanda Lillywhite and Yikang Liu and Liu, {Yanyan Y.} and {L{\'o}pez -Castro}, Alejandra and Xavier L{\'o}pez-Gil and Zilu Ma and Eilidh MacNicol and Dan Madularu and Francesca Mandino and Sabina Marciano and McAuslan, {Matthew J.} and Patrick McCunn and Alison McIntosh and Xianzong Meng and Lisa Meyer-Baese and Stephan Missault and Federico Moro and Naessens, {Daphne M. P.} and Nava-Gomez, {Laura J.} and Hiroi Nonaka and Ortiz, {Juan J.} and Jaakko Paasonen and Peeters, {Lore M.} and Micka{\"e}l Pereira and Perez, {Pablo D.} and Marjory Pompilus and Malcolm Prior and Rustam Rakhmatullin and Reimann, {Henning M.} and Jonathan Reinwald and {del Rio}, {Rodrigo Triana} and Alejandro Rivera-Olvera and Daniel Ruiz-P{\'e}rez and Gabriele Russo and Rutten, {Tobias J.} and Rie Ryoke and Markus Sack and Piergiorgio Salvan and Sanganahalli, {Basavaraju G.} and Aileen Schroeter and Seewoo, {Bhedita J.} and Erwan Selingue and Aline Seuwen and Bowen Shi and Nikoloz Sirmpilatze and Smith, {Joanna A. B.} and Corrie Smith and Filip Sobczak and Stenroos, {Petteri J.} and Milou Straathof and Sandra Strobelt and Akira Sumiyoshi and Kengo Takahashi and Torres-Garc{\'i}a, {Maria E.} and Raul Tudela and {van den Berg}, Monica and {van der Marel}, Kajo and {van Hout}, {Aran T. B.} and Roberta Vertullo and Benjamin Vidal and Vrooman, {Ro{\"e}l M.} and Wang, {Victora X.} and Isabel Wank and Watson, {David J. G.} and Ting Yin and Yongzhi Zhang and Stefan Zurbruegg and Sophie Achard and Sarael Alcauter and Auer, {Dorothee P.} and Barbier, {Emmanuel L.} and Baudewig, {J. rgen} and Beckmann, {Christian F.} and Nicolau Beckmann and Becq, {Guillaume J. P. C.} and Blezer, {Erwin L. A.} and Radu Bolbos and Susann Boretius and Sandrine Bouvard and Eike Budinger and Buxbaum, {Joseph D.} and Diana Cash and Victoria Chapman and Kai-Hsiang Chuang and Luisa Ciobanu and Coolen, {Bram F.} and Dalley, {Jeffrey W.} and Marc Dhenain and Dijkhuizen, {Rick M.} and Oscar Esteban and Cornelius Faber and Marcelo Febo and Feindel, {Kirk W.} and Gianluigi Forloni and Fouquet, {J. r{\'e}mie} and Garza-Villarreal, {Eduardo A.} and Natalia Gass and Glennon, {Jeffrey C.} and Alessandro Gozzi and Olli Gr{\"o}hn and Andrew Harkin and Arend Heerschap and Xavier Helluy and Kristina Herfert and Arnd Heuser and Homberg, {Judith R.} and Houwing, {Danielle J.} and Fahmeed Hyder and Ielacqua, {Giovanna Diletta} and Jelescu, {Ileana O.} and Heidi Johansen-Berg and Gen Kaneko and Ryuta Kawashima and Keilholz, {Shella D.} and Keliris, {Georgios A.} and Clare Kelly and Christian Kerskens and Khokhar, {Jibran Y.} and Kind, {Peter C.} and Jean-Baptiste Langlois and Lerch, {Jason P.} and L{\'o}pez-Hidalgo, {Monica A.} and Denise Manahan-Vaughan and Fabien Marchand and Mars, {Rogier B.} and Gerardo Marsella and Edoardo Micotti and Emma Mu{\~n}oz-Moreno and Jamie Near and Thoralf Niendorf and Otte, {Willem M.} and Patricia Pais-Rold{\'a}n and Wen-Ju Pan and Prado-Alcal{\'a}, {Roberto A.} and Quirarte, {Gina L.} and Jennifer Rodger and Tim Rosenow and Cassandra Sampaio-Baptista and Alexander Sartorius and Sawiak, {Stephen J.} and Scheenen, {Tom W. J.} and Noam Shemesh and Shih, {Yen-Yu Ian} and Amir Shmuel and Guadalupe Soria and Ron Stoop and Thompson, {Garth J.} and Till, {Sally M.} and Nick Todd and {van der Linden}, Annemie and {van der Toorn}, Annette and {van Tilborg}, {Geralda A. F.} and Christian Vanhove and Andor Veltien and Marleen Verhoye and Lydia Wachsmuth and Wolfgang Weber-Fahr and Patricia Wenk and Xin Yu and Valerio Zerbi and Nanyin Zhang and Zhang, {Baogui B.} and Luc Zimmer and Devenyi, {Gabriel A.} and Chakravarty, {M. Mallar} and Andreas Hess",

note = "Funding Information: This research was enabled, in part, by support provided by Compute Ontario ( https://www.computeontario.ca/ ) and Compute Canada ( www.computecanada.ca ). For the purpose of open access, we have applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. This research was funded by: the National Institutes of Health (K01EB023983, R03DA042971, R21AG065819, K25DA047458, I015I01CX000642-04, R01NS085200, R01MH098003, RF1MH114224, T32AA007573, R01MH067528, P30NS05219, T32GM007205, R01MH111416, R01NS078095, R01EB029857, F31 MH115656 and 1R21MH116473-01A1); the Wellcome Trust (212934/Z/18/Z, 109062/Z/15/Z, 110027/Z/15/Z, 204814/Z/16/Z and 203139/Z/16/Z); the Dutch Research Council (OCENW.KLEIN.334, 021.002.053, 016.130.662 and 016.168.038); the German Research Foundation (SA 1869/15-1, SA 2897/2-1, SFB 1436/B06, SFB874/B3 project no.: 122679504, SFB 1280/A04 project no.: 316803389); the French National Research Agency (ANR-15-IDEX-02 and ANR-11-INBS-0006); Programa de Apoyo a Proyectos de Investigaci{\'o}n e Innovaci{\'o}n Tecnol{\'o}gica (IN212219, IA202120 and IA201622); the UK Medical Research Council (MR/N013700/1 and 1653552); the Portuguese Foundation for Science and Technology (LISBOA-01-0145-FEDER-022170 and 275-FCT-PTDC/BBB/IMG/5132/2014); the Swiss National Science Foundation (PCEFP3_203005 and PCEFP2_194260); King{\textquoteright}s College London, Biotechnology and Biological Sciences Research Council (BB/N009088/1); the European Community{\textquoteright}s Seventh Framework Program (FP7/2007-2013); TACTICS (278948); the Brain and Behaviour Foundation (NARSAD, 25861); the Dutch Brain Foundation (F2014(1)-06); the National Science Foundation (DMR-1644779, DMR-1533260, DMR-2128556); the Human Brain Project (945539); the Canadian Institutes of Health Research (PJT-148751, PJT-173442 and MOP-102599); the Natural Sciences and Engineering Research Council of Canada (RGPIN-2020-05917, RGPIN-375457-09 and RGPIN-2015-05103); the Horizon 2020 Framework Programme of the European Union (740264 and 802371); the Academy of Finland (298007); the European Research Council (679058 and 802371); Innosuisse (18546.1); the Research Foundation – Flanders (12W1619N, FWO-G048917N and G045420N); the Stichting Alzheimer Onderzoek (SAO-FRA-20180003); Special Research Programmes (1158); CIBER-BBN; Instituto de Salut Carlos III - FEDER (PI18/00893); Versus Arthritis (20777); the Brain Behavior Foundation (25861); the Telethon Foundation (GGP19177); Eurostars (E!114985); the Brain Canada Foundation platform support grant (PSG15-3755); the National Natural Science Foundation of China (81950410637); Science Foundation Ireland (20/FFPP/8799); Trinity Foundation (RCN 20028626); Consejo Nacional de Ciencia y Tecnologia Ciencia de Frontera (171874); PAPIIT-DGAPA (IA208022); Fonds de recherche du Qu{\'e}bec – Nature et technologies; the Forrest Research Foundation; the Australian National Imaging Facility; the University of Western Australia; the National Health and Medical Research Council of the Australian Government; the Perron Institute for Neurological and Translational Science; McGill University{\textquoteright}s Faculty of Medicine; the Seaver Foundation; Autism Speaks; the Centre d{\textquoteright}Imagerie BioM{\'e}dicale of the UNIL, UNIGE, HUG, CHUV, EPFL; the Leenaards and Louis-Jeantet Foundations; the DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain; the Synapsis Foundation; the Simons Initiative for the Developing Brain; the Patrick Wild Centre; the Department of Biotechnology India; Utrecht University High Potential Program; ERA-NET NEURON Neuromarket; Mannheim Advanced Clinician Scientist Program; ICON – Interfaces and Interventions in Complex Chronic Conditions; the Werner Siemens Foundation; the Lisboa Regional Operational Programme; the Japan Ministry of Education, Culture, Sports, Science and Technology (MEXT); ShanghaiTech University; the Shanghai Municipal Government; and the Interdisciplinary Center for Clinical Research M{\"u}nster (PIX). Publisher Copyright: {\textcopyright} 2023, The Author(s), under exclusive licence to Springer Nature America, Inc.",

year = "2023",

month = apr,

doi = "https://doi.org/10.1038/s41593-023-01286-8",

language = "English",

volume = "26",

pages = "673--681",

journal = "Nature neuroscience",

issn = "1097-6256",

publisher = "Nature Publishing Group",

number = "4",

}

Grandjean, J, Desrosiers-Gregoire, G, Anckaerts, C, Angeles-Valdez, D, Ayad, F, Barrière, DA, Blockx, I, Bortel, A, Broadwater, M, Cardoso, BM, Célestine, M, Chavez-Negrete, JE, Choi, S, Christiaen, E, Clavijo, P, Colon-Perez, L, Cramer, S, Daniele, T, Dempsey, E, Diao, Y, Doelemeyer, A, Dopfel, D, Dvořáková, L, Falfán-Melgoza, C, Fernandes, FF, Fowler, CF, Fuentes-Ibañez, A, Garin, C, Gelderman, E, Golden, CEM, Guo, CCG, Henckens, MJAG, Hennessy, LA, Herman, P, Hofwijks, N, Horien, C, Ionescu, TM, Jones, J, Kaesser, J, Kim, E, Lambers, H, Lazari, A, Lee, S-H, Lillywhite, A, Liu, Y, Liu, YY, López -Castro, A, López-Gil, X, Ma, Z, MacNicol, E, Madularu, D, Mandino, F, Marciano, S, McAuslan, MJ, McCunn, P, McIntosh, A, Meng, X, Meyer-Baese, L, Missault, S, Moro, F, Naessens, DMP, Nava-Gomez, LJ, Nonaka, H, Ortiz, JJ, Paasonen, J, Peeters, LM, Pereira, M, Perez, PD, Pompilus, M, Prior, M, Rakhmatullin, R, Reimann, HM, Reinwald, J, del Rio, RT, Rivera-Olvera, A, Ruiz-Pérez, D, Russo, G, Rutten, TJ, Ryoke, R, Sack, M, Salvan, P, Sanganahalli, BG, Schroeter, A, Seewoo, BJ, Selingue, E, Seuwen, A, Shi, B, Sirmpilatze, N, Smith, JAB, Smith, C, Sobczak, F, Stenroos, PJ, Straathof, M, Strobelt, S, Sumiyoshi, A, Takahashi, K, Torres-García, ME, Tudela, R, van den Berg, M, van der Marel, K, van Hout, ATB, Vertullo, R, Vidal, B, Vrooman, RM, Wang, VX, Wank, I, Watson, DJG, Yin, T, Zhang, Y, Zurbruegg, S, Achard, S, Alcauter, S, Auer, DP, Barbier, EL, Baudewig, JR, Beckmann, CF, Beckmann, N, Becq, GJPC, Blezer, ELA, Bolbos, R, Boretius, S, Bouvard, S, Budinger, E, Buxbaum, JD, Cash, D, Chapman, V, Chuang, K-H, Ciobanu, L, Coolen, BF, Dalley, JW, Dhenain, M, Dijkhuizen, RM, Esteban, O, Faber, C, Febo, M, Feindel, KW, Forloni, G, Fouquet, JR, Garza-Villarreal, EA, Gass, N, Glennon, JC, Gozzi, A, Gröhn, O, Harkin, A, Heerschap, A, Helluy, X, Herfert, K, Heuser, A, Homberg, JR, Houwing, DJ, Hyder, F, Ielacqua, GD, Jelescu, IO, Johansen-Berg, H, Kaneko, G, Kawashima, R, Keilholz, SD, Keliris, GA, Kelly, C, Kerskens, C, Khokhar, JY, Kind, PC, Langlois, J-B, Lerch, JP, López-Hidalgo, MA, Manahan-Vaughan, D, Marchand, F, Mars, RB, Marsella, G, Micotti, E, Muñoz-Moreno, E, Near, J, Niendorf, T, Otte, WM, Pais-Roldán, P, Pan, W-J, Prado-Alcalá, RA, Quirarte, GL, Rodger, J, Rosenow, T, Sampaio-Baptista, C, Sartorius, A, Sawiak, SJ, Scheenen, TWJ, Shemesh, N, Shih, Y-YI, Shmuel, A, Soria, G, Stoop, R, Thompson, GJ, Till, SM, Todd, N, van der Linden, A, van der Toorn, A, van Tilborg, GAF, Vanhove, C, Veltien, A, Verhoye, M, Wachsmuth, L, Weber-Fahr, W, Wenk, P, Yu, X, Zerbi, V, Zhang, N, Zhang, BB, Zimmer, L, Devenyi, GA, Chakravarty, MM & Hess, A 2023, 'A consensus protocol for functional connectivity analysis in the rat brain', Nature neuroscience, vol. 26, no. 4, pp. 673-681. https://doi.org/10.1038/s41593-023-01286-8

TY - JOUR

T1 - A consensus protocol for functional connectivity analysis in the rat brain

AU - Grandjean, Joanes

AU - Desrosiers-Gregoire, Gabriel

AU - Anckaerts, Cynthia

AU - Angeles-Valdez, Diego

AU - Ayad, Fadi

AU - Barrière, David A.

AU - Blockx, Ines

AU - Bortel, Aleksandra

AU - Broadwater, Margaret

AU - Cardoso, Beatriz M.

AU - Célestine, Marina

AU - Chavez-Negrete, Jorge E.

AU - Choi, Sangcheon

AU - Christiaen, Emma

AU - Clavijo, Perrin

AU - Colon-Perez, Luis

AU - Cramer, Samuel

AU - Daniele, Tolomeo

AU - Dempsey, Elaine

AU - Diao, Yujian

AU - Doelemeyer, Arno

AU - Dopfel, David

AU - Dvořáková, Lenka

AU - Falfán-Melgoza, Claudia

AU - Fernandes, Francisca F.

AU - Fowler, Caitlin F.

AU - Fuentes-Ibañez, Antonio

AU - Garin, Clément

AU - Gelderman, Eveline

AU - Golden, Carla E. M.

AU - Guo, Chao C. G.

AU - Henckens, Marloes J. A. G.

AU - Hennessy, Lauren A.

AU - Herman, Peter

AU - Hofwijks, Nita

AU - Horien, Corey

AU - Ionescu, Tudor M.

AU - Jones, Jolyon

AU - Kaesser, Johannes

AU - Kim, Eugene

AU - Lambers, Henriette

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N1 - Funding Information: This research was enabled, in part, by support provided by Compute Ontario ( https://www.computeontario.ca/ ) and Compute Canada ( www.computecanada.ca ). For the purpose of open access, we have applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. This research was funded by: the National Institutes of Health (K01EB023983, R03DA042971, R21AG065819, K25DA047458, I015I01CX000642-04, R01NS085200, R01MH098003, RF1MH114224, T32AA007573, R01MH067528, P30NS05219, T32GM007205, R01MH111416, R01NS078095, R01EB029857, F31 MH115656 and 1R21MH116473-01A1); the Wellcome Trust (212934/Z/18/Z, 109062/Z/15/Z, 110027/Z/15/Z, 204814/Z/16/Z and 203139/Z/16/Z); the Dutch Research Council (OCENW.KLEIN.334, 021.002.053, 016.130.662 and 016.168.038); the German Research Foundation (SA 1869/15-1, SA 2897/2-1, SFB 1436/B06, SFB874/B3 project no.: 122679504, SFB 1280/A04 project no.: 316803389); the French National Research Agency (ANR-15-IDEX-02 and ANR-11-INBS-0006); Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica (IN212219, IA202120 and IA201622); the UK Medical Research Council (MR/N013700/1 and 1653552); the Portuguese Foundation for Science and Technology (LISBOA-01-0145-FEDER-022170 and 275-FCT-PTDC/BBB/IMG/5132/2014); the Swiss National Science Foundation (PCEFP3_203005 and PCEFP2_194260); King’s College London, Biotechnology and Biological Sciences Research Council (BB/N009088/1); the European Community’s Seventh Framework Program (FP7/2007-2013); TACTICS (278948); the Brain and Behaviour Foundation (NARSAD, 25861); the Dutch Brain Foundation (F2014(1)-06); the National Science Foundation (DMR-1644779, DMR-1533260, DMR-2128556); the Human Brain Project (945539); the Canadian Institutes of Health Research (PJT-148751, PJT-173442 and MOP-102599); the Natural Sciences and Engineering Research Council of Canada (RGPIN-2020-05917, RGPIN-375457-09 and RGPIN-2015-05103); the Horizon 2020 Framework Programme of the European Union (740264 and 802371); the Academy of Finland (298007); the European Research Council (679058 and 802371); Innosuisse (18546.1); the Research Foundation – Flanders (12W1619N, FWO-G048917N and G045420N); the Stichting Alzheimer Onderzoek (SAO-FRA-20180003); Special Research Programmes (1158); CIBER-BBN; Instituto de Salut Carlos III - FEDER (PI18/00893); Versus Arthritis (20777); the Brain Behavior Foundation (25861); the Telethon Foundation (GGP19177); Eurostars (E!114985); the Brain Canada Foundation platform support grant (PSG15-3755); the National Natural Science Foundation of China (81950410637); Science Foundation Ireland (20/FFPP/8799); Trinity Foundation (RCN 20028626); Consejo Nacional de Ciencia y Tecnologia Ciencia de Frontera (171874); PAPIIT-DGAPA (IA208022); Fonds de recherche du Québec – Nature et technologies; the Forrest Research Foundation; the Australian National Imaging Facility; the University of Western Australia; the National Health and Medical Research Council of the Australian Government; the Perron Institute for Neurological and Translational Science; McGill University’s Faculty of Medicine; the Seaver Foundation; Autism Speaks; the Centre d’Imagerie BioMédicale of the UNIL, UNIGE, HUG, CHUV, EPFL; the Leenaards and Louis-Jeantet Foundations; the DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain; the Synapsis Foundation; the Simons Initiative for the Developing Brain; the Patrick Wild Centre; the Department of Biotechnology India; Utrecht University High Potential Program; ERA-NET NEURON Neuromarket; Mannheim Advanced Clinician Scientist Program; ICON – Interfaces and Interventions in Complex Chronic Conditions; the Werner Siemens Foundation; the Lisboa Regional Operational Programme; the Japan Ministry of Education, Culture, Sports, Science and Technology (MEXT); ShanghaiTech University; the Shanghai Municipal Government; and the Interdisciplinary Center for Clinical Research Münster (PIX). Publisher Copyright: © 2023, The Author(s), under exclusive licence to Springer Nature America, Inc.

PY - 2023/4

Y1 - 2023/4

N2 - Task-free functional connectivity in animal models provides an experimental framework to examine connectivity phenomena under controlled conditions and allows for comparisons with data modalities collected under invasive or terminal procedures. Currently, animal acquisitions are performed with varying protocols and analyses that hamper result comparison and integration. Here we introduce StandardRat, a consensus rat functional magnetic resonance imaging acquisition protocol tested across 20 centers. To develop this protocol with optimized acquisition and processing parameters, we initially aggregated 65 functional imaging datasets acquired from rats across 46 centers. We developed a reproducible pipeline for analyzing rat data acquired with diverse protocols and determined experimental and processing parameters associated with the robust detection of functional connectivity across centers. We show that the standardized protocol enhances biologically plausible functional connectivity patterns relative to previous acquisitions. The protocol and processing pipeline described here is openly shared with the neuroimaging community to promote interoperability and cooperation toward tackling the most important challenges in neuroscience.

AB - Task-free functional connectivity in animal models provides an experimental framework to examine connectivity phenomena under controlled conditions and allows for comparisons with data modalities collected under invasive or terminal procedures. Currently, animal acquisitions are performed with varying protocols and analyses that hamper result comparison and integration. Here we introduce StandardRat, a consensus rat functional magnetic resonance imaging acquisition protocol tested across 20 centers. To develop this protocol with optimized acquisition and processing parameters, we initially aggregated 65 functional imaging datasets acquired from rats across 46 centers. We developed a reproducible pipeline for analyzing rat data acquired with diverse protocols and determined experimental and processing parameters associated with the robust detection of functional connectivity across centers. We show that the standardized protocol enhances biologically plausible functional connectivity patterns relative to previous acquisitions. The protocol and processing pipeline described here is openly shared with the neuroimaging community to promote interoperability and cooperation toward tackling the most important challenges in neuroscience.

UR - http://www.scopus.com/inward/record.url?scp=85150875109&partnerID=8YFLogxK

U2 - https://doi.org/10.1038/s41593-023-01286-8

DO - https://doi.org/10.1038/s41593-023-01286-8

M3 - Article

C2 - 36973511

SN - 1097-6256

VL - 26

SP - 673

EP - 681

JO - Nature neuroscience

JF - Nature neuroscience

IS - 4

ER -

A consensus protocol for functional connectivity analysis in the rat brain

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