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; Jürgen 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; Jérémie 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: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, Jürgen 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, Jérémie 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 › peer-review

6 Scopus citations

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 (US)
Pages (from-to)	673-681
Number of pages	9
Journal	Nature Neuroscience
Volume	26
Issue number	4
DOIs	https://doi.org/10.1038/s41593-023-01286-8
State	Published - Apr 2023

All Science Journal Classification (ASJC) codes

Neuroscience(all)

Access to Document

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{27081b3cb45e4cd3968c634634c3d371,

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 Lee, {Sung Ho} 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 J{\"u}rgen Baudewig 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 Chuang, {Kai Hsiang} 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 J{\'e}r{\'e}mie Fouquet 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 Langlois, {Jean Baptiste} 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 Pan, {Wen Ju} 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 = "Publisher Copyright: {\textcopyright} 2023, The Author(s), under exclusive licence to Springer Nature America, Inc.",

year = "2023",

month = apr,

doi = "10.1038/s41593-023-01286-8",

language = "English (US)",

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, SH, 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, J, Beckmann, CF, Beckmann, N, Becq, GJPC, Blezer, ELA, Bolbos, R, Boretius, S, Bouvard, S, Budinger, E, Buxbaum, JD, Cash, D, Chapman, V, Chuang, KH, Ciobanu, L, Coolen, BF, Dalley, JW, Dhenain, M, Dijkhuizen, RM, Esteban, O, Faber, C, Febo, M, Feindel, KW, Forloni, G, Fouquet, J, 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, JB, 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, WJ, Prado-Alcalá, RA, Quirarte, GL, Rodger, J, Rosenow, T, Sampaio-Baptista, C, Sartorius, A, Sawiak, SJ, Scheenen, TWJ, Shemesh, N, Shih, YYI, 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

AU - Lazari, Alberto

AU - Lee, Sung Ho

AU - Lillywhite, Amanda

AU - Liu, Yikang

AU - Liu, Yanyan Y.

AU - López -Castro, Alejandra

AU - López-Gil, Xavier

AU - Ma, Zilu

AU - MacNicol, Eilidh

AU - Madularu, Dan

AU - Mandino, Francesca

AU - Marciano, Sabina

AU - McAuslan, Matthew J.

AU - McCunn, Patrick

AU - McIntosh, Alison

AU - Meng, Xianzong

AU - Meyer-Baese, Lisa

AU - Missault, Stephan

AU - Moro, Federico

AU - Naessens, Daphne M.P.

AU - Nava-Gomez, Laura J.

AU - Nonaka, Hiroi

AU - Ortiz, Juan J.

AU - Paasonen, Jaakko

AU - Peeters, Lore M.

AU - Pereira, Mickaël

AU - Perez, Pablo D.

AU - Pompilus, Marjory

AU - Prior, Malcolm

AU - Rakhmatullin, Rustam

AU - Reimann, Henning M.

AU - Reinwald, Jonathan

AU - Del Rio, Rodrigo Triana

AU - Rivera-Olvera, Alejandro

AU - Ruiz-Pérez, Daniel

AU - Russo, Gabriele

AU - Rutten, Tobias J.

AU - Ryoke, Rie

AU - Sack, Markus

AU - Salvan, Piergiorgio

AU - Sanganahalli, Basavaraju G.

AU - Schroeter, Aileen

AU - Seewoo, Bhedita J.

AU - Selingue, Erwan

AU - Seuwen, Aline

AU - Shi, Bowen

AU - Sirmpilatze, Nikoloz

AU - Smith, Joanna A.B.

AU - Smith, Corrie

AU - Sobczak, Filip

AU - Stenroos, Petteri J.

AU - Straathof, Milou

AU - Strobelt, Sandra

AU - Sumiyoshi, Akira

AU - Takahashi, Kengo

AU - Torres-García, Maria E.

AU - Tudela, Raul

AU - van den Berg, Monica

AU - van der Marel, Kajo

AU - van Hout, Aran T.B.

AU - Vertullo, Roberta

AU - Vidal, Benjamin

AU - Vrooman, Roël M.

AU - Wang, Victora X.

AU - Wank, Isabel

AU - Watson, David J.G.

AU - Yin, Ting

AU - Zhang, Yongzhi

AU - Zurbruegg, Stefan

AU - Achard, Sophie

AU - Alcauter, Sarael

AU - Auer, Dorothee P.

AU - Barbier, Emmanuel L.

AU - Baudewig, Jürgen

AU - Beckmann, Christian F.

AU - Beckmann, Nicolau

AU - Becq, Guillaume J.P.C.

AU - Blezer, Erwin L.A.

AU - Bolbos, Radu

AU - Boretius, Susann

AU - Bouvard, Sandrine

AU - Budinger, Eike

AU - Buxbaum, Joseph D.

AU - Cash, Diana

AU - Chapman, Victoria

AU - Chuang, Kai Hsiang

AU - Ciobanu, Luisa

AU - Coolen, Bram F.

AU - Dalley, Jeffrey W.

AU - Dhenain, Marc

AU - Dijkhuizen, Rick M.

AU - Esteban, Oscar

AU - Faber, Cornelius

AU - Febo, Marcelo

AU - Feindel, Kirk W.

AU - Forloni, Gianluigi

AU - Fouquet, Jérémie

AU - Garza-Villarreal, Eduardo A.

AU - Gass, Natalia

AU - Glennon, Jeffrey C.

AU - Gozzi, Alessandro

AU - Gröhn, Olli

AU - Harkin, Andrew

AU - Heerschap, Arend

AU - Helluy, Xavier

AU - Herfert, Kristina

AU - Heuser, Arnd

AU - Homberg, Judith R.

AU - Houwing, Danielle J.

AU - Hyder, Fahmeed

AU - Ielacqua, Giovanna Diletta

AU - Jelescu, Ileana O.

AU - Johansen-Berg, Heidi

AU - Kaneko, Gen

AU - Kawashima, Ryuta

AU - Keilholz, Shella D.

AU - Keliris, Georgios A.

AU - Kelly, Clare

AU - Kerskens, Christian

AU - Khokhar, Jibran Y.

AU - Kind, Peter C.

AU - Langlois, Jean Baptiste

AU - Lerch, Jason P.

AU - López-Hidalgo, Monica A.

AU - Manahan-Vaughan, Denise

AU - Marchand, Fabien

AU - Mars, Rogier B.

AU - Marsella, Gerardo

AU - Micotti, Edoardo

AU - Muñoz-Moreno, Emma

AU - Near, Jamie

AU - Niendorf, Thoralf

AU - Otte, Willem M.

AU - Pais-Roldán, Patricia

AU - Pan, Wen Ju

AU - Prado-Alcalá, Roberto A.

AU - Quirarte, Gina L.

AU - Rodger, Jennifer

AU - Rosenow, Tim

AU - Sampaio-Baptista, Cassandra

AU - Sartorius, Alexander

AU - Sawiak, Stephen J.

AU - Scheenen, Tom W.J.

AU - Shemesh, Noam

AU - Shih, Yen Yu Ian

AU - Shmuel, Amir

AU - Soria, Guadalupe

AU - Stoop, Ron

AU - Thompson, Garth J.

AU - Till, Sally M.

AU - Todd, Nick

AU - Van Der Linden, Annemie

AU - van der Toorn, Annette

AU - van Tilborg, Geralda A.F.

AU - Vanhove, Christian

AU - Veltien, Andor

AU - Verhoye, Marleen

AU - Wachsmuth, Lydia

AU - Weber-Fahr, Wolfgang

AU - Wenk, Patricia

AU - Yu, Xin

AU - Zerbi, Valerio

AU - Zhang, Nanyin

AU - Zhang, Baogui B.

AU - Zimmer, Luc

AU - Devenyi, Gabriel A.

AU - Chakravarty, M. Mallar

AU - Hess, Andreas

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

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

U2 - 10.1038/s41593-023-01286-8

DO - 10.1038/s41593-023-01286-8

M3 - Article

C2 - 36973511

AN - SCOPUS:85150875109

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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