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

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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 languageEnglish (US)
Pages (from-to)673-681
Number of pages9
JournalNature Neuroscience
Volume26
Issue number4
DOIs
StatePublished - Apr 2023

All Science Journal Classification (ASJC) codes

  • General Neuroscience

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