A consensus protocol for functional connectivity analysis in the rat brain
Joanes Grandjean, Gabriel Desrosiers-Grégoire, Cynthia Anckaerts, Diego Ángeles-Valdéz, Fadi Ayad, David André Barrière, Ines Blockx, Aleksandra Bortel, Margaret Broadwater, Beatriz M Cardoso, Marina Célestine, Jorge E. Chavez-Negrete, Sangcheon Choi, Emma Christiaen, Perrin Clavijo, Luis M. Colón-Pérez, Samuel Cramer, Tolomeo Daniele, Elaine Dempsey, Yujian Diao, Arno Doelemeyer, David Dopfel, Lenka Dvořáková, Claudia Falfán-Melgoza, Francisca F. Fernandes, Caitlin Fowler, Antonio Fuentes-Ibañez, Clément M. Garin, Eveline Gelderman, Carla E. M. Golden, Chao Guo, Marloes J. A. G. Henckens, Lauren A. Hennessy, Péter Hermán, Nita Hofwijks, Corey Horien, Tudor M. Ionescu, Jolyon A. 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 José Ortiz, Jaakko Paasonen, Lore M. Peeters, Mickaël Pereira, Pablo D. Pérez, Marjory Pompilus, M. J. W. 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 Stenroos, Milou Straathof, Sandra Strobelt, Akira Sumiyoshi, Kengo Takahashi, Maria E. Torres-García, Raúl Tudela, Monica van den Berg, Kajo van der Marel
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.