StandardRat: A multi-center consensus protocol to enhance functional connectivity specificity in the rat brain
Authors: Grandjean Joanes , Desrosiers-Gregoire Gabriel , Anckaerts Cynthia , Angeles-Valdez Diego , Ayad Fadi , Barrière David A , Blockx Ines , Bortel Aleksandra B , Broadwater Margaret , Cardoso Beatriz M , Célestine Marina , Chavez-Negrete Jorge E , Choi Sangcheon , Christiaen Emma , Clavijo Perrin , Colon-Perez Luis , Cramer Samuel , Daniele Tolomeo , Dempsey Elaine , Diao Yujian , Doelemeyer Arno , Dopfel David , Dvořáková Lenka , Falfán-Melgoza Claudia , Fernandes Francisca F , Fowler Caitlin F , Fuentes-Ibañez Antonio , Garin Clément , Gelderman Eveline , Golden Carla EM , Guo Chao CG , Henckens Marloes JAG , Hennessy Lauren A , Herman Peter , Hofwijks Nita , Horien Corey , Ionescu Tudor M , Jones Jolyon , Kaesser Johannes , Kim Eugene , Lambers Henriette , Lazari Alberto , Lee Sung-Ho , Lillywhite Amanda , Liu Yikang , Liu Yanyan Y , López-Castro Alejandra , López-Gil Xavier , Ma Zilu , MacNicol Eilidh , Madularu Dan , Mandino Francesca , Marciano Sabina , McAuslan Matthew J , McCunn Patrick , McIntosh Alison , Meng Xianzong , Meyer-Baese Lisa , Missault Stephan , Moro Federico , Naessens Daphne , Nava-Gomez Laura J , Nonaka Hiroi , Ortiz Juan J , Paasonen Jaakko , Peeters Lore M , Pereira Mickaël , Perez Pablo D , Pompilus Marjory , Prior Malcolm , Rakhmatullin Rustam , Reimann Henning M , Reinwald Jonathan , de Rio Rodrigo Triana , Rivera-Olvera Alejandro , Ruiz-Pérez Daniel , Russo Gabriele , Rutten Tobias J , Ryoke Rie , Sack Markus , Salvan Piergiorgio , Sanganahalli Basavaraju G , Schroeter Aileen , Seewoo Bhedita J , Selingue Erwan , Seuwen Aline , Shi Bowen , Sirmpilatze Nikoloz , Smith Joanna AB , Smith Corrie , Sobczak Filip , Stenroos Petteri J , Straathof Milou , Strobelt Sandra , Sumiyoshi Akira , Takahashi Kengo , Torres-García Maria E , Tudela Raul , van den Berg Monica , van der Marel Kajo , van Hout Aran TB , Vertullo Roberta , Vidal Benjamin , Vrooman Roel M , Wang Victora X , Wank Isabel , Watson David JG , Yin Ting , Zhang Yongzhi , Zurbruegg Stefan , Achard Sophie , Alcauter Sarael , Auer Dorothee P , Barbier Emmanuel L , Baudewig Jürgen , Beckmann Christian F , Beckmann Nicolau , Becq Guillaume JPC , Blezer Erwin LA , Bolbos Radu , Boretius Susann , Bouvard Sandrine , Budinger Eike , Buxbaum Joseph D , Cash Diana , Chapman Victoria , Chuang Kai-Hsiang , Ciobanu Luisa , Coolen Bram , Dalley Jeffrey W , Dhenain Marc , Dijkhuizen Rick M , Esteban Oscar , Faber Cornelius , Febo Marcelo , Feindel Kirk W , Forloni Gianluigi , Fouquet Jérémie , Garza-Villarreal Eduardo A , Gass Natalia , Glennon Jeffrey C , Gozzi Alessandro , Gröhn Olli , Harkin Andrew , Heerschap Arend , Helluy Xavier , Herfert Kristina , Heuser Arnd , Homberg Judith R , Houwing Danielle J , Hyder Fahmeed , Ielacqua Giovanna Diletta , Jelescu Ileana O , Johansen-Berg Heidi , Kaneko Gen , Kawashima Ryuta , Keilholz Shella D , Keliris Georgios A , Kelly Clare , Kerskens Christian , Khokhar Jibran Y , Kind Peter C , Langlois Jean-Baptiste , Lerch Jason P , López-Hidalgo Monica A , Manahan-Vaughan Denise , Marchand Fabien , Mars Rogier B , Marsella Gerardo , Micotti Edoardo , Muñoz-Moreno Emma , Near Jamie , Niendorf Thoralf , Otte Willem M , Pais Patricia , Pan Wen-Ju , Prado-Alcalá Roberto A , Quirarte Gina L , Rodger Jennifer , Rosenow Tim , Baptista Cassandra Sampaio , Sartorius Alexander , Sawiak Stephen J , Scheenen Tom WJ , Shemesh Noam , Shih Yen-Yu Ian , Shmuel Amir , Soria Guadalupe , Stoop Ron , Thompson Garth J , Till Sally M , Todd Nick , Van Der Linden Annemie , van der Toorn Annette , van Tilborg Geralda AF , Vanhove Christian , Veltien Andor , Verhoye Marleen , Wachsmuth Lydia , Weber-Fahr Wolfgang , Wenk Patricia , Yu Xin , Zerbi Valerio , Zhang Nanyin , Zhang Baogui B , Zimmer Luc , Devenyi Gabriel A , Chakravarty M Mallar , Hess Andreas 
Published: April 2022

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