A consensus protocol for functional connectivity analysis in the rat brain
Creators: name: Zimmer, Luc
name: Manahan-Vaughan, Denise
name: Dempsey, Elaine
name: Langlois, Jean-Baptiste
name: Clavijo, Perrin
name: Reinwald, Jonathan
name: Mars, Rogier B.
name: Gröhn, Olli
name: Ma, Zilu
name: Herfert, Kristina
name: Zhang, Yongzhi
name: van Tilborg, Geralda A. F.
name: Barbier, Emmanuel L.
name: Kawashima, Ryuta
name: Pereira, Mickaël
name: Zerbi, Valerio
name: Khokhar, Jibran Y.
name: Seuwen, Aline
name: Rakhmatullin, Rustam
name: Fowler, Caitlin F.
name: Otte, Willem M.
name: Schroeter, Aileen
name: Dvořáková, Lenka
name: Ruiz-Pérez, Daniel
name: Rodger, Jennifer
name: Esteban, Oscar
name: Takahashi, Kengo
name: Lee, Sung-Ho
name: Becq, Guillaume J. P. C.
name: Jelescu, Ileana O.
name: Cramer, Samuel
name: Keliris, Georgios A.
name: Salvan, Piergiorgio
name: Doelemeyer, Arno
name: Marsella, Gerardo
name: MacNicol, Eilidh
name: Dhenain, Marc
name: López -Castro, Alejandra
name: McCunn, Patrick
name: Feindel, Kirk W.
name: Mandino, Francesca
name: Gelderman, Eveline
name: Zhang, Nanyin
name: Herman, Peter
name: Thompson, Garth J.
name: Gozzi, Alessandro
name: Budinger, Eike
name: Ciobanu, Luisa
name: Johansen-Berg, Heidi
name: Ryoke, Rie
name: Wang, Victora X.
name: Kelly, Clare
name: Peeters, Lore M.
name: Nonaka, Hiroi
name: Wenk, Patricia
name: Strobelt, Sandra
name: Beckmann, Nicolau
name: Shemesh, Noam
name: Sartorius, Alexander
name: Coolen, Bram F.
name: Verhoye, Marleen
name: Faber, Cornelius
name: Sack, Markus
name: Russo, Gabriele
name: Grandjean, Joanes
name: Del Rio, Rodrigo Triana
name: Pais-Roldán, Patricia
name: Prado-Alcalá, Roberto A.
name: Falfán-Melgoza, Claudia
name: Célestine, Marina
name: Naessens, Daphne M. P.
name: Rosenow, Tim
name: Ayad, Fadi
name: Glennon, Jeffrey C.
name: Meyer-Baese, Lisa
name: Vertullo, Roberta
name: Smith, Corrie
name: Golden, Carla E. M.
name: Paasonen, Jaakko
name: Barrière, David A.
name: Van Der Linden, Annemie
name: Nava-Gomez, Laura J.
name: Gass, Natalia
name: Near, Jamie
name: Colon-Perez, Luis
name: Forloni, Gianluigi
name: Ionescu, Tudor M.
name: Wachsmuth, Lydia
name: Achard, Sophie
name: Soria, Guadalupe
name: Zhang, Baogui B.
name: Devenyi, Gabriel A.
name: López-Hidalgo, Monica A.
name: Yin, Ting
name: Till, Sally M.
name: Beckmann, Christian F.
name: Kind, Peter C.
name: Pompilus, Marjory
name: Reimann, Henning M.
name: Auer, Dorothee P.
name: Marchand, Fabien
name: Boretius, Susann
name: Liu, Yikang
name: van der Marel, Kajo
name: van der Toorn, Annette
name: Chapman, Victoria
name: Torres-García, Maria E.
name: Wank, Isabel
name: Selingue, Erwan
name: Fernandes, Francisca F.
name: Moro, Federico
name: Sanganahalli, Basavaraju G.
name: Helluy, Xavier
name: Dopfel, David
name: Meng, Xianzong
name: Blockx, Ines
name: Hyder, Fahmeed
name: Dijkhuizen, Rick M.
name: Muñoz-Moreno, Emma
name: Smith, Joanna A. B.
name: Sumiyoshi, Akira
name: Lazari, Alberto
name: Bortel, Aleksandra
name: Garza-Villarreal, Eduardo A.
name: Desrosiers-Gregoire, Gabriel
name: Shih, Yen-Yu Ian
name: Chavez-Negrete, Jorge E.
name: Heuser, Arnd
name: Sirmpilatze, Nikoloz
name: Garin, Clément M.
name: Lerch, Jason P.
name: Horien, Corey
name: Straathof, Milou
name: Hennessy, Lauren A.
name: Perez, Pablo D.
name: Lambers, Henriette
name: Stoop, Ron
name: Quirarte, Gina L.
name: Sawiak, Stephen J.
name: Yu, Xin
name: Blezer, Erwin L. A.
name: Buxbaum, Joseph D.
name: Seewoo, Bhedita J.
name: Vrooman, Roël M.
name: Harkin, Andrew
name: Madularu, Dan
name: Micotti, Edoardo
name: Weber-Fahr, Wolfgang
name: Vidal, Benjamin
name: Homberg, Judith R.
name: López-Gil, Xavier
name: McIntosh, Alison
name: Marciano, Sabina
name: Kim, Eugene
name: Chakravarty, M. Mallar
name: Daniele, Tolomeo
name: Scheenen, Tom W. J.
name: Choi, Sangcheon
name: Shi, Bowen
name: Liu, Yanyan Y.
name: van Hout, Aran T. B.
name: Fuentes-Ibañez, Antonio
name: Veltien, Andor
name: Hofwijks, Nita
name: Stenroos, Petteri J.
name: Henckens, Marloes J. A. G.
name: Kaneko, Gen
name: Kerskens, Christian
name: Broadwater, Margaret
name: Prior, Malcolm
name: Keilholz, Shella D.
name: Anckaerts, Cynthia
name: Ortiz, Juan J.
name: Rivera-Olvera, Alejandro
name: Tudela, Raul
name: Hess, Andreas
name: Kaesser, Johannes
name: Shmuel, Amir
name: Cardoso, Beatriz M.
name: Todd, Nick
name: Angeles-Valdez, Diego
name: Ielacqua, Giovanna Diletta
name: Christiaen, Emma
name: Diao, Yujian
name: Dalley, Jeffrey W.
name: Chuang, Kai-Hsiang
name: Febo, Marcelo
name: Zurbruegg, Stefan
name: Vanhove, Christian
name: Watson, David J. G.
name: Baudewig, Jürgen
name: Rutten, Tobias J.
name: Alcauter, Sarael
name: Pan, Wen-Ju
name: Sampaio-Baptista, Cassandra
name: Bolbos, Radu
name: Bouvard, Sandrine
name: van den Berg, Monica
name: Missault, Stephan
name: Cash, Diana
name: Sobczak, Filip
name: Lillywhite, Amanda
name: Guo, Chao C. G.
name: Heerschap, Arend
name: Niendorf, Thoralf
name: Fouquet, Jérémie
name: Houwing, Danielle J.
name: Jones, Jolyon
name: McAuslan, Matthew J.
Publisher: name: Springer Nature
Year: 2023

description: <p>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.</p>