{Reference Type}: Journal Article
{Title}: A consensus protocol for functional connectivity analysis in the rat brain.
{Author}: 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 CM;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 YI;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;
{Journal}: Nat Neurosci
{Volume}: 26
{Issue}: 4
{Year}: 04 2023
{Factor}: 28.771
{DOI}: 10.1038/s41593-023-01286-8
{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.