Bibliography

ATS+11

Brian B Avants, Nicholas J Tustison, Gang Song, Philip A Cook, Arno Klein, and James C Gee. A reproducible evaluation of ANTs similarity metric performance in brain image registration. Neuroimage, 54(3):2033–2044, February 2011.

BMFS09

Christian F Beckmann, Clare E Mackay, Nicola Filippini, and Stephen M Smith. Group comparison of resting-state FMRI data using multi-subject ICA and dual regression. Neuroimage, 47(Suppl 1):S148, 2009.

BS04

Christian F Beckmann and Stephen M Smith. Probabilistic independent component analysis for functional magnetic resonance imaging. IEEE Trans. Med. Imaging, 23(2):137–152, February 2004.

BZYHH95

Bharat Biswal, F Zerrin Yetkin, Victor M Haughton, and James S Hyde. Functional connectivity in the motor cortex of resting human brain using echo-planar MRI. Magn. Reson. Med., 34(4):537–541, 1995.

Car13

Joshua Carp. Optimizing the order of operations for movement scrubbing: comment on power et al. Neuroimage, 76:436–438, August 2013.

DGDGMC23

Gabriel Desrosiers-Gregoire, Gabriel A Devenyi, Joanes Grandjean, and M Mallar Chakravarty. Rodent automated bold improvement of EPI sequences (RABIES): a standardized image processing and data quality platform for rodent fMRI. *status needed for bibtex rendering with Sphinx*, September 2023.

EMB+19

Oscar Esteban, Christopher J Markiewicz, Ross W Blair, Craig A Moodie, A Ilkay Isik, Asier Erramuzpe, James D Kent, Mathias Goncalves, Elizabeth DuPre, Madeleine Snyder, Hiroyuki Oya, Satrajit S Ghosh, Jessey Wright, Joke Durnez, Russell A Poldrack, and Krzysztof J Gorgolewski. fMRIPrep: a robust preprocessing pipeline for functional MRI. Nat. Methods, 16(1):111–116, January 2019.

FWH+96

Karl J Friston, Steven Williams, Robert Howard, Richard S J Frackowiak, and Robert Turner. Movement-Related effects in fMRI time-series. 1996.

GAC+16

Krzysztof J Gorgolewski, Tibor Auer, Vince D Calhoun, R Cameron Craddock, Samir Das, Eugene P Duff, Guillaume Flandin, Satrajit S Ghosh, Tristan Glatard, Yaroslav O Halchenko, Daniel A Handwerker, Michael Hanke, David Keator, Xiangrui Li, Zachary Michael, Camille Maumet, B Nolan Nichols, Thomas E Nichols, John Pellman, Jean-Baptiste Poline, Ariel Rokem, Gunnar Schaefer, Vanessa Sochat, William Triplett, Jessica A Turner, Gaël Varoquaux, and Russell A Poldrack. The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Sci Data, 3:160044, June 2016.

GCA+20

Joanes Grandjean, Carola Canella, Cynthia Anckaerts, Gülebru Ayrancı, Salma Bougacha, Thomas Bienert, David Buehlmann, Ludovico Coletta, Daniel Gallino, Natalia Gass, Clément M Garin, Nachiket Abhay Nadkarni, Neele S Hübner, Meltem Karatas, Yuji Komaki, Silke Kreitz, Francesca Mandino, Anna E Mechling, Chika Sato, Katja Sauer, Disha Shah, Sandra Strobelt, Norio Takata, Isabel Wank, Tong Wu, Noriaki Yahata, Ling Yun Yeow, Yohan Yee, Ichio Aoki, M Mallar Chakravarty, Wei-Tang Chang, Marc Dhenain, Dominik von Elverfeldt, Laura-Adela Harsan, Andreas Hess, Tianzi Jiang, Georgios A Keliris, Jason P Lerch, Andreas Meyer-Lindenberg, Hideyuki Okano, Markus Rudin, Alexander Sartorius, Annemie Van der Linden, Marleen Verhoye, Wolfgang Weber-Fahr, Nicole Wenderoth, Valerio Zerbi, and Alessandro Gozzi. Common functional networks in the mouse brain revealed by multi-centre resting-state fMRI analysis. Neuroimage, 205:116278, January 2020.

LGWC19

Martin A Lindquist, Stephan Geuter, Tor D Wager, and Brian S Caffo. Modular preprocessing pipelines can reintroduce artifacts into fMRI data. Hum. Brain Mapp., 40(8):2358–2376, June 2019.

MGG+04

Adolf Mathias, Florian Grond, Ramon Guardans, Detlef Seese, Miguel Canela, and Hans H Diebner. Algorithms for spectral analysis of irregularly sampled time series. J. Stat. Softw., 11(1):1–27, 2004.

MNC+14

John Muschelli, Mary Beth Nebel, Brian S Caffo, Anita D Barber, James J Pekar, and Stewart H Mostofsky. Reduction of motion-related artifacts in resting state fMRI using aCompCor. Neuroimage, 96:22–35, August 2014.

NSOngurB17

Lisa D Nickerson, Stephen M Smith, Döst Öngür, and Christian F Beckmann. Using dual regression to investigate network shape and amplitude in functional connectivity analyses. Front. Neurosci., 11:115, 2017.

PBS+12

Jonathan D Power, Kelly A Barnes, Abraham Z Snyder, Bradley L Schlaggar, and Steven E Petersen. Spurious but systematic correlations in functional connectivity MRI networks arise from subject motion. Neuroimage, 59(3):2142–2154, February 2012.

PML+14

Jonathan D Power, Anish Mitra, Timothy O Laumann, Abraham Z Snyder, Bradley L Schlaggar, and Steven E Petersen. Methods to detect, characterize, and remove motion artifact in resting state fMRI. Neuroimage, 84:320–341, January 2014.

PPLM17

Jonathan D Power, Mark Plitt, Timothy O Laumann, and Alex Martin. Sources and implications of whole-brain fMRI signals in humans. Neuroimage, 146:609–625, February 2017.

PMvR+15

Raimon H R Pruim, Maarten Mennes, Daan van Rooij, Alberto Llera, Jan K Buitelaar, and Christian F Beckmann. ICA-AROMA: a robust ICA-based strategy for removing motion artifacts from fMRI data. Neuroimage, 112:267–277, May 2015.

WPG+17

Sijia Wang, Daniel J Peterson, J C Gatenby, Wenbin Li, Thomas J Grabowski, and Tara M Madhyastha. Evaluation of field map and nonlinear registration methods for correction of susceptibility artifacts in diffusion MRI. Front. Neuroinform., 11:17, February 2017.

ZGRW15

Valerio Zerbi, Joanes Grandjean, Markus Rudin, and Nicole Wenderoth. Mapping the mouse brain with rs-fMRI: an optimized pipeline for functional network identification. Neuroimage, 123:11–21, December 2015.