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.

ATS09

Brian B Avants, Nick Tustison, and Gang Song. Advanced normalization tools (ANTS). Insight J., 2:1–35, 2009.

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.

BMZ+10

Bharat B Biswal, Maarten Mennes, Xi-Nian Zuo, Suril Gohel, Clare Kelly, Steve M Smith, Christian F Beckmann, Jonathan S Adelstein, Randy L Buckner, Stan Colcombe, Anne-Marie Dogonowski, Monique Ernst, Damien Fair, Michelle Hampson, Matthew J Hoptman, James S Hyde, Vesa J Kiviniemi, Rolf Kötter, Shi-Jiang Li, Ching-Po Lin, Mark J Lowe, Clare Mackay, David J Madden, Kristoffer H Madsen, Daniel S Margulies, Helen S Mayberg, Katie McMahon, Christopher S Monk, Stewart H Mostofsky, Bonnie J Nagel, James J Pekar, Scott J Peltier, Steven E Petersen, Valentin Riedl, Serge A R B Rombouts, Bart Rypma, Bradley L Schlaggar, Sein Schmidt, Rachael D Seidler, Greg J Siegle, Christian Sorg, Gao-Jun Teng, Juha Veijola, Arno Villringer, Martin Walter, Lihong Wang, Xu-Chu Weng, Susan Whitfield-Gabrieli, Peter Williamson, Christian Windischberger, Yu-Feng Zang, Hong-Ying Zhang, F Xavier Castellanos, and Michael P Milham. Toward discovery science of human brain function. Proc. Natl. Acad. Sci. U. S. A., 107(10):4734–4739, March 2010.

Car13

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

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.

GBM+11

Krzysztof Gorgolewski, Christopher D Burns, Cindee Madison, Dav Clark, Yaroslav O Halchenko, Michael L Waskom, and Satrajit S Ghosh. Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python. Front. Neuroinform., 5:13, August 2011.

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.

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.

ManjonCoupeMartiBonmati+10

José V Manjón, Pierrick Coupé, Luis Martí-Bonmatí, D Louis Collins, and Montserrat Robles. Adaptive non-local means denoising of MR images with spatially varying noise levels. J. Magn. Reson. Imaging, 31(1):192–203, January 2010.

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.

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.

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.

SZE98

J G Sled, A P Zijdenbos, and A C Evans. A nonparametric method for automatic correction of intensity nonuniformity in MRI data. IEEE Trans. Med. Imaging, 17(1):87–97, February 1998.

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.