neuRosim: An R package for generating fMRI data

Journal of Statistical Software

Volumn 44, Issue 10, 2011, Pages 1-18

  Welvaert, Marijke ^a   Durnez, Joke ^a   Moerkerke, Beatrijs ^a   Verdoolaege, Geert ^a   Rosseel, Yves ^a  

^a GHENT UNIVERSITY   (Belgium)

Author keywords

Data generation; fMRI; Simulation

Indexed keywords

EID: 84856270891     PISSN: None     EISSN: 15487660     Source Type: Journal    
DOI: 10.18637/jss.v044.i10     Document Type: Article

References (42)

1. Ashburner J, Barnes G, Chen CC, Daunizeau J, Flandin G, Friston K, Gitelman D, Kiebel S, Kilner J, Litvak V, Moran R, Penny W, Stephan K, Gitelman D, Henson R, Hutton C, Glauche V, Mattoutee J, Phillips C (2009). SPM8 Manual, Wellcome Trust Centre for Neuroimaging, University College London.
2. Bellec P, Perlbarg V, Evans A (2009). "Bootstrap Generation and Evaluation of an fMRI Simulation Database. " Magnetic Resonance Imaging, 27, 1382-1396.
3. Bianciardi M, Cerasa A, Patria F, Hagberg G (2004). "Evaluation of Mixed Effects in Event-Related fMRI Studies: Impact of First-Level Design and Filtering. " NeuroImage, 22, 1351-1370.
4. Biswal B, DeYoe E, Hyde J (1996). "Reduction of Physiological Fluctuations in fMRI Using Digital Filters. " Magnetic Resonance in Medicine, 35, 107-113.
5. Bloch F (1946). "Nuclear Induction. " Physical Review, 70(7-8), 460-474.
6. Bullmore E, Brammer M, Williams S, Rabe-Hesketh S, Janot N, David A, Mellers J, Howard R, Sham P (1996). "Statistical Methods of Estimation and Inference for Functional MR Image Analysis. " Magnetic Resonance in Medicine, 35, 261-277.
7. Buxton R, Uludffag K, Dubowitz D, Liu T (2004). "Modeling the Hemodynamic Response to Brain Activation. " NeuroImage, 23, S220-S233.
8. Cox R (1996). "AFNI: Software for Analysis and Visualization of Functional Magnetic Resonance Neuroimages. " Computers and Biomedical Research, 29, 162-173.
9. David O, Guillemain I, Saillet S, Reyt S, Deransart C, Segebarth C, Depaulis A (2008). "Identifying Neural Drivers with Functional MRI: An Electrophysiological Validation. " PLoS Biology, 6(12), e315.
10. Drobnjak I, Gavaghan D, Süli E, Pitt-Francis J, Jenkinson M (2006). "Development of a fMRI Simulator for Modelling Realistic Rigid-Body Motion Artifacts. " Magnetic Resonance in Medicine, 56(2), 364-380.
11. Drysdale P, Huber J, Robinson P, Aquino K (2010). "Spatiotemporal BOLD Dynamics from a Poroelastic Hemodynamic model. " Journal of Theoretical Biology, 265(4), 524-34.
12. Friston K, Fletcher P, Josephs O, Holmes A, Rugg M, Turner R (1998). "Event-Related fMRI: Characterizing Differential Responses. " NeuroImage, 7, 30-40.
13. Glover G (1999). "Deconvolution of Impulse Response in Event-Related BOLD fMRI. " Neu-roImage, 9, 416-429.
14. Granert O (2010). Rniftilib: R Interface to NIFTICLIB (V1.1.0), R package version 0.0-29, URL http://CRAN.R-project.org/package=Rniftilib.
15. Grinband J, Wager T, Lindquist M, Ferrera V, Hirsch J (2008). "Detection of Time-Varying Signals in Event-Related fMRI Designs. " NeuroImage, 43, 509-520.
16. Gudbjartsson H, Patz S (1995). "The Rician Distribution of Noisy MRI Data. " Magnetic Resonance in Medicine, 34(6), 910-914.
17. Haacke E, Brown R, Thompson M, Venkatesan R (1999). Magnetic Resonance Imaging: Principles and Sequence Design, John Wiley & Sons, New York.
18. Hansen L, Nielsen F, Strother S, Lange N (2001). "Consensus Inference in Neuroimaging. " NeuroImage, 13, 1212-1218.
19. Henson R, Shallice T, Gorno-Tempini ML, Dolan R (2002). "Face Repetition Effects in Implicit and Explicit Memory Tests as Measured by fMRI. " Cerebral Cortex, 12, 178-186.
20. Hyde J, Biswal B, Jesmanowicz A (2001). "High-Resolution fMRI Using Multislice Partial k-Space GR-EPI With Cubic Voxels. " Magnetic Resonance in Medicine, 46, 114-125.
21. Krüger G, Glover G (2001). "Physiological Noise in Oxygenation-Sensitive Magnetic Resonance Imaging. " Magnetic Resonance in Medicine, 46, 631-637.
22. Lange N (1999). "Statistical Thinking in Functional and Structural Magnetic Resonance Neuroimaging. " Statistics in Medicine, 18, 2401-2407.
23. Lange N, Strother S, Anderson J, Nielsen F, Holmes A, Kolenda T, Savoy R, Hansen L (1999). "Plurality and Resemblance in fMRI Data Analysis. " NeuroImage, 10, 282-303.
24. Lazar N (2008). The Statistical Analysis of Functional MRI Data, Springer-Verlag.
25. Lee J, Hu J, Gao J, Crosson B, Peck K, Wierenga C, McGregor K, Zhao Q, White K (2008). "Discriminating Brain Activity from Task-Related Artifacts in Functional MRI: Fractal Scaling Analysis Simulation and Application. " NeuroImage, 40, 197-212.
26. Lei X, Qiu C, Xu P, Yao D (2010). "A Parallel Framework for Simultaneous EEG/fMRI Analysis: Methodology and Simulation. " NeuroImage, 52, 1123-1134.
27. Liao W, Chen H, Yang Q, Lei X (2008). "Analysis of fMRI Data Using Improved Self-Organizing Mapping and Spatio-Temporal Metric Hierarchical Clustering. " IEEE Transactions of Medical Imaging, 27, 1472-1483.
28. Lin QH, Liu J, Zheng YR, Liang H, Calhoun V (2010). "Semiblind Spatial ICA of fMRI Using Spatial Constraints. " Human Brain Mapping, 31, 1076-1088.
29. Locascio J, Jennings P, Moore C, Corkin S (1997). "Time Series Analysis in the Time Domain and Resampling Methods for Studies of Functional Magnetic Resonance Brain Imaging. " Human Brain Mapping, 5, 168-193.
30. Logan B, Rowe D (2004). "An Evaluation of Thresholding Techniques in fMRI Analysis. " NeuroImage, 22, 95-108.
31. Purdon P, Weisskoff R (1998). "Effect of Temporal Autocorrelation Due to Physiological Noise and Stimulus Paradigm on Voxel-Level False-Positive Rates in fMRI. " Human Brain Mapping, 6, 239-249.
32. R Development Core Team (2011). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http: //www.R-project.org/.
33. Rowe D, Logan B (2004). "A Complex Way to Compute fMRI Activation. " NeuroImage, 23, 1078-1092.
34. Skudlarski P, Constable R, Gore J (1999). "ROC Analysis of Statistical Methods Used in Functional MRI: Individual Subjects. " NeuroImage, 9, 311-329.
35. Smith A, Lewis B, Ruttimann U, Ye F, Sinnwell T, Yang Y, Duyn J, Frank J (1999). "Investigation of Low Frequency Drift in fMRI Signal. " NeuroImage, 9, 526-533.
36. Smith S, Jenkinson M, Woolrich M, Beckmann C, Behrens T, Johansen-Berg H, Bannister P, De Luca M, Drobnjak I, Flitney D, Niazy R, Saunders J, Vickers J, Zhang Y, De Stefano N, Brady J, Matthews P (2004). "Advances in Functional and Structural MR Image Analysis and Implementation as FSL. " NeuroImage, 23, S208-S219.
37. Soetaert K, Petzoldt T, Setzer RW (2010). "Solving Differential Equations in R: Package deSolve. " Journal of Statistical Software, 33(9), 1-25. URL http://www.jstatsoft.org/ v33/i09/.
38. Sotero R, Trujillo-Barreto N (2008). "Biophysical Model for Integrating Neuronal Activity, EEG, fMRI and Metabolism. " NeuroImage, 39, 290-309.
39. Sotero R, Trujillo-Barreto N, Jimffenez J, Carbonell F, Rodrffffguez-Rojas R (2009). "Identiffcation and Comparison of Stochastic Metabolic/Hemodynamic Models (sMHM) for the Generation of the BOLD Signal. " Journal of Computational Neuroscience, 26, 251-269.
40. Weibull A, Gustavsson H, Mattsson S, Svensson J (2008). "Investigation of Spatial Resolution, Partial Volume Effects and Smoothing in Functional MRI Using Artiffcial 3D Time Series. " NeuroImage, 41, 346-353.
41. Whitcher B, Schmid V, Thornton A (2011a). oro. nifti: Rigorous-NIfTI Input / Output, R package version 0.2.6, URL http://CRAN.R-project.org/package=oro.nifti.
42. Whitcher B, Schmid VJ, Thornton A (2011b). "Working with the DICOM and NIfTI Data Standards in R. " Journal of Statistical Software, 44(6), 1-28. URL http://www. jstatsoft.org/v44/i06/.