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Imaging Library-Preprocessing

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Imaging Library - Preprocessing


Artifact Detection/Quality Assurance


Andersson, J.L.R., Hutton, C, Ashburner, C., Turner, R., and Friston, K. (2001). Modeling geometric deformations in EPI time series. NeuroImage, 13, 903-919. [pdf]


Ardekani, B.A., Bachman, A.H., and Helpern, J.A. (2001). A quantitative comparison of motion detection algorithms in fMRI. Magnetic Resonance Imaging, 19, 959-963. [pdf]


Birn, R.M., Bandettini, P.A., Coz, R.W., and Shaker, R. (1999). Event-related fMRI of tasks involving brief motion. Human Brain Mapping, 7, 106-114. [pdf]


Bullmore, E.T., Brammer, M.J., Rabe-Hesketh, S.R., Curtis, V.A., Morris, R.G., Williams, S.C.R., Sharma, T., and McGuire, P.K. (1999). Methods for diagnosis and treatment of stimulus-correlated motion in generic brain activation studies using fMRI. Human Brain Mapping, 7, 38-48. [pdf]


Diedrichsen, J. and Shadmehr, R. (2005). Detecting and adjusting for artifacts in fMRI time series data. NeuroImage, 27, 624-634. [pdf]


Field, A.S., Yen, Y.F., Burdette, J.H., and Elster, A.D. (2000). False cerebral activation on BOLD functional MR images: study of love-amplitude motion weakly correlated to stimulus. American Journal of Neuroradiology, 21, 1388-1396. [pdf]


Freire, L. and Mangin, J.F. (2001). Motion correction algorithms may create spurious brain activations in the absence of subject motion. NeuroImage, 14, 709-722. [pdf]


Grootoonk, S., Hutton, C., Ashburner, J., Howseman, A.M., Josephs, O., Rees, G., Friston, K.J., and Turner, R. (2000). Characterization and correction of interpolation effects in the realignment of fMRI time series. NeuroImage, 11, 49-57. [pdf]


Morgan, V.L., Pickens, D.R., Hartmann, S.L., and Prince, R.R. (2001). Comparison of functional MRI image realignment tools using a computer-generated phantom. Magnetic Resonance Imaging, 46, 510-514. [pdf]


Stocker, T., Schneider, F., Klein, M., Habel, U., Kellermann, T., Zilles, K., and Shah, N.J. (2005). Automated quality assurance routines for fMRI data applied to a multicenter study. Human Brain Mapping, 25, 237-246. [pdf]


Ward, H.A., Riederer, S.J., Grimm, R.C., Ehman, R.L., Felmlee, J.P., and Jack, Jr., C.R. (2000). Prospective multiaxial motion correction for fMRI. Magnetic Resonance in Medicine, 43, 459-469. [pdf]

 

Slice Timing


Calhoun, V. et al. (2000). Improved fMRI slice timing correction: interpolation errors and wrap-around effects. Proceedings, ISMRM, 9th Annual Meeting, Denver, CO, 810. [pdf]

Henson et al. (1999). The slice-timing problem in event-related fMRI. NeuroImage, 9, S125. [pdf]


Van de Moortele et al. (1998). Slice-dependent time shift efficiently corrected by interpolation in multi-slice EPI fMRI series. NeuroImage, 7(4), S607. [pdf]


Van de Moortele et al. (1999). Latencies in fMRI time-series: effect of slice acquisition order and perception. Nuclear Magnetic Resonance in Biomedicine, 10, 230-236. [pdf]

 

Motion Correction/Realignment


Andersson, J.L.R., Hutton, C., Ashburner, J., Turner, R., and Friston, K. (2001). Modeling geometric distortions in EPI time series. NeuroImage, 13, 903-919. [pdf]


Ardekani, B.A., Bachman, A.H., and Helpern, J.A. (2001). A quantitative comparison of motion detection algorithms. Magnetic Resonance Imaging, 19, 959-963. [pdf]


Birn, R.M., Bandettini, P.A., Cox, R.W., and Shaker, R. (1999). Event-related fMRI of tasks involving brief motion. Human Brain Mapping, 7, 106-115. [pdf]


Bullmore, E.T., Brammer, M.J., Rabe-Hesketh, S., Curtis, V.A., Morris, R.G., Williams, S.C.R., Sharma, T., and McGuire, P.K. (1999). Methods for diagnosis and treatment of stimulus-correlated motion in generic brain activation studies using fMRI. Human Brain Mapping, 7, 38-48. [pdf]


Field, A.S., Yen, Y.-F., Burdette, J.H., and Elster, A.D. (2000). False cerebral activation on BOLD functional MR images: study of low-amplitude motion weakly correlated to stimulus. American Journal of Neuroradiology, 21, 1388-1396. [pdf]


Freire, L. and Mangin, J.F. (2001). Motion correction algorithms may create spurious brain activations in the absence of subject motion. NeuroImage, 14, 709-722. [pdf]


Friston K.J., Williams S.R., Howard R., Frackowiak R.S.J., and Turner R. (1995). Movement-related effect in fMRI time-series. Magnetic Resonance in Medicine, 35, 346-355. [pdf]


Glover, G.H., Li, T.-Q., and Ress, D. (2000). Image-based method for retrospective correction of physiological motion effects in fMRI: RETROICOR. agnetic Resonance in Medicine, 44, 162-169. [pdf]


Grootonk, S., Hutton, C., Ashburner, J., Howseman, A.M., Josephs, O., Rees, G., Friston, K.J., and Turner, R. (2000). Characterization and correction of interpolation effects in the realignment of fMRI time series. NeuroImage, 11, 49-57. [pdf]


Hutton C., Bork A., Josephs O., Deichmann R, Ashburner J., and Turner R. (2002). Image distortion correction in fMRI: a quantitative evaluation. NeuroImage, 16, 217-240. [pdf]


Jezzard P. and Balaban R.S. (1995). Correction for geometric distortions in echoplanar images from B0 field variations. Magnetic Resonance in Medicine, 34, 65-73. [abstract]

Morgan et al. (2001). Comparison of functional MRI image realignment tools using a computer-generated phantom. Magnetic Resonance in Medicine, 46, 510-514. [pdf]


Ward et al. (2001). Prospective multiaxial motion correction for fMRI. Magnetic Resonance in Medicine, 43, 459-469. [pdf]

 

Coregistration


Ashburner & Friston (1997). Multimodal image coregistration and partitioning - a unified framework. NeuroImage, 6, 209-217. [pdf]


Maes et al. (1997). Multimodality image registration by maximization of mutual information. IEEE Transactions on Medical Imaging, 16(2), 187-198. [pdf]


Nestares & Heeger (2000). Robust multiresolution alignment of MRI brain volumes. Magnetic Resonance in Medicine, 43(5), 705-15. [pdf]


Zhu & Cochoff (2002). Influence of implementation parameters on registration of MR and SPECT brain images by maximization of mutual information. Journal of Nuclear Medicine, 43(2), 160-166. [pdf]

 

Normalization


Ashburner & Friston (1999). Nonlinear spatial normalization using basis functions. Human Brain Mapping, 7(4), 254-66. [pdf]

Brett et al. (2001). Spatial normalization of brain images with focal lesions using cost function masking. NeuroImage, 14(2), 507-12. [pdf]


Crivello et al. (2002). Comparison of spatial normalization procedures and their impact on functional maps. Human Brain Mapping, 16(4), 228-50. [pdf]


Kochunov et al. (2000). Evaluation of octree regional spatial normalization method for regional anatomical matching. Human Brain Mapping, 11(3), 193-206. [pdf]


Salmond et al. (2002). The precision of anatomical normalization in the medial temporal lobe using spatial basis functions. NeuroImage, 17, 507-12. [pdf]


Wilke et al. (2002). Assessment of spatial normalization of whole-brain magnetic resonance images in children. Human Brain Mapping, 17, 48-60. [pdf]

 

Smoothing


Hopfinger et al. (2000). A study of analysis parameters that influence the sensitivity of event-related fMRI analyses. NeuroImage, 11, 326-333. [pdf]


Kiebel & Friston (2002). Anatomically informed basis functions in multisubject studies. Human Brain Mapping, 16, 36-46. [pdf]


LaConte et al. (2003). The evaluation of preprocessing choices in single-subject BOLD fMRI using NPAIRS performance metrics. NeuroImage, 18, 10-27. [pdf]


Skudlarski et al. (1999). ROC analysis of statistical methods used in functional MRI: individual subjects. NeuroImage, 9, 311-329. [pdf]


White et al. (2001). Anatomic and functional variability: the effects of filter size in group fMRI data analysis. NeuroImage, 13, 577-588. [pdf]


Zarahn et al. (1997). Empirical analyses of BOLD fMRI statistics I: Spatially unsmoothed data collected under null-hypothesis conditions. NeuroImage, 5, 179-197. [pdf]

 

Additional information