Abstract
It has been reported that resting state fluctuation amplitude (RSFA) exhibits extremely large inter-site variability, which limits its application in multisite studies. Although global normalization (GN) based approaches are efficient in reducing the site effects, they may cause spurious results. In this study, our purpose was to find alternative strategies to minimize the substantial site effects for RSFA, without the risk of introducing artificial findings. We firstly modified the ALFF algorithm so that it is conceptually validated and insensitive to data length, then found that (a) global mean amplitude of low-frequency fluctuation (ALFF) covaried only with BOLD signal intensity, while global mean fractional ALFF (fALFF) was significantly correlated with TRs across different sites; (b) The inter-site variations in raw RSFA values were significant across the entire brain and exhibited similar trends between gray matter and white matter; (c) For ALFF, signal intensity rescaling could dramatically reduce inter-site variability by several orders, but could not fully removed the globally distributed inter-site variability. For fALFF, the global site effects could be completely removed by TR controlling; (d) Meanwhile, the magnitude of the inter-site variability of fALFF could also be reduced to an acceptable level, as indicated by the detection power of fALFF in multisite data quite close to that in monosite data. Thus our findings suggest GN based harmonization methods could be replaced with only controlling for confounding factors including signal scaling, TR and full-band power.
Similar content being viewed by others
References
Abbott, C., Juarez, M., White, T., Gollub, R. L., Pearlson, G. D., Bustillo, J., et al. (2011). Antipsychotic dose and diminished neural modulation: A multi-site fMRI study. Progress in Neuro-Psychopharmacology and Biological Psychiatry, 35(2), 473–482.
Abraham, A., Milham, M. P., Di Martino, A., Craddock, R. C., Samaras, D., Thirion, B., et al. (2017). Deriving reproducible biomarkers from multi-site resting-state data: An autism-based example. Neuroimage, 147, 736–745.
Ashburner, J. (2007). A fast diffeomorphic image registration algorithm. Neuroimage, 38(1), 95–113.
Baria, A. T., Baliki, M. N., Parrish, T., & Apkarian, A. V. (2011). Anatomical and functional assemblies of brain BOLD oscillations. The Journal of Neuroscience, 31(21), 7910–7919.
Beall, E. B., & Lowe, M. J. (2010). The non-separability of physiologic noise in functional connectivity MRI with spatial ICA at 3T. Journal of Neuroscience Methods, 191(2), 263–276.
Biswal, B., Yetkin, F. Z., Haughton, V. M., Hyde, J. S. (1995) Functional connectivity in the motor cortex of resting human brain using echo-planar mri. Magnetic Resonance in Medicine, 34 (4):537–541.
Biswal, B. B., Mennes, M., Zuo, X. N., Gohel, S., Kelly, C., Smith, S. M., Beckmann, C. F., Adelstein, J. S., Buckner, R. L., Colcombe, S., Dogonowski, A. M., Ernst, M., Fair, D., Hampson, M., Hoptman, M. J., Hyde, J. S., Kiviniemi, V. J., Kötter, R., Li, S. J., Lin, C. P., Lowe, M. J., Mackay, C., Madden, D. J., Madsen, K. H., Margulies, D. S., Mayberg, H. S., McMahon, K., Monk, C. S., Mostofsky, S. H., Nagel, B. J., Pekar, J. J., Peltier, S. J., Petersen, S. E., Riedl, V., Rombouts, S. A., Rypma, B., Schlaggar, B. L., Schmidt, S., Seidler, R. D., Siegle, G. J., Sorg, C., Teng, G. J., Veijola, J., Villringer, A., Walter, M., Wang, L., Weng, X. C., Whitfield-Gabrieli, S., Williamson, P., Windischberger, C., Zang, Y. F., Zhang, H. Y., Castellanos, F. X., & Milham, M. P. (2010). Toward discovery science of human brain function. Proceedings of the National Academy of Sciences of the United States of America, 107(10), 4734–4739.
Boubela, R. N., Kalcher, K., Huf, W., Kronnerwetter, C., Filzmoser, P., & Moser, E. (2013). Beyond noise: Using temporal ICA to extract meaningful information from high-frequency fMRI signal fluctuations during rest. Frontiers in Human Neuroscience, 7.
Caramanos, Z., Fonov, V. S., Francis, S. J., Narayanan, S., Pike, G. B., Collins, D. L., & Arnold, D. L. (2010). Gradient distortions in MRI: Characterizing and correcting for their effects on SIENA-generated measures of brain volume change. NeuroImage, 49(2), 1601–1611.
Castellanos, F. X., Di Martino, A., Craddock, R. C., Mehta, A. D., & Milham, M. P. (2013). Clinical applications of the functional connectome. Neuroimage, 80, 527–540. https://doi.org/10.1016/j.neuroimage.2013.04.083.
Chen, N. K., Dickey, C. C., Yoo, S. S., Guttmann, C. R., & Panych, L. P. (2003). Selection of voxel size and slice orientation for fMRI in the presence of susceptibility field gradients: Application to imaging of the amygdala. NeuroImage, 19, 817–825.
Cheng, W., Palaniyappan, L., Li, M., Kendrick, K. M., Zhang, J., Luo, Q., et al. (2015). Voxel-based, brain-wide association study of aberrant functional connectivity in schizophrenia implicates thalamocortical circuitry. NPJ Schizophrenia, 1, 15016.
Cordes, D., Haughton, V. M., Arfanakis, K., Wendt, G. J., Turski, P. A., Moritz, C. H., et al. (2000). Mapping functionally related regions of brain with functional connectivity MR imaging. AJNR. American Journal of Neuroradiology, 21, 1636–1644.
Dagli, M. S., Ingeholm, J. E., & Haxby, J. V. (1999). Localization of cardiac-induced signal change in fMRI. Neuroimage, 9, 407–415.
Dansereau, C., Benhajali, Y., Risterucci, C., Pich, E. M., Orban, P., Arnold, D., & Bellec, P. (2017). Statistical power and prediction accuracy in multisite resting-state fMRI connectivity. Neuroimage, 149, 220–232.
Deichmann, R., Gottfried, J. A., Hutton, C., & Turner, R. (2003). Optimized EPI for fMRI studies of the orbitofrontal cortex. NeuroImage, 19, 430–441.
Di Martino, A., Yan, C. G., Li, Q., Denio, E., Castellanos, F. X., Alaerts, K., et al. (2014). The autism brain imaging data exchange: Towards a large-scale evaluation of the intrinsic brain architecture in autism. Molecular Psychiatry, 19(6), 659–667.
Edward, V., Windischberger, C., Cunnington, R., Erdler, M., Lanzenberger, R., Mayer, D., Endl, W., & Beisteiner, R. (2000). Quantification of fMRI artifact reduction by a novel plaster cast head holder. Human Brain Mapping, 11(3), 207–213.
Fair, D. A., Nigg, J. T., Iyer, S., Bathula, D., Mills, K. L., Dosenbach, N. U., et al. (2012). Distinct neural signatures detected for ADHD subtypes after controlling for micro-movements in resting state functional connectivity MRI data. Frontiers in Systems Neuroscience, 6, 80.
Fan, L., Li, H., Zhuo, J., Zhang, Y., Wang, J., Chen, L., Yang, Z., Chu, C., Xie, S., Laird, A. R., Fox, P. T., Eickhoff, S. B., Yu, C., & Jiang, T. (2016). The human Brainnetome atlas: A new brain atlas based on connectional architecture. Cerebral Cortex, 26, 3508–3526.
Feinberg, D. A., & Yacoub, E. (2012). The rapid development of high speed, resolution and precision in fMRI. Neuroimage, 62(2), 720–725.
Feinberg, D. A., Moeller, S., Smith, S. M., Auerbach, E., Ramanna, S., Gunther, M., Glasser, M. F., Miller, K. L., Ugurbil, K., & Yacoub, E. (2010). Multiplexed echo planar imaging for sub-second whole brain FMRI and fast diffusion imaging. PLoS One, 5(12), e15710.
Fox, M. D., & Greicius, M. (2010). Clinical applications of resting state functional connectivity. Frontiers in Systems Neuroscience, 4, 19.
Fox, M. D., & Raichle, M. E. (2007). Spontaneous fluctuations in brain activity observed with functional magnetic resonance imaging. Nature Reviews. Neuroscience, 8(9), 700–711.
Fox, M. D., Snyder, A. Z., Vincent, J. L., Corbetta, M., Van Essen, D. C., Raichle, M.E. (2005). The human brain is intrinsically organized into dynamic, anticorrelated functional networks. Proceedings of the National Academy of Sciences of the U S A 102(27), 9673–9678.
Fransson, P. (2005). Spontaneous low-frequency BOLD signal fluctuations: An fMRI investigation of the resting-state default mode of brain function hypothesis. Human Brain Mapping, 26(1), 15–29.
Friston, K. J., Williams, S., Howard, R., Frackowiak, R. S., & Turner, R. (1996). Movement-related effects in fMRI time-series. Magnetic Resonance in Medicine, 35, 346–355.
Fryer, S. L., Roach, B. J., Ford, J. M., Turner, J. A., van Erp, T. G., Voyvodic, J., et al. (2015). Relating intrinsic low-frequency BOLD cortical oscillations to cognition in schizophrenia. Neuropsychopharmacology, 40(12), 2705–2714.
Glover, G. H. (2012). Spiral imaging in fMRI. Neuroimage, 62(2), 706–712.
Greicius, M. D., Krasnow, B., Reiss, A. L., & Menon, V. (2003). Functional connectivity in the resting brain: A network analysis of the default mode hypothesis. Proceedings of the National Academy of Sciences of the United States of America, 100(1), 253–258.
Greicius, M. D., Kiviniemi, V., Tervonen, O., Vainionpaa, V., Alahuhta, S., Reiss, A. L., et al. (2008). Persistent default-mode network connectivity during light sedation. Human Brain Mapping, 29(7), 839–847.
Hohenfeld, C., Werner, C. J., & Reetz, K. (2018). Resting-state connectivity in neurodegenerative disorders: Is there potential for an imaging biomarker? Neuroimage Clin, 18, 849–870.
Jao, T., Vertes, P. E., Alexander-Bloch, A. F., Tang, I. N., Yu, Y. C., Chen, J. H., et al. (2013). Volitional eyes opening perturbs brain dynamics and functional connectivity regardless of light input. Neuroimage, 69, 21–34.
Jenkinson, M., Bannister, P., Brady, M., & Smith, S. (2002). Improved optimization for the robust and accurate linear registration and motion correction of brain images. Neuroimage, 17(2), 825–841.
Jia, X. Z., Sun, J. W., Ji, G. J., Liao, W., Lv, Y. T., Wang, J., Wang, Z., Zhang, H., Liu, D. Q., & Zang, Y. F. (2020). Percent amplitude of fluctuation: A simple measure for resting-state fMRI signal at single voxel level. PLoS One, 15(1), e0227021 https://doi.org/10.1371/journal.pone.0227021.
Jiang, X., Dai, X., Kale Edmiston, E., Zhou, Q., Xu, K., Zhou, Y., Wu, F., Kong, L., Wei, S., Zhou, Y., Chang, M., Geng, H., Wang, D., Wang, Y., Cui, W., Wang, F., & Tang, Y. (2017). Alteration of cortico-limbic-striatal neural system in major depressive disorder and bipolar disorder. Journal of Affective Disorders, 221, 297–303.
Kirilina, E., Lutti, A., Poser, B. A., Blankenburg, F., & Weiskopf, N. (2016). The quest for the best: The impact of different EPI sequences on the sensitivity of random effect fMRI group analyses. NeuroImage, 126, 49–59.
Liu, D., Dong, Z., Zuo, X., Wang, J., & Zang, Y. (2013). Eyes-open/eyes-closed dataset sharing for reproducibility evaluation of resting state fMRI data analysis methods. Neuroinformatics, 11(4), 469–476.
Lowe, M. J., Mock, B. J., & Sorenson, J. A. (1998). Functional connectivity in single and multislice Echoplanar imaging using resting-state fluctuations. Neuroimage, 7, 119–132.
Lui, S., Yao, L., Xiao, Y., Keedy, S. K., Reilly, J. L., Keefe, R. S., Tamminga, C. A., Keshavan, M. S., Pearlson, G. D., Gong, Q., & Sweeney, J. A. (2015). Resting-state brain function in schizophrenia and psychotic bipolar probands and their first-degree relatives. Psychological Medicine, 45(1), 97–108.
McAvoy, M., Larson-Prior, L., Nolan, T. S., Vaishnavi, S. N., Raichle, M. E., & d'Avossa, G. (2008). Resting states affect spontaneous BOLD oscillations in sensory and paralimbic cortex. Journal of Neurophysiology, 100(2), 922–931.
Merboldt, K. D., Fransson, P., Bruhn, H., & Frahm, J. (2001). Functional MRI of the human amygdala? Neuroimage, 14(2), 253–257.
Moeller, S., Yacoub, E., Olman, C. A., Auerbach, E., Strupp, J., Harel, N., & Uğurbil, K. (2010). Multiband multislice GE-EPI at 7 tesla, with 16-fold acceleration using partial parallel imaging with application to high spatial and temporal whole-brain fMRI. Magnetic Resonance in Medicine, 63(5), 1144–1153.
Nielsen, J. A., Zielinski, B. A., Fletcher, P. T., Alexander, A. L., Lange, N., Bigler, E. D., et al. (2013). Multisite functional connectivity MRI classification of autism: ABIDE results. Frontiers in Human Neuroscience, 7, 599.
Orban, P., Dansereau, C., Desbois, L., Mongeau-Perusse, V., Giguere, C. E., Nguyen, H., et al. (2018). Multisite generalizability of schizophrenia diagnosis classification based on functional brain connectivity. Schizophrenia Research, 192, 167–171.
Power, J. D., Schlaggar, B. L., & Petersen, S. E. (2014). Studying brain organization via spontaneous fMRI signal. Neuron, 84(4), 681–696.
Shang, C. Y., Yan, C. G., Lin, H. Y., Tseng, W. Y., Castellanos, F. X., & Gau, S. S. (2016). Differential effects of methylphenidate and atomoxetine on intrinsic brain activity in children with attention deficit hyperactivity disorder. Psychological Medicine, 46(15), 3173–3185.
Tadayonnejad, R., Yang, S., Kumar, A., & Ajilore, O. (2015). Clinical, cognitive, and functional connectivity correlations of resting-state intrinsic brain activity alterations in unmedicated depression. Journal of Affective Disorders, 172, 241–250.
Tam, A., Dansereau, C., Badhwar, A., Orban, P., Belleville, S., Chertkow, H., et al. (2015). Common effects of amnestic mild cognitive impairment on resting-state connectivity across four independent studies. Frontiers in Aging Neuroscience, 7, 242.
Teipel, S. J., Wohlert, A., Metzger, C., Grimmer, T., Sorg, C., Ewers, M., Meisenzahl, E., Klöppel, S., Borchardt, V., Grothe, M. J., Walter, M., & Dyrba, M. (2017). Multicenter stability of resting state fMRI in the detection of Alzheimer's disease and amnestic MCI. Neuroimage Clin, 14, 183–194.
Van den Heuvel, M. P., & Hulshoff Pol, H. E. (2010). Exploring the brain network: A review on resting-state fMRI functional connectivity. European Neuropsychopharmacology, 20(8), 519–534.
Wang, Z., Yan, C., Zhao, C., Qi, Z., Zhou, W., Lu, J., He, Y., & Li, K. (2011). Spatial patterns of intrinsic brain activity in mild cognitive impairment and Alzheimer's disease: A resting-state functional MRI study. Human Brain Mapping, 32(10), 1720–1740.
Wang, J. B., Zheng, L. J., Cao, Q. J., Wang, Y. F., Sun, L., Zang, Y. F., et al. (2017). Inconsistency in abnormal brain activity across cohorts of ADHD-200 in children with attention deficit hyperactivity disorder. Frontiers in Neuroscience, 11, 320.
Wang, J., Zhang, J. R., Zang, Y. F., & Wu, T. (2018). Consistent decreased activity in the putamen in Parkinson's disease: A meta-analysis and an independent validation of resting-state fMRI. Gigascience, 7(6).
Weiskopf, N., Hutton, C., Josephs, O., & Deichmann, R. (2006). Optimal EPI parameters for reduction of susceptibility-induced BOLD sensitivity losses: A whole-brain analysis at 3 T and 1.5 T. Neuroimage, 33(2), 493–504.
Xia, M., Si, T., Sun, X., Ma, Q., Liu, B., Wang, L., et al. (2019). Reproducibility of functional brain alterations in major depressive disorder: Evidence from a multisite resting-state functional MRI study with 1,434 individuals. Neuroimage, 289, 700–714.
Yan, C. G., Craddock, R. C., Zuo, X. N., Zang, Y. F., & Milham, M. P. (2013). Standardizing the intrinsic brain: Towards robust measurement of inter-individual variation in 1000 functional connectomes. Neuroimage, 80, 246–262.
Yan, C. G., Wang, X. D., Zuo, X. N., & Zang, Y. F. (2016). DPABI: Data Processing & Analysis for (resting-state) brain imaging. Neuroinformatics, 14(3), 339–351.
Yang, H., Long, X. Y., Yang, Y., Yan, H., Zhu, C. Z., Zhou, X. P., et al. (2007). Amplitude of low frequency fluctuation within visual areas revealed by resting-state functional MRI. Neuroimage, 36(1), 144–152.
Yu, R., Chien, Y. L., Wang, H. L., Liu, C. M., Liu, C. C., Hwang, T. J., Hsieh, M. H., Hwu, H. G., & Tseng, W. Y. (2014). Frequency-specific alternations in the amplitude of low-frequency fluctuations in schizophrenia. Human Brain Mapping, 35(2), 627–637.
Zang, Y. F., He, Y., Zhu, C. Z., Cao, Q. J., Sui, M. Q., Liang, M., Tian, L. X., Jiang, T. Z., & Wang, Y. F. (2007). Altered baseline brain activity in children with ADHD revealed by resting-state functional MRI. Brain and Development, 29(2), 83–91.
Zhang, D., & Raichle, M. E. (2010). Disease and the brain's dark energy. Nature Reviews. Neurology, 6(1), 15–28.
Zhang, Z., Lu, G., Zhong, Y., Tan, Q., Chen, H., Liao, W., Tian, L., Li, Z., Shi, J., & Liu, Y. (2010). fMRI study of mesial temporal lobe epilepsy using amplitude of low-frequency fluctuation analysis. Human Brain Mapping, 31(12), 1851–1861.
Zhang, Z., Liao, W., Zuo, X. N., Wang, Z., Yuan, C., Jiao, Q., Chen, H., Biswal, B. B., Lu, G., & Liu, Y. (2011). Resting-state brain organization revealed by functional covariance networks. PLoS One, 6(12), e28817.
Zhang, Z., Xu, Q., Liao, W., Wang, Z., Li, Q., Yang, F., Zhang, Z., Liu, Y., & Lu, G. (2015). Pathological uncoupling between amplitude and connectivity of brain fluctuations in epilepsy. Human Brain Mapping, 36(7), 2756–2766.
Zou, Q. H., Zhu, C. Z., Yang, Y., Zuo, X. N., Long, X. Y., Cao, Q. J., Wang, Y. F., & Zang, Y. F. (2008). An improved approach to detection of amplitude of low-frequency fluctuation (ALFF) for resting-state fMRI: Fractional ALFF. Journal of Neuroscience Methods, 172(1), 137–141.
Zuo, X. N., Di Martino, A., Kelly, C., Shehzad, Z. E., Gee, D. G., Klein, D. F., et al. (2010). The oscillating brain: Complex and reliable. Neuroimage, 49(2), 1432–1445.
Acknowledgments
This work was supported by the Natural Science Foundation of China (81201083) and the MOE (Ministry of Education in China) Project of Humanities and Social Sciences (16YJCZH057).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of Interest
The authors have no conflicts of interest to declare.
Ethical Approval
The public multisite data used in this study were acquired from human participants. The institutional review boards of each site approved submission of anonymized data. Written informed consent was obtained from each participant.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
ESM 1
(PDF 548 kb)
Rights and permissions
About this article
Cite this article
Wang, X., Wang, Q., Zhang, P. et al. Reducing Inter-Site Variability for Fluctuation Amplitude Metrics in Multisite Resting State BOLD-fMRI Data. Neuroinform 19, 23–38 (2021). https://doi.org/10.1007/s12021-020-09463-x
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12021-020-09463-x