Skip to main content
Top
Published in: Neuroinformatics 3/2016

01-07-2016 | Software Original Article

DPABI: Data Processing & Analysis for (Resting-State) Brain Imaging

Authors: Chao-Gan Yan, Xin-Di Wang, Xi-Nian Zuo, Yu-Feng Zang

Published in: Neuroinformatics | Issue 3/2016

Login to get access

Abstract

Brain imaging efforts are being increasingly devoted to decode the functioning of the human brain. Among neuroimaging techniques, resting-state fMRI (R-fMRI) is currently expanding exponentially. Beyond the general neuroimaging analysis packages (e.g., SPM, AFNI and FSL), REST and DPARSF were developed to meet the increasing need of user-friendly toolboxes for R-fMRI data processing. To address recently identified methodological challenges of R-fMRI, we introduce the newly developed toolbox, DPABI, which was evolved from REST and DPARSF. DPABI incorporates recent research advances on head motion control and measurement standardization, thus allowing users to evaluate results using stringent control strategies. DPABI also emphasizes test-retest reliability and quality control of data processing. Furthermore, DPABI provides a user-friendly pipeline analysis toolkit for rat/monkey R-fMRI data analysis to reflect the rapid advances in animal imaging. In addition, DPABI includes preprocessing modules for task-based fMRI, voxel-based morphometry analysis, statistical analysis and results viewing. DPABI is designed to make data analysis require fewer manual operations, be less time-consuming, have a lower skill requirement, a smaller risk of inadvertent mistakes, and be more comparable across studies. We anticipate this open-source toolbox will assist novices and expert users alike and continue to support advancing R-fMRI methodology and its application to clinical translational studies.
Literature
go back to reference ADHD-200-Consortium. (2012). The ADHD-200 Consortium: a model to advance the translational potential of neuroimaging in clinical neuroscience. Frontiers in Systems Neuroscience, 6, 62. doi:10.3389/fnsys.2012.00062. ADHD-200-Consortium. (2012). The ADHD-200 Consortium: a model to advance the translational potential of neuroimaging in clinical neuroscience. Frontiers in Systems Neuroscience, 6, 62. doi:10.​3389/​fnsys.​2012.​00062.
go back to reference Anderson, J. S., Druzgal, T. J., Froehlich, A., DuBray, M. B., Lange, N., Alexander, A. L., Abildskov, T., Nielsen, J. A., Cariello, A. N., Cooperrider, J. R., Bigler, E. D., & Lainhart, J. E. (2011). Decreased interhemispheric functional connectivity in autism. Cerebral Cortex, 21(5), 1134–1146. doi:10.1093/cercor/bhq190.CrossRefPubMed Anderson, J. S., Druzgal, T. J., Froehlich, A., DuBray, M. B., Lange, N., Alexander, A. L., Abildskov, T., Nielsen, J. A., Cariello, A. N., Cooperrider, J. R., Bigler, E. D., & Lainhart, J. E. (2011). Decreased interhemispheric functional connectivity in autism. Cerebral Cortex, 21(5), 1134–1146. doi:10.​1093/​cercor/​bhq190.CrossRefPubMed
go back to reference 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.CrossRefPubMed 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.CrossRefPubMed
go back to reference 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., Kotter, 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. doi:10.1073/pnas.0911855107.CrossRefPubMedPubMedCentral 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., Kotter, 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. doi:10.​1073/​pnas.​0911855107.CrossRefPubMedPubMedCentral
go back to reference Buckner, R. L., Sepulcre, J., Talukdar, T., Krienen, F. M., Liu, H., Hedden, T., Andrews-Hanna, J. R., Sperling, R. A., & Johnson, K. A. (2009). Cortical hubs revealed by intrinsic functional connectivity: mapping, assessment of stability, and relation to Alzheimer’s disease. Journal of Neuroscience, 29(6), 1860–1873. doi:10.1523/JNEUROSCI.5062-08.2009.CrossRefPubMedPubMedCentral Buckner, R. L., Sepulcre, J., Talukdar, T., Krienen, F. M., Liu, H., Hedden, T., Andrews-Hanna, J. R., Sperling, R. A., & Johnson, K. A. (2009). Cortical hubs revealed by intrinsic functional connectivity: mapping, assessment of stability, and relation to Alzheimer’s disease. Journal of Neuroscience, 29(6), 1860–1873. doi:10.​1523/​JNEUROSCI.​5062-08.​2009.CrossRefPubMedPubMedCentral
go back to reference Di Martino, A., Yan, C. G., Li, Q., Denio, E., Castellanos, F. X., Alaerts, K., Anderson, J. S., Assaf, M., Bookheimer, S. Y., Dapretto, M., Deen, B., Delmonte, S., Dinstein, I., Ertl-Wagner, B., Fair, D. A., Gallagher, L., Kennedy, D. P., Keown, C. L., Keysers, C., Lainhart, J. E., Lord, C., Luna, B., Menon, V., Minshew, N. J., Monk, C. S., Mueller, S., Muller, R. A., Nebel, M. B., Nigg, J. T., O’Hearn, K., Pelphrey, K. A., Peltier, S. J., Rudie, J. D., Sunaert, S., Thioux, M., Tyszka, J. M., Uddin, L. Q., Verhoeven, J. S., Wenderoth, N., Wiggins, J. L., Mostofsky, S. H., & Milham, M. P. (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. doi:10.1038/mp.2013.78.CrossRefPubMed Di Martino, A., Yan, C. G., Li, Q., Denio, E., Castellanos, F. X., Alaerts, K., Anderson, J. S., Assaf, M., Bookheimer, S. Y., Dapretto, M., Deen, B., Delmonte, S., Dinstein, I., Ertl-Wagner, B., Fair, D. A., Gallagher, L., Kennedy, D. P., Keown, C. L., Keysers, C., Lainhart, J. E., Lord, C., Luna, B., Menon, V., Minshew, N. J., Monk, C. S., Mueller, S., Muller, R. A., Nebel, M. B., Nigg, J. T., O’Hearn, K., Pelphrey, K. A., Peltier, S. J., Rudie, J. D., Sunaert, S., Thioux, M., Tyszka, J. M., Uddin, L. Q., Verhoeven, J. S., Wenderoth, N., Wiggins, J. L., Mostofsky, S. H., & Milham, M. P. (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. doi:10.​1038/​mp.​2013.​78.CrossRefPubMed
go back to reference Eklund, A., Nichols, T., Knutsson, H. (2015). Can parametric statistical methods be trusted for fMRI based group studies? arXiv preprint arXiv:1511.01863. Eklund, A., Nichols, T., Knutsson, H. (2015). Can parametric statistical methods be trusted for fMRI based group studies? arXiv preprint arXiv:1511.01863.
go back to reference Fair, D., Nigg, J.T., Iyer, S., Bathula, D., Mills, K.L., Dosenbach, N.U., Schlaggar, B.L., Mennes, M., Gutman, D., Bangaru, S., Buitelaar, J.K., Dickstein, D.P., Di Martino, A., Kennedy, D.N., Kelly, C., Luna, B., Schweitzer, J.B., Velanova, K., Wang, Y.-F., Mostofsky, S.H., Castellanos, F.X., Milham, M.P. (2012). Distinct neural signatures detected for ADHD subtypes after controlling for micro-movements in resting state functional connectivity MRI data. Front Syst Neurosci, 6, doi:10.3389/fnsys.2012.00080. Fair, D., Nigg, J.T., Iyer, S., Bathula, D., Mills, K.L., Dosenbach, N.U., Schlaggar, B.L., Mennes, M., Gutman, D., Bangaru, S., Buitelaar, J.K., Dickstein, D.P., Di Martino, A., Kennedy, D.N., Kelly, C., Luna, B., Schweitzer, J.B., Velanova, K., Wang, Y.-F., Mostofsky, S.H., Castellanos, F.X., Milham, M.P. (2012). Distinct neural signatures detected for ADHD subtypes after controlling for micro-movements in resting state functional connectivity MRI data. Front Syst Neurosci, 6, doi:10.​3389/​fnsys.​2012.​00080.
go back to reference Fox, M. D., & Raichle, M. E. (2007). Spontaneous fluctuations in brain activity observed with functional magnetic resonance imaging. Nature Review Neuroscience, 8(9), 700–711.CrossRef Fox, M. D., & Raichle, M. E. (2007). Spontaneous fluctuations in brain activity observed with functional magnetic resonance imaging. Nature Review Neuroscience, 8(9), 700–711.CrossRef
go back to reference 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(3), 346–355.CrossRefPubMed 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(3), 346–355.CrossRefPubMed
go back to reference Huettel, S., Song, A., McCarthy, G. (2004). Functional magnetic resonance imaging: Sinauer Associates Sunderland, MA. Huettel, S., Song, A., McCarthy, G. (2004). Functional magnetic resonance imaging: Sinauer Associates Sunderland, MA.
go back to reference 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.CrossRefPubMed 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.CrossRefPubMed
go back to reference Kelly, C., Biswal, B. B., Craddock, R. C., Castellanos, F. X., & Milham, M. P. (2012). Characterizing variation in the functional connectome: promise and pitfalls. Trends in Cognitive Science, 16(3), 181–188. doi:10.1016/j.tics.2012.02.001.CrossRef Kelly, C., Biswal, B. B., Craddock, R. C., Castellanos, F. X., & Milham, M. P. (2012). Characterizing variation in the functional connectome: promise and pitfalls. Trends in Cognitive Science, 16(3), 181–188. doi:10.​1016/​j.​tics.​2012.​02.​001.CrossRef
go back to reference Lowe, M. J., Mock, B. J., & Sorenson, J. A. (1998). Functional connectivity in single and multislice echoplanar imaging using resting-state fluctuations. NeuroImage, 7(2), 119–132.CrossRefPubMed Lowe, M. J., Mock, B. J., & Sorenson, J. A. (1998). Functional connectivity in single and multislice echoplanar imaging using resting-state fluctuations. NeuroImage, 7(2), 119–132.CrossRefPubMed
go back to reference Muller, R., & Buttner, P. (1994). A critical discussion of intraclass correlation coefficients. Statistics in Medicine, 13(23–24), 2465–2476.CrossRefPubMed Muller, R., & Buttner, P. (1994). A critical discussion of intraclass correlation coefficients. Statistics in Medicine, 13(23–24), 2465–2476.CrossRefPubMed
go back to reference Satterthwaite, T. D., Elliott, M. A., Gerraty, R. T., Ruparel, K., Loughead, J., Calkins, M. E., Eickhoff, S. B., Hakonarson, H., Gur, R. C., Gur, R. E., & Wolf, D. H. (2013). An improved framework for confound regression and filtering for control of motion artifact in the preprocessing of resting-state functional connectivity data. NeuroImage, 64, 240–256. doi:10.1016/j.neuroimage.2012.08.052.CrossRefPubMed Satterthwaite, T. D., Elliott, M. A., Gerraty, R. T., Ruparel, K., Loughead, J., Calkins, M. E., Eickhoff, S. B., Hakonarson, H., Gur, R. C., Gur, R. E., & Wolf, D. H. (2013). An improved framework for confound regression and filtering for control of motion artifact in the preprocessing of resting-state functional connectivity data. NeuroImage, 64, 240–256. doi:10.​1016/​j.​neuroimage.​2012.​08.​052.CrossRefPubMed
go back to reference Sawiak, S., Williams, G., Wood, N., Morton, A., Carpenter, T. (2009). SPMMouse: A new toolbox for SPM in the animal brain. ISMRM 17th Scientific Meeting & Exhibition, April, pp. 18-24. Sawiak, S., Williams, G., Wood, N., Morton, A., Carpenter, T. (2009). SPMMouse: A new toolbox for SPM in the animal brain. ISMRM 17th Scientific Meeting & Exhibition, April, pp. 18-24.
go back to reference Schwarz, A. J., Danckaert, A., Reese, T., Gozzi, A., Paxinos, G., Watson, C., Merlo-Pich, E. V., & Bifone, A. (2006). A stereotaxic MRI template set for the rat brain with tissue class distribution maps and co-registered anatomical atlas: application to pharmacological MRI. NeuroImage, 32(2), 538–550. doi:10.1016/j.neuroimage.2006.04.214.CrossRefPubMed Schwarz, A. J., Danckaert, A., Reese, T., Gozzi, A., Paxinos, G., Watson, C., Merlo-Pich, E. V., & Bifone, A. (2006). A stereotaxic MRI template set for the rat brain with tissue class distribution maps and co-registered anatomical atlas: application to pharmacological MRI. NeuroImage, 32(2), 538–550. doi:10.​1016/​j.​neuroimage.​2006.​04.​214.CrossRefPubMed
go back to reference Shannon, B. J., Dosenbach, R. A., Su, Y., Vlassenko, A. G., Larson-Prior, L. J., Nolan, T. S., Snyder, A. Z., & Raichle, M. E. (2013). Morning-evening variation in human brain metabolism and memory circuits. Journal of Neurophysiology, 109(5), 1444–1456. doi:10.1152/jn.00651.2012.CrossRefPubMed Shannon, B. J., Dosenbach, R. A., Su, Y., Vlassenko, A. G., Larson-Prior, L. J., Nolan, T. S., Snyder, A. Z., & Raichle, M. E. (2013). Morning-evening variation in human brain metabolism and memory circuits. Journal of Neurophysiology, 109(5), 1444–1456. doi:10.​1152/​jn.​00651.​2012.CrossRefPubMed
go back to reference Shehzad, Z., Kelly, A. M., Reiss, P. T., Gee, D. G., Gotimer, K., Uddin, L. Q., Lee, S. H., Margulies, D. S., Roy, A. K., Biswal, B. B., Petkova, E., Castellanos, F. X., & Milham, M. P. (2009). The resting brain: unconstrained yet reliable. Cerebral Cortex, 19(10), 2209–2229. doi:10.1093/cercor/bhn256.CrossRefPubMedPubMedCentral Shehzad, Z., Kelly, A. M., Reiss, P. T., Gee, D. G., Gotimer, K., Uddin, L. Q., Lee, S. H., Margulies, D. S., Roy, A. K., Biswal, B. B., Petkova, E., Castellanos, F. X., & Milham, M. P. (2009). The resting brain: unconstrained yet reliable. Cerebral Cortex, 19(10), 2209–2229. doi:10.​1093/​cercor/​bhn256.CrossRefPubMedPubMedCentral
go back to reference Shrout, P. E., & Fleiss, J. L. (1979). Intraclass correlations: uses in assessing rater reliability. Psychological Bulletin, 86(2), 420–428.CrossRefPubMed Shrout, P. E., & Fleiss, J. L. (1979). Intraclass correlations: uses in assessing rater reliability. Psychological Bulletin, 86(2), 420–428.CrossRefPubMed
go back to reference Simmons, A., Moore, E., & Williams, S. C. (1999). Quality control for functional magnetic resonance imaging using automated data analysis and Shewhart charting. Magnetic Resonance in Medicine, 41(6), 1274–1278.CrossRefPubMed Simmons, A., Moore, E., & Williams, S. C. (1999). Quality control for functional magnetic resonance imaging using automated data analysis and Shewhart charting. Magnetic Resonance in Medicine, 41(6), 1274–1278.CrossRefPubMed
go back to reference Vanhoutte, G., Verhoye, M., & Van der Linden, A. (2006). Changing body temperature affects the T2* signal in the rat brain and reveals hypothalamic activity. Magnetic Resonance in Medicine, 55(5), 1006–1012. doi:10.1002/mrm.20861.CrossRefPubMed Vanhoutte, G., Verhoye, M., & Van der Linden, A. (2006). Changing body temperature affects the T2* signal in the rat brain and reveals hypothalamic activity. Magnetic Resonance in Medicine, 55(5), 1006–1012. doi:10.​1002/​mrm.​20861.CrossRefPubMed
go back to reference Zang, Y. F., Jiang, T. Z., Lu, Y. L., He, Y., & Tian, L. X. (2004). Regional homogeneity approach to fMRI data analysis. NeuroImage, 22(1), 394–400.CrossRefPubMed Zang, Y. F., Jiang, T. Z., Lu, Y. L., He, Y., & Tian, L. X. (2004). Regional homogeneity approach to fMRI data analysis. NeuroImage, 22(1), 394–400.CrossRefPubMed
go back to reference 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 Dev, 29(2), 83–91.CrossRefPubMed 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 Dev, 29(2), 83–91.CrossRefPubMed
go back to reference Zuo, X. N., Kelly, C., Di Martino, A., Mennes, M., Margulies, D. S., Bangaru, S., Grzadzinski, R., Evans, A. C., Zang, Y. F., Castellanos, F. X., & Milham, M. P. (2010b). Growing together and growing apart: regional and sex differences in the lifespan developmental trajectories of functional homotopy. Journal of Neuroscience, 30(45), 15034–15043. doi:10.1523/JNEUROSCI.2612-10.2010.CrossRefPubMedPubMedCentral Zuo, X. N., Kelly, C., Di Martino, A., Mennes, M., Margulies, D. S., Bangaru, S., Grzadzinski, R., Evans, A. C., Zang, Y. F., Castellanos, F. X., & Milham, M. P. (2010b). Growing together and growing apart: regional and sex differences in the lifespan developmental trajectories of functional homotopy. Journal of Neuroscience, 30(45), 15034–15043. doi:10.​1523/​JNEUROSCI.​2612-10.​2010.CrossRefPubMedPubMedCentral
go back to reference Zuo, X. N., Ehmke, R., Mennes, M., Imperati, D., Castellanos, F. X., Sporns, O., & Milham, M. P. (2012). Network centrality in the human functional connectome. Cerebral Cortex, 22(8), 1862–1875. doi:10.1093/cercor/bhr269.CrossRefPubMed Zuo, X. N., Ehmke, R., Mennes, M., Imperati, D., Castellanos, F. X., Sporns, O., & Milham, M. P. (2012). Network centrality in the human functional connectome. Cerebral Cortex, 22(8), 1862–1875. doi:10.​1093/​cercor/​bhr269.CrossRefPubMed
go back to reference Zuo, X. N., Xu, T., Jiang, L., Yang, Z., Cao, X. Y., He, Y., Zang, Y. F., Castellanos, F. X., & Milham, M. P. (2013). Toward reliable characterization of functional homogeneity in the human brain: preprocessing, scan duration, imaging resolution and computational space. NeuroImage, 65, 374–386. doi:10.1016/j.neuroimage.2012.10.017.CrossRefPubMed Zuo, X. N., Xu, T., Jiang, L., Yang, Z., Cao, X. Y., He, Y., Zang, Y. F., Castellanos, F. X., & Milham, M. P. (2013). Toward reliable characterization of functional homogeneity in the human brain: preprocessing, scan duration, imaging resolution and computational space. NeuroImage, 65, 374–386. doi:10.​1016/​j.​neuroimage.​2012.​10.​017.CrossRefPubMed
Metadata
Title
DPABI: Data Processing & Analysis for (Resting-State) Brain Imaging
Authors
Chao-Gan Yan
Xin-Di Wang
Xi-Nian Zuo
Yu-Feng Zang
Publication date
01-07-2016
Publisher
Springer US
Published in
Neuroinformatics / Issue 3/2016
Print ISSN: 1539-2791
Electronic ISSN: 1559-0089
DOI
https://doi.org/10.1007/s12021-016-9299-4

Other articles of this Issue 3/2016

Neuroinformatics 3/2016 Go to the issue