Reproducibility of neuroimaging analyses across operating systems

Frontiers in Neuroinformatics

Volumn 9, Issue APR, 2015, Pages

  Glatard, Tristan ^a,b   Lewis, Lindsay B ^a   da Silva, Rafael Ferreira ^c   Adalat, Reza ^a   Beck, Natacha ^a   Lepage, Claude ^a   Rioux, Pierre ^a   Rousseau, Marc Etienne ^a   Sherif, Tarek ^a   Deelman, Ewa ^c   Khalili Mahani, Najmeh ^a   Evans, Alan C ^a  

^a MCGILL UNIVERSITY   (Canada)

^b UNIVERSITÉ DE LYON   (France)

^c UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

CIVET; Freesurfer; FSL; Operating systems; Reproducibility

Indexed keywords

ARTICLE; BRAIN CORTEX; BRAIN REGION; COMPUTER MODEL; COMPUTER PROGRAM; CORTICAL THICKNESS (BRAIN); DATA PROCESSING; FUNCTIONAL MAGNETIC RESONANCE IMAGING; HISTOGRAM; HUMAN; INDEPENDENT COMPONENT ANALYSIS; MATHEMATICAL COMPUTING; MEASUREMENT; NEUROANATOMY; NEUROIMAGING; REPRODUCIBILITY; RESTING STATE NETWORK; STRUCTURE ANALYSIS;

EID: 84928663156     PISSN: 16625196     EISSN: 16625196     Source Type: Journal    
DOI: 10.3389/fninf.2015.00012     Document Type: Article

References (18)

1. Ad-Dabbagh, Y., Einarson, D., Lyttelton, O., Muehlboeck, J.-S., Mok, K., Ivanov, O., et al. (2006). "The CIVET image-processing environment: a fully automated comprehensive pipeline for anatomical neuroimaging research, " in Proceedings of the 12th Annual Meeting of the Organization for Human Brain Mapping. (Florence).
2. Bailey, D., Barrio, R., and Borwein, J. (2012). High-precision computation: mathematical physics and dynamics. Appl. Math. Comput. 218, 10106-10121. doi: 10. 1016/j. amc. 2012. 03. 087.
3. Beckmann, C. F., and Smith, S. M. (2004). Probabilistic independent component analysis for functional magnetic resonance imaging. IEEE Trans. Med. Imaging 23, 137-152. doi: 10. 1109/TMI. 2003. 822821.
4. Dice, L. (1945). Measures of the amount of ecologic association between species. Ecology 26, 297-302. doi: 10. 2307/1932409.
5. Fischl, B. (2012). FreeSurfer. Neuroimage 62, 774-781. doi: 10. 1016/j. neuroimage. 2012. 01. 021.
6. Glatard, T., Rousseau, M., Rioux, P., Adalat, R., and Evans, A. C. (2014). "Controlling the deployment of virtual machines on clusters and clouds for scientific computing in CBRAIN, " in 14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (Chicago), 384-393.
7. Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., et al. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. PLoS ONE 7: e38234. doi: 10. 1371/journal. pone. 0038234.
8. Halchenko, Y. O., and Hanke, M. (2012). Open is not enough. Let's take the next step: an integrated, community-driven computing platform for neuroscience. Front. Neuroinform. 6: 22. doi: 10. 3389/fninf. 2012. 00022.
9. Hanke, M., and Halchenko, Y. O. (2011). Neuroscience Runs on GNU/Linux. Front. Neuroinform. 5: 8. doi: 10. 3389/fninf. 2011. 00008.
10. Jenkinson, M., Beckmann, C. F., Behrens, T. E. J., Woolrich, M. W., and Smith, S. M. (2012). FSL. Neuroimage 62, 782-790. doi: 10. 1016/j. neuroimage. 2011. 09. 015.
11. Krefting, D., Scheel, M., Freing, A., Specovius, S., Paul, F., and Brandt, A. (2011). "Reliability of quantitative neuroimage analysis using freesurfer in distributed environments, " in MICCAI Workshop on High-Performance and Distributed Computing for Medical Imaging. (Toronto, ON).
12. Mazziotta, J., Toga, A., Evans, A., Fox, P., Lancaster, J., Zilles, K., et al. (2001). A probabilistic atlas and reference system for the human brain: international Consortium for Brain Mapping (ICBM). Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci. 356, 1293-1322. doi: 10. 1098/rstb. 2001. 0915.
13. Minka, T. (2000). Automatic Choice of Dimensionality for PCA. Technical report, Technical Report 514, MIT Media Lab Vision and Modeling Group.
14. Patenaude, B., Smith, S. M., Kennedy, D. N., and Jenkinson, M. (2011). A Bayesian model of shape and appearance for subcortical brain segmentation. Neuroimage 56, 907-922. doi: 10. 1016/j. neuroimage. 2011. 02. 046.
15. Sherif, T., Rioux, P., Rousseau, M.-E., Kassis, N., Beck, N., Glatard, T., et al. (2014). CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research. Front. Neurosci. 8: 54. doi: 10. 3389/fninf. 2014. 00054.
16. Smith, S. M. (2002). Fast robust automated brain extraction. Hum. Brain Mapp. 17, 143-155. doi: 10. 1002/hbm. 10062.
17. Worsley, K., Taylor, J., Carbonell, F., Chung, M., Duerden, E., Bernhardt, B., et al. (2009). SurfStat: a matlab toolbox for the statistical analysis of univariate and multivariate surface and volumetric data using linear mixed effects models and random field theory. Neuroimage 47, S102. doi: 10. 1016/S1053-8119(09)70882-1.
18. Zhang, Y., Brady, M., and Smith, S. (2001). Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm. IEEE Trans. Med. Imaging 20, 45-57. doi: 10. 1109/42. 906424.