The pipeline system for Octave and Matlab (PSOM): A lightweight scripting framework and execution engine for scientific workflows

Frontiers in Neuroinformatics

Volumn 6, Issue MARCH, 2012, Pages

  Bellec, Pierre ^a,b   Lavoie Courchesne, Sébastien ^a,b,c   Dickinson, Phil ^a,c   Lerch, Jason P ^d,e   Zijdenbos, Alex P ^f   Evans, Alan C ^c  

^a CENTRE DE RECHERCHE   (Canada)

^b UNIVERSITÉ DE MONTRÉAL   (Canada)

^c MCGILL UNIVERSITY   (Canada)

^d HOSPITAL FOR SICK CHILDREN   (Canada)

^e UNIVERSITY OF TORONTO   (Canada)

^f Biospective Inc   (Canada)

Author keywords

High performance computing; Matlab; Neuroimaging; Octave; Open source; Parallel computing; Pipeline; Workflow

Indexed keywords

ANALYTICAL PARAMETERS; ARTICLE; COMPUTER PROGRAM; CONCEPTUAL FRAMEWORK; DATA ANALYSIS; DATA BASE; DOCUMENTATION; FUNCTIONAL MAGNETIC RESONANCE IMAGING; IMAGING SOFTWARE; NEUROIMAGING; PIPELINE COMPOSITION; PIPELINE EXECUTION; PIPELINE MAPPING; PIPELINE PROVENANCE; PIPELINE SYSTEM FOR OCTAVE AND MATLAB; QUALITY CONTROL;

EID: 84858060836     PISSN: 16625196     EISSN: None     Source Type: Journal    
DOI: 10.3389/fninf.2012.00007     Document Type: Article

References (47)

1. Ad-Dab'bagh, Y., Einarson, D., Lyttelton, O., Muehlboeck, J. S., Mok, K., Ivanov, O., Vincent, R. D., Lepage, C., Lerch, J., Fombonne, E., Evans, A. C., 2006. The CIVET Image-Processing Environment: A Fully Automated Comprehensive Pipeline for Anatomical Neuroimaging Research. In: Corbetta, M. (Ed.), Proceedings of the 12th Annual Meeting of the Human Brain Mapping Organization. Neuroimage, Florence, Italy.
2. Armstrong, T. G., 2011. Integrating task parallelism into the python programming language. Master's thesis, The University of Chicago.
3. Ashburner, J., Oct. 2011. SPM: A history. NeuroImage. URL http://dx.doi.Org/10.1016/j.neuroimage.2011.10.025
4. Baker, H. G., Hewitt, C., 1977. The Incremental Garbage Collection of Processes. Tech. rep., Cambridge, MA, USA. URL http://portal.acm.org/citation.cfm?id=889254
5. Bellec, P., Carbonell, F. M., Perlbarg, V., Lepage, C., Lyttelton, O., Fonov, V., Janke, A., Tohka, J., Evans, A. C., 2011. A neuroimaging analysis kit for Matlab and Octave. In: Proceedings of the 17th International Conference on Functional Mapping of the Human Brain. pp. In Press+.
6. Bellec, P., Perlbarg, V., Evans, A. C., Jun. 2009. Bootstrap generation and evaluation of an fMRI simulation database. Magnetic Resonance Imaging 27, 1382-1396. URL http://dx.doi.org/10.1016/j.mri.2009.05.034
7. Bellec, P., Petrides, M., Rosa-Neto, P., Evans, A. C., 2010a. Stable group clusters in resting-state fMRI at multiple scales: from systems to regions. In: Proceedings of the 16th International Conference on Functional Mapping of the Human Brain.
8. Bellec, P., Rosa-Neto, P., Lyttelton, O. C., Benali, H., Evans, A. C., Jul. 2010b. Multi-level bootstrap analysis of stable clusters in resting-state fMRI. NeuroImage 51 (3), 1126-1139. URL http://dx.doi.org/10.1016/j.neuroimage.2010.02.082
9. Biswal, B. B., Mennes, M., Zuo, X.-N. N., Gohel, S., Kelly, C., Smith, S. M., Beckmann, C. F., Adelstein, J. S., Buckner, R. L., Colcombe, S., Dogonowski, A.-M. M., Ernst, M., Fair, D., Hampson, M., Hoptman, M. J., Hyde, J. S., Kiviniemi, V. J., Kotter, R., Li, S.-J. J., Lin, C.-P. 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. J., Veijola, J., Villringer, A., Walter, M., Wang, L., Weng, X.-C. C., Whitfield-Gabrieli, S., Williamson, P., Windischberger, C., Zang, Y.-F. F., Zhang, H.-Y. Y., Castellanos, F. X., Milham, M. P., Mar. 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. URL http://dx.doi.org/10.1073/pnas.0911855107
10. Bose, R., Foster, I., Moreau, L., Sep. 2006. Report on the International Provenance and Annotation Workshop: (IPAW'06) 3-5 May 2006, Chicago. SIG-MOD Rec. 35, 51-53. URL http://dx.doi.org/10.1145/1168092.1168102
11. Burton, A., Mar. 2011. Big science for a big problem: ADNI enters its second phase. Lancet neurology 10 (3), 206-207. URL http://dx.doi.org/10.1016/S1474-4422(11)70031-X
12. Callahan, S. P., Freire, J., Santos, E., Scheidegger, C. E., Silva, C. T., Vo, H. T., 2006. VisTrails: visualization meets data management. In: Proceedings of the 2006 ACM SIGMOD international conference on Management of data. SIGMOD '06. ACM, New York, NY, USA, pp. 745-747. URL http://dx.doi.org/10.1145/1142473.1142574
13. Carbonell, F. M., Bellec, P., Shmuel, A., Feb. 2012. Global and system-specific resting-state BOLD fluctuations are uncorrelated: principal component analysis reveals anti-correlated networks. Brain Connectivity, 120208060948009+. URL http://dx.doi.org/10.1089/brain.2011.0065
14. Chao-Gan, Y., Yu-Feng, Z., 2010. DPARSF: A MATLAB Toolbox for "Pipeline" Data Analysis of Resting-State fMRI. Frontiers in systems neuroscience 4. URL http://dx.doi.org/10.3389/fnsys.2010.00013
15. Collins, D. L., Neelin, P., Peters, T. M., Evans, A. C., 1994. Automatic 3D intersubject registration of MR volumetric data in standardized Talairach space. Journal of computer assisted tomography 18 (2), 192-205. URL http://view.ncbi.nlm.nih.gov/pubmed/8126267
16. Dansereau, C. L., Pittau, F., Bellec, P., Gotman, J., Grova, C., 2011. Detection of abnormal resting state networks in epileptic patients. In: 17th International Conference on Functional Mapping of the Human Brain.
17. Das, S., Zijdenbos, A. P., Vins, D., Harlap, J., Evans, A. C., 2012. LORIS: a web-based data management system for multi-center studies. Frontiers in Neuroinformatics 5. URL http://www.frontiersin.org/neuroinformatics/10.3389/fninf. 2011.00037/abstract
18. Deelman, E., Gannon, D., Shields, M., Taylor, I., May 2009. Workflows and e-Science: An overview of workflow system features and capabilities. Future Generation Computer Systems 25 (5), 528-540. URL http://dx.doi.org/10.1016/j.future.2008.06.012
19. Deelman, E., Singh, G., Su, M. H., Blythe, J., Gil, Y., Kesselman, C., Mehta, G., Vahi, K., Berriman, G. B., Good, J., Laity, A., Jacob, J. C., Katz, D. S., Jul. 2005. Pegasus: A framework for mapping complex scientific workflows onto distributed systems. Sci. Program. 13, 219-237. URL http://portal.acm.org/citation.cfm?id=1239649.1239653
20. Dinov, I. D., Van Horn, J. D., Lozev, K. M., Magsipoc, R., Petrosyan, P., Liu, Z., Mackenzie-Graham, A., Eggert, P., Parker, D. S., Toga, A. W., 2009. Efficient, Distributed and Interactive Neuroimaging Data Analysis Using the LONI Pipeline. Frontiers in neuroinformatics 3. URL http://dx.doi.org/10.3389/neuro.11.022.2009
21. Evans, A. C., Mar. 2006. The NIH MRI study of normal brain development. NeuroImage 30 (1), 184-202. URL http://dx.doi.org/10.1016/j.neuroimage.2005.09.068
22. Fonov, V., Evans, A. C., Botteron, K., Almli, C. R., McKinstry, R. C., Collins, D. L., Brain Development Cooperative Group, Jan. 2011. Unbiased average age-appropriate atlases for pediatric studies. NeuroImage 54 (1), 313-327. URL http://dx.doi.org/10.1016/j.neuroimage.2010.07.033
23. Frisoni, G. B., Redolfi, A., Manset, D., Rousseau, M.-E. E., Toga, A., Evans, A. C., Aug. 2011. Virtual imaging laboratories for marker discovery in neu-rodegenerative diseases. Nature reviews. Neurology 7 (8), 429-438. URL http://dx.doi.org/10.1038/nrneurol.2011.99
24. Ganjavi, H., Lewis, J. D., Bellec, P., MacDonald, P. A., Waber, D. P., Evans, A. C., Karama, S., Brain Development Cooperative Group, 2011. Negative associations between corpus callosum midsagittal area and IQ in a representative sample of healthy children and adolescents. PloS one 6 (5). URL http://dx.doi.org/10.1371/journal.pone.0019698
25. Goecks, J., Nekrutenko, A., Taylor, J., Galaxy Team, Aug. 2010. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome biology 11 (8), R86+. URL http://dx.doi.org/10.1186/gb-2010-11-8-r86
26. Gorgolewski, K., Burns, C. D., Madison, C., Clark, D., Halchenko, Y. O., Waskom, M. L., Ghosh, S. S., 2011. Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python. Frontiers in Neuroinformatics 5. URL http://dx.doi.org/10.3389/fninf.2011.00013
27. Harrison, A., Taylor, I., Wang, I., Shields, M., Aug. 2008. WS-RF Workflow in Triana. Int. J. High Perform. Comput. Appl. 22, 268-283. URL http://dx.doi.org/10.1177/1094342007086226
28. Kassis, N., Gong, G., Rousseau, M. E., Adalat, R., Evans, A. C., 2011. Brain-Browser: Web-based 3D Visualization for the maCaCC Dataset and other Surface Data. In: 17th International Conference on Functional Mapping of the Human Brain.
29. Laguitton, S., Riviere, D., Vincent, T., Fischer, C., Geffroy, D., Souedet, N., Denghien, I., Cointepas, Y., Sep. 2011. Soma-workflow: a unified and simple interface to parallel computing resources.
30. Lavoie-Courchesne, S., Rioux, P., Chouinard-Decorte, F., Sherif, T., Rousseau, M. E., Das, S., Adalat, R., Doyon, J., Craddock, C., Margulies, D., Chu, C., Lyttelton, O., Evans, A. C., Bellec, P., Feb. 2012. Integration of a neuroimaging processing pipeline into a pan-canadian computing grid. Journal of Physics: Conference Series 341 (1), 012032+. URL http://dx.doi.org/10.1088/1742-6596/341/1/012032
31. Liu, H., Stufflebeam, S. M., Sepulcre, J., Hedden, T., Buckner, R. L., Dec. 2009. Evidence from intrinsic activity that asymmetry of the human brain is controlled by multiple factors. Proceedings of the National Academy of Sciences 106 (48), 20499-20503. URL http://dx.doi.org/10.1073/pnas.0908073106
32. Ludäscher, B., Altintas, I., Berkley, C., Higgins, D., Jaeger, E., Jones, M., Lee, E.A., Tao, J., Zhao, Y., Aug. 2006. Scientific workflow management and the Kepler system: Research Articles. Concurr. Comput.: Pract. Exper. 18 (10), 1039-1065. URL http://dx.doi.org/10.1002/cpe.v18:10
33. Machado, A., Lina, J. M., Tremblay, J., Lassonde, M., Nguyen, D. K., Lesage, F., Grova, C., May 2011. Detection of hemodynamic responses to epileptic activity using simultaneous Electro-EncephaloGraphy (EEG)/Near Infra Red Spectroscopy (NIRS) acquisitions. NeuroImage 56 (1), 114-125. URL http://dx.doi.org/10.1016/j.neuroimage.2010.12.026
34. MacKenzie-Graham, A. J., Van Horn, J. D., Woods, R. P., Crawford, K. L., Toga, A. W., Aug. 2008. Provenance in neuroimaging. NeuroImage 42 (1), 178-195. URL http://dx.doi.org/10.1016/j.neuroimage.2008.04.186
35. Marcus, D., Olsen, T., Ramaratnam, M., Buckner, R., Mar. 2007. The extensible neuroimaging archive toolkit. Neuroinformatics 5 (1), 11-33. URL http://dx.doi.org/10.1385/NI:5:1:11
36. Mesirov, J. P., Jan. 2010. Accessible Reproducible Research. Science 327 (5964), 415-416. URL http://dx.doi.org/10.1126/science.1179653
37. Moeller, F., Maneshi, M., Pittau, F., Gholipour, T., Bellec, P., Dubeau, F., Grova, C., Gotman, J., Mar. 2011. Functional connectivity in patients with idiopathic generalized epilepsy. Epilepsia 52 (3), 515-522. URL http://dx.doi.org/10.1111/j.1528-1167.2010.02938.x
38. Oinn, T., Greenwood, M., Addis, M., Alpdemir, M. N., Ferris, J., Glover, K., Goble, C., Goderis, A., Hull, D., Marvin, D., Li, P., Lord, P., Pocock, M. R., Senger, M., Stevens, R., Wipat, A., Wroe, C., 2006. Taverna: lessons in creating a workflow environment for the life sciences. Concurrency and Computation: Practice and Experience 18 (10), 1067-1100. URL http://dx.doi.org/10.1002/cpe.993
39. Orban, P., Doyon, J., Hoge, R., Bellec, P., 2011. Stable clusters of brain regions associated with distinct motor task-evoked hemodynamic responses. In: Proceedings of the 17th International Conference on Functional Mapping of the Human Brain.
40. Perlbarg, V., Bellec, P., Anton, J.-L., Pélégrini-Issac, M., Doyon, J., Benali, H., Jan. 2007. CORSICA: correction of structured noise in fMRI by automatic identification of ICA components. Magnetic Resonance Imaging 25 (1), 35-46. URL http://dx.doi.org/10.1016/j.mri.2006.09.042
41. Poinot, M., 2010. Five Good Reasons to Use the Hierarchical Data Format. Computing in Science & Engineering 12 (5), 84-90. URL http://dx.doi.org/10.1109/MCSE.2010.107
42. Schoemaker, D., Soder, R. B., Sziklas, V., Rowley, J., Carbonnell, F., Mohades, S., Fonov, V., Bellec, P., Dagher, A., Schmuel, A., Gauthier, S., Rosa Neto, P., 2011. Hippocampal resting connectivity lateralize memory function in aMCI brain networks. In: Alzheimer's Association 2011 International Conference on Alzheimer's Disease (ICAD).
43. Stef-Praun, T., Clifford, B., Foster, I., Hasson, U., Hategan, M., Small, S. L., Wilde, M., Zhao, Y., 2007. Accelerating medical research using the swift workflow system. Studies in health technology and informatics 126, 207-216. URL http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2676238/
44. Tadel, F., Baillet, S., Mosher, J. C., Pantazis, D., Leahy, R. M., 2011. Brainstorm: A User-Friendly Application for MEG/EEG Analysis. Computational Intelligence and Neuroscience 2011, 1-13. URL http://dx.doi.org/10.1155/2011/879716
45. Wilde, M., Hategan, M., Wozniak, J. M., Clifford, B., Katz, D. S., Foster, I., Sep. 2011. Swift: A language for distributed parallel scripting. Parallel Computing 37 (9), 633-652. URL http://dx.doi.org/10.1016/j.parco.2011.05.005
46. Worsley, K. J., Liao, C. H., Aston, J., Petre, V., Duncan, G. H., Morales, F., Evans, A. C., Jan. 2002. A general statistical analysis for fMRI data. NeuroImage 15 (1), 1-15. URL http://dx.doi.org/10.1006/nimg.2001.0933
47. Zijdenbos, A. P., Jimenez, A., Evans, A. C., 1998. Pipelines: Large Scale Automatic Analysis of 3D Brain Data Sets. In: Proceedings of the 4th International Conference on Functional Mapping of the Human Brain.