Acknowledging Pipeline

Publications and Print Materials

Papers, technical reports and other printed materials utilizing Pipeline use should cite the relevant publications, as appropriate:

Fu, K., Nathan, R., Dinov, ID, Li, J.,  Toga. AW (2016) T2-Imaging Changes in the Nigrosome-1 Relate to Clinical Measures of Parkinson’s Disease. Frontiers in Neurology, DOI: 10.3389/fneur.2016.00174

Dinov, I.D., Heavner, B., Tang, M. et al. (2016) Predictive Big Data Analytics: A Study of Parkinson’s Disease Using Large, Complex, Heterogeneous, Incongruent, Multi-Source and Incomplete Observations. PLOS One, DOI: 10.1371/journal.pone.0157077

Torgerson, C.M., Quinn, C., Dinov, I. et al. (2015) Interacting with the National Database for Autism Research (NDAR) via the LONI Pipeline workflow environment. Brain Imaging and Behavior, 9: 89. 10.1007/s11682-015-9354-z

Toga, WA, Dinov, ID. (2015) Sharing big biomedical data. Journal of Big Data., 2(7):1-12. DOI: 10.1186/s40537-015-0016-1

Moon, Seok WooDinov, Ivo D.Kim, JaebumZamanyan, Alen, Hobel, SamThompson, Paul M, Toga, Arthur W. (2015) Structural NeuroImaging Genetics Interactions in Patients with Alzheimer’s Disease. Journal of Alzheimer’s Disease, 48:4 DOI: 103233/JAD-150335

Woo MS, Dinov, ID, Hobel, S, Zamanyan, A, Choi, YC, Thompson, PM, Toga, AW and Alzheimer’s Disease Neuroimaging Initiative (ADNI) (2015) Structural Brain Changes in Early-Onset Alzheimer’s Disease Subjects Using the LONI Pipeline Environment. Journal of Neuroimaging., in press. DOI: 10.1111/jon.12252

Dinov ID, Petrosyan P, Liu Z, Eggert P, Hobel S, Vespa P, Woo Moon S, Van Horn JD, Franco J and Toga AW. (2014) High-throughput neuroimaging-genetics computational infrastructure. Front. Neuroinform., 8:41. doi: 10.3389/fninf.2014.00041

Dinov, ID, Petrosyan, P, Liu, Z, Eggert, P, Zamanyan, A, Torri, F, Macciardi, F, Hobel, S, Moon, SW, Sung, YH, Jiang, Z, Labus, J, Kurth, F, Ashe-McNalley, C, Mayer, E, Vespa, PM, Van Horn, JD, Toga, AW. (2013) The Perfect Neuroimaging-Genetics-Computation Storm: Collision of Petabytes of Data, Millions of Hardware Devices and Thousands of Software Tools, Brain Imaging and Behavior, 8(2):311-322, DOI: 10.1007/s11682-013-9248-x.

Torri, F., Dinov, ID, Zamanyan, A, Hobel, S, Genco, A, Petrosyan, P, Clark, AP, Liu, Z, Eggert, P, Pierce, J, Knowles, JA, Ames, J, Kesselman, C, Toga, AW, Potkin, SG, Vawter, MP, Macciardi, F. (2012) Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows, Genes, 3(3):545-575; doi:10.3390/genes3030545.

Dinov, ID, Torri, F, Macciardi, F, Petrosyan, P, Liu, Z, Zamanyan, A, Eggert, P, Pierce, J, Genco, A, Knowles, JA, Clark, AP, Van Horn, JD, Ames, J, Kesselman, C, Toga, AW. (2011) Applications of the Pipeline Environment for Visual Informatics and Genomics Computations, BMC Bioinformatics, 12:304, doi:10.1186/1471-2105-12-304.

Dinov ID, Lozev K, Petrosyan P, Liu Z, Eggert P, Pierce, J, Zamanyan, A, Chakrapani, S, Van Horn, JD, Parker, DS, Magsipoc, R, Leung, K, Gutman, B, Woods, RP, Toga, AW. (2010) Neuroimaging Study Designs, Computational Analyses and Data Provenance Using the LONI Pipeline. PLoS ONE 5(9): e13070. doi:10.1371/journal.pone.0013070

Dinov I, Van Horn JD, Lozev KM, Magsipoc R, Petrosyan P, Liu Z, MacKenzie-Graham A, Eggert P, Parker DS and Toga AW (2009) Efficient, Distributed and Interactive Neuroimaging Data Analysis using the LONI Pipeline. Front. Neuroinform.,  3(22):1-10. doi:10.3389/neuro.11.022.2009.

Leung, K, Parker, D, Cunha, A, Hojatkashani, C, Dinov, I, Toga, A (2008) IRMA: An Image Registration Meta-Algorithm. Lecture Notes in Computer Science, Springer Berlin/Heidelberg, vol 5069:612-617 DOI: 10.1007/978-3-540-69497-7_46

Rex, DE, Shattuck, DW, Woods, RP, Narr, KL, Luders, E, Rehm, K, Stolzner, SE, Rottenberg, DA, Toga, AW (2004) A meta-algorithm for brain extraction in MRI NeuroImage, Volume 23, Issue 2, October 2004, Pages 625-637, ISSN 1053-8119, DOI: 10.1016/j.neuroimage.2004.06.019.

Rex, DE, Ma, JQ, and Toga, AW. (2003) The LONI Pipeline Processing Environment. Neuroimage, 19(3): 1033-48. doi:10.1016/S1053-8119(03)00185-X.

Visual Materials

Graphics, video and media projects that use the Pipeline environment should cite it as in quotations below:

“This project utilizes the LONI Pipeline environment, which was developed by the Laboratory of Neuro Imaging.”


The LONI Pipeline environment ( is developed by the Laboratory of Neuro Imaging, and partially funded by NIH grants 9P41EB015922-15, 2-P41-RR-013642-15, R01 MH71940 and U54 RR021813.

keywords: cite, credit, acknowledgment