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Neuroimaging Data Provenance Using the LONI Pipeline Workflow Environment [chapter]

Allan J. MacKenzie-Graham, Arash Payan, Ivo D. Dinov, John D. Van Horn, Arthur W. Toga
2008 Lecture Notes in Computer Science  
We have developed a provenance framework for describing the current and retrospective data state integrated with the LONI Pipeline workflow environment.  ...  The LONI Pipeline (http://pipeline.loni.ucla.edu) is a Java-based workflow environment for the construction and execution of data processing streams.  ...  The LONI Pipeline differs from many similar workflow environments.  ... 
doi:10.1007/978-3-540-89965-5_22 fatcat:3kobwveadjgnliynzohjgcapdi

Neuroimaging Study Designs, Computational Analyses and Data Provenance Using the LONI Pipeline

Ivo Dinov, Kamen Lozev, Petros Petrosyan, Zhizhong Liu, Paul Eggert, Jonathan Pierce, Alen Zamanyan, Shruthi Chakrapani, John Van Horn, D. Stott Parker, Rico Magsipoc, Kelvin Leung (+4 others)
2010 PLoS ONE  
Citation: Dinov I, Lozev K, Petrosyan P, Liu Z, Eggert P, et al. (2010) Neuroimaging Study Designs, Computational Analyses and Data Provenance Using the LONI Pipeline. PLoS ONE 5(9): e13070.  ...  Our solution is based on the LONI Pipeline environment [3,4], a graphical workflow environment for constructing and executing complex data processing protocols.  ...  Peter Lyster), and many general users for their patience with beta-testing the LONI Pipeline and for providing useful feedback about its state, functionality and usability.  ... 
doi:10.1371/journal.pone.0013070 pmid:20927408 pmcid:PMC2946935 fatcat:gfcxghw435ejfh7ah3j4m5nnta

Provenance in neuroimaging

Allan J. MacKenzie-Graham, John D. Van Horn, Roger P. Woods, Karen L. Crawford, Arthur W. Toga
2008 NeuroImage  
Provenance, the description of the history of a set of data, has grown more important with the proliferation of research consortia-related efforts in neuroimaging.  ...  We have drafted a mechanism for describing provenance in a simple and easy to use environment, alleviating the burden of documentation from the user while still providing a rich description of an image's  ...  In order to address this issue we have used the LONI Pipeline Processing Environment (LONI Pipeline; http://pipeline.loni.ucla.edu) (Rex et al., 2003) to capture workflow provenance and description.  ... 
doi:10.1016/j.neuroimage.2008.04.186 pmid:18519166 pmcid:PMC2664747 fatcat:ue56gsjx7bgqnk7dx4lfiky444

Integration of Behavioral, Structural, Functional, and Genetic Data for the Study of Autism Spectrum Disorders [chapter]

Carinna M. Torgerson, Andrei Irimia, S.-Y. Matthew Goh, John D. Van Horn
2015 Lecture Notes in Computer Science  
To encourage fusion of data across modalities, we have integrated a direct National Database for Autism Research (NDAR) data sharing capability into the LONI Pipeline processing environment, which allows  ...  As the designated Data Coordinating Center in the Autism Center of Excellence (ACE) network, the Laboratory of Neuro Imaging (LONI) is faced with the task of efficiently organizing data from behavioral  ...  In our role as the DCC, we sought to overcome this barrier partly by using the LONI Pipeline processing environment, where researchers can create simple data analysis workflows by utilizing some of the  ... 
doi:10.1007/978-3-319-21843-4_16 fatcat:xrnjaazuhrdbfcnvcorfjlsxwi

Interacting with the National Database for Autism Research (NDAR) via the LONI Pipeline workflow environment

Carinna M. Torgerson, Catherine Quinn, Ivo Dinov, Zhizhong Liu, Petros Petrosyan, Kevin Pelphrey, Christian Haselgrove, David N. Kennedy, Arthur W. Toga, John Darrell Van Horn
2015 Brain Imaging and Behavior  
To illustrate the use of NDAR and LONI Pipeline for performing several commonly performed neuroimaging processing steps and analyses, this paper presents example workflows useful for ASD neuroimaging researchers  ...  NDAR has recently made its database accessible through the LONI Pipeline processing environment to enable large-scale analyses of cortical architecture and function via local, cluster, or "cloud"-based  ...  Finally, we acknowledge the dedicated staff of the Institute for Neuroimaging and Informatics at the University of Southern California.  ... 
doi:10.1007/s11682-015-9354-z pmid:25666423 pmcid:PMC4447326 fatcat:symi75dpargr5jde6xajjnelia

Is it time to re-prioritize neuroimaging databases and digital repositories?

John Darrell Van Horn, Arthur W. Toga
2009 NeuroImage  
We feature the LONI IDA as an example of an archive being used as a source for brain atlas workflow construction, list several instances of other successful uses of image databases, and comment on archive  ...  In this article, we review the progress made in neuroimaging databases, their role in data sharing, data management, potential for the construction of brain atlases, recording data provenance, and value  ...  Acknowledgments The authors express their gratitude to our colleagues in the Laboratory of Neuro Imaging (LONI) and those collaborators at our partner laboratories who utilize LONI database and computational  ... 
doi:10.1016/j.neuroimage.2009.03.086 pmid:19371790 pmcid:PMC2754579 fatcat:qxjviytffrexbf7wrn2xfkrns4

High-throughput neuroimaging-genetics computational infrastructure

Ivo D. Dinov, Petros Petrosyan, Zhizhong Liu, Paul Eggert, Sam Hobel, Paul Vespa, Seok Woo Moon, John D. Van Horn, Joseph Franco, Arthur W. Toga
2014 Frontiers in Neuroinformatics  
All data analytics were performed using the LONI Pipeline environment (Dinov et al., 2010; Torri et al., 2012) .  ...  provenance in the form of complex graphical workflows.  ... 
doi:10.3389/fninf.2014.00041 pmid:24795619 pmcid:PMC4005931 fatcat:dcvv5nyiifg47mb33r67qjmf2q

A Serverless Tool for Platform Agnostic Computational Experiment Management [article]

Gregory Kiar, Shawn T Brown, Tristan Glatard, Alan C Evans
2018 arXiv   pre-print
these problems using their own datasets, pipelines, and environments.  ...  Neuroscience has been carried into the domain of big data and high performance computing (HPC) on the backs of initiatives in data collection and an increasingly compute-intensive tools.  ...  Tools and Versions The following is a list of tools and data used in this manuscript, and their respective versions. 2).  ... 
arXiv:1809.07693v1 fatcat:4v33y6ggqzaqdjtrungvm6hol4

Workflow Reuse in Practice: A Study of Neuroimaging Pipeline Users

Daniel Garijo, Oscar Corcho, Yolanda Gil, Meredith N. Braskie, Derrek Hibar, Xue Hua, Neda Jahanshad, Paul Thompson, Arthur W. Toga
2014 2014 IEEE 10th International Conference on e-Science  
This paper reports on a study of the current use of workflows and workflow fragments in labs that use the LONI Pipeline, a popular workflow system used mainly for neuroimaging research that enables users  ...  We also report on a survey of researchers in a lab that has the LONI Pipeline installed, asking them about their experiences with reuse of workflow fragments and the actual benefits they perceive.  ...  ACKNOWLEDGMENTS This research was supported in part by the US National Science Foundation with awards IIS-1344272 and ICER-1343800 (to YG), and by the Spanish Science and Innovation Ministry (MICINN) with  ... 
doi:10.1109/escience.2014.33 dblp:conf/eScience/GarijoCGBHHJTT14 fatcat:o7axyyj53zhftmmmo45j73rvwi

A Serverless Tool for Platform Agnostic Computational Experiment Management

Gregory Kiar, Shawn T. Brown, Tristan Glatard, Alan C. Evans
2019 Frontiers in Neuroinformatics  
these problems using their own datasets, pipelines, and environments.  ...  Neuroscience has been carried into the domain of big data and high performance computing (HPC) on the backs of initiatives in data collection and an increasingly compute-intensive tools.  ...  ACKNOWLEDGMENTS The authors would like to thank Pierre Rioux and Valerie Hayot-Sasson for their insight and many helpful discussions.  ... 
doi:10.3389/fninf.2019.00012 pmid:30890927 pmcid:PMC6411646 fatcat:7uwik54sbjddxd3w553xilt2ha

Gene Interactions and Structural Brain Change in Early-Onset Alzheimer's Disease Subjects Using the Pipeline Environment

Seok Woo Moon, Ivo D. Dinov, Alen Zamanyan, Ran Shi, Alex Genco, Sam Hobel, Paul M. Thompson, Arthur W. Toga
2015 Psychiatry Investigation  
The 15 most important neuroimaging markers were extracted with the Global Shape Analysis (GSA) Pipeline workflow.  ...  However, larger sample sizes are needed to ensure that the effects will be detectable for a reasonable false-positive error rate using the GSA and Plink Pipeline workflows.  ...  Acknowledgments Data used in preparation of this article were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database (http://ADNI.loni. usc.edu).  ... 
doi:10.4306/pi.2015.12.1.125 pmid:25670955 pmcid:PMC4310910 fatcat:doi73ulumnfltg3pwxxbh5zdpq

An Integrated e-Science Analysis Base for Computation Neuroscience Experiments and Analysis

Kamran Munir, Saad Liaquat Kiani, Khawar Hasham, Richard McClatchey, Andrew Branson, Jetendr Shamdasani
2013 Procedia - Social and Behavioral Sciences  
data analysis environment with the necessary building blocks for neuroscientists to optimally exploit neuroscience workflows, large image datasets and algorithms in order to conduct analyses.  ...  The N4U Analysis Base enables such analyses by indexing and interlinking the neuroimaging and clinical study datasets stored on the N4U Grid infrastructure, algorithms and scientific workflow definitions  ...  Acknowledgements This work is funded by the EU 7 th Framework Programme under the N4U project (reference 283562).  ... 
doi:10.1016/j.sbspro.2013.02.026 fatcat:bnqtqmkvcfaynjsyftz332y54u

Using Make for Reproducible and Parallel Neuroimaging Workflow and Quality-Assurance

Mary K. Askren, Trevor K. McAllister-Day, Natalie Koh, Zoé Mestre, Jennifer N. Dines, Benjamin A. Korman, Susan J. Melhorn, Daniel J. Peterson, Matthew Peverill, Xiaoyan Qin, Swati D. Rane, Melissa A. Reilly (+5 others)
2016 Frontiers in Neuroinformatics  
This approach reduces the technical skill and time required to write, debug, and maintain neuroimaging workflows in a dynamic environment, where pipelines are often modified to accommodate new best practices  ...  The contribution of this paper is to describe how we can program neuroimaging workflow using Make, a software development tool designed for describing how to build executables from source files.  ...  ACKNOWLEDGMENTS This research was supported by grants from the National Institutes of Health 1RC4NS073008-01, P50NS062684, the Eunice Kennedy Shriver National Institute of Child Health and Human Development  ... 
doi:10.3389/fninf.2016.00002 pmid:26869916 pmcid:PMC4735413 fatcat:xmg3rv2ltvgihptu56bkgutjq4

Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python

Krzysztof Gorgolewski, Christopher D. Burns, Cindee Madison, Dav Clark, Yaroslav O. Halchenko, Michael L. Waskom, Satrajit S. Ghosh
2011 Frontiers in Neuroinformatics  
We would like to thank James Bednar, Stephan Gerhard, and Helen Ramsden for providing feedback during the preparation of the manuscript.  ...  We would also like to thank the developers of FreeSurfer, FSL, and SPM for being supportive of the project and providing valuable feedback on technical issues.  ...  Although it provides a helpful graphical interface, the LONI Pipeline environment does not provide an easy option to script a workflow or for rapidly exploring parametric variations within a workflow (  ... 
doi:10.3389/fninf.2011.00013 pmid:21897815 pmcid:PMC3159964 fatcat:vzgm5hzdu5dwxor7fhtehusb3m

Providing traceability for neuroimaging analyses

Richard McClatchey, Andrew Branson, Ashiq Anjum, Peter Bloodsworth, Irfan Habib, Kamran Munir, Jetendr Shamdasani, Kamran Soomro
2013 International Journal of Medical Informatics  
It introduces the use of the CRISTAL software to provide provenance management as one of a number of services delivered on a SOA, deployed to manage neuroimaging projects that have been studying biomarkers  ...  Over the past decade, we have been working with mammographers, paediatricians and neuroscientists in three generations of projects to provide the data management and provenance services now required for  ...  Acknowledgements The authors wish to thank their institutes and the European Commission for their support and to  ... 
doi:10.1016/j.ijmedinf.2013.05.005 pmid:23763909 fatcat:c3yyjdxqizgp7hlowa32zfthny
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