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Neuroimaging Data Provenance Using the LONI Pipeline Workflow Environment
[chapter]
2008
Lecture Notes in Computer Science
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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
2010
PLoS ONE
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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
2008
NeuroImage
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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]
2015
Lecture Notes in Computer Science
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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
2015
Brain Imaging and Behavior
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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?
2009
NeuroImage
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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
2014
Frontiers in Neuroinformatics
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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]
2018
arXiv
pre-print
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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
2014
2014 IEEE 10th International Conference on e-Science
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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
2019
Frontiers in Neuroinformatics
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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
2015
Psychiatry Investigation
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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
2013
Procedia - Social and Behavioral Sciences
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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
2016
Frontiers in Neuroinformatics
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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
2011
Frontiers in Neuroinformatics
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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
2013
International Journal of Medical Informatics
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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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