Neuroimaging study designs, computational analyses and data provenance using the LONI pipeline.
Ivo D. Dinov,Kamen Lozev,Petros Petrosyan,Zhizhong Liu,Paul Eggert,Jonathan Pierce,Alen Zamanyan,Shruthi Chakrapani,John D. Van Horn,D. Stott Parker,Rico Magsipoc,Kelvin T. Leung,Boris A. Gutman,Roger P. Woods,Arthur W. Toga +14 more
TLDR
The LONI Pipeline features include distributed grid-enabled infrastructure, virtualized execution environment, efficient integration, data provenance, validation and distribution of new computational tools, automated data format conversion, and an intuitive graphical user interface.Abstract:
Modern computational neuroscience employs diverse software tools and multidisciplinary expertise to analyze heterogeneous brain data. The classical problems of gathering meaningful data, fitting specific models, and discovering appropriate analysis and visualization tools give way to a new class of computational challenges—management of large and incongruous data, integration and interoperability of computational resources, and data provenance. We designed, implemented and validated a new paradigm for addressing these challenges in the neuroimaging field. Our solution is based on the LONI Pipeline environment [3], [4], a graphical workflow environment for constructing and executing complex data processing protocols. We developed study-design, database and visual language programming functionalities within the LONI Pipeline that enable the construction of complete, elaborate and robust graphical workflows for analyzing neuroimaging and other data. These workflows facilitate open sharing and communication of data and metadata, concrete processing protocols, result validation, and study replication among different investigators and research groups. The LONI Pipeline features include distributed grid-enabled infrastructure, virtualized execution environment, efficient integration, data provenance, validation and distribution of new computational tools, automated data format conversion, and an intuitive graphical user interface. We demonstrate the new LONI Pipeline features using large scale neuroimaging studies based on data from the International Consortium for Brain Mapping [5] and the Alzheimer's Disease Neuroimaging Initiative [6]. User guides, forums, instructions and downloads of the LONI Pipeline environment are available at http://pipeline.loni.ucla.edu.read more
Citations
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Journal ArticleDOI
Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python
Krzysztof J. Gorgolewski,Christopher Burns,Cindee Madison,Dav Clark,Yaroslav O. Halchenko,Michael Waskom,Satrajit S. Ghosh +6 more
TL;DR: Nipype solves issues by providing Interfaces to existing neuroimaging software with uniform usage semantics and by facilitating interaction between these packages using Workflows, and provides an environment that encourages interactive exploration of algorithms, eases the design of Workflows within and between packages, and reduces the learning Curve.
Journal ArticleDOI
Blood-brain barrier breakdown is an early biomarker of human cognitive dysfunction.
Daniel A. Nation,Melanie D. Sweeney,Axel Montagne,Abhay P. Sagare,Lina M. D'Orazio,Maricarmen Pachicano,Farshid Sepehrband,Amy R. Nelson,David P. Buennagel,Michael G. Harrington,Tammie L.S. Benzinger,Anne M. Fagan,John M. Ringman,Lon S. Schneider,John C. Morris,Helena C. Chui,Meng Law,Arthur W. Toga,Berislav V. Zlokovic +18 more
TL;DR: Neuroimaging and cerebrospinal fluid analyses in humans reveal that loss of blood–brain barrier integrity and brain capillary pericyte damage are early biomarkers of cognitive impairment that occur independently of changes in amyloid-β and tau.
Journal ArticleDOI
APOE4 leads to blood–brain barrier dysfunction predicting cognitive decline
Axel Montagne,Daniel A. Nation,Abhay P. Sagare,Giuseppe Barisano,Melanie D. Sweeney,Ararat Chakhoyan,Maricarmen Pachicano,Elizabeth Joe,Amy R. Nelson,Lina M. D'Orazio,David P. Buennagel,Michael G. Harrington,Tammie L.S. Benzinger,Anne M. Fagan,John M. Ringman,Lon S. Schneider,John C. Morris,Eric M. Reiman,Richard J. Caselli,Helena C. Chui,Julia Tcw,Yining Chen,Judy Pa,Peter S. Conti,Meng Law,Meng Law,Arthur W. Toga,Berislav V. Zlokovic +27 more
TL;DR: The findings suggest that breakdown of the BBB contributes to APOE4-associated cognitive decline independently of Alzheimer’s disease pathology, and might be a therapeutic target inAPOE4 carriers.
Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python
Krzysztof J. Gorgolewski,Christopher Burns,Cindee Madison,Dav Clark,Yaroslav O. Halchenko,Michael Waskom,Satrajit S. Ghosh +6 more
TL;DR: Neuroimaging in Python: Pipelines and interfaces as discussed by the authors is an open-source, community-developed, software package and scriptable library for neuroimaging analysis using Python.
Journal ArticleDOI
Making big data open: Data sharing in neuroimaging
TL;DR: The state of data sharing for task-based functional MRI (fMRI) data is outlined, with a focus on various forms of data and their relative utility for subsequent analyses.
References
More filters
Journal ArticleDOI
Advances in functional and structural MR image analysis and implementation as FSL.
Stephen M. Smith,Mark Jenkinson,Mark W. Woolrich,Mark W. Woolrich,Christian F. Beckmann,Behrens Tej.,Heidi Johansen-Berg,Peter R. Bannister,M De Luca,Ivana Drobnjak,D E Flitney,Rami K. Niazy,J Saunders,J Vickers,Yongyue Zhang,N. De Stefano,J M Brady,Paul M. Matthews +17 more
TL;DR: A review of the research carried out by the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB) on the development of new methodologies for the analysis of both structural and functional magnetic resonance imaging data.
Journal ArticleDOI
AFNI: software for analysis and visualization of functional magnetic resonance neuroimages
TL;DR: A package of computer programs for analysis and visualization of three-dimensional human brain functional magnetic resonance imaging (FMRI) results is described and techniques for automatically generating transformed functional data sets from manually labeled anatomical data sets are described.
Journal ArticleDOI
The Alzheimer's Disease Neuroimaging Initiative (ADNI): MRI methods.
Clifford R. Jack,Matt A. Bernstein,Nick C. Fox,Paul M. Thompson,Gene E. Alexander,Danielle J Harvey,Bret J. Borowski,Paula J. Britson,Jennifer L. Whitwell,Chadwick P. Ward,Anders M. Dale,Joel P. Felmlee,Jeffrey L. Gunter,Derek L. G. Hill,Ronald J. Killiany,Norbert Schuff,Sabrina Fox-Bosetti,Chen Lin,Colin Studholme,Charles DeCarli,Gunnar Krueger,Heidi A. Ward,Gregory J. Metzger,Katherine T. Scott,Richard Philip Mallozzi,Daniel J. Blezek,Joshua Levy,Josef Phillip Debbins,Adam S. Fleisher,Marilyn S. Albert,Robert C. Green,George Bartzokis,Gary H. Glover,John P. Mugler,Michael W. Weiner +34 more
TL;DR: The approach taken in ADNI to standardization across sites and platforms of the MRI protocol, postacquisition corrections, and phantom‐based monitoring of all scanners could be used as a model for other multisite trials.
Journal ArticleDOI
Automatic 3D intersubject registration of MR volumetric data in standardized Talairach space
TL;DR: A fully automatic registration method to map volumetric data into stereotaxic space that yields results comparable with those of manually based techniques and therefore does not suffer the drawbacks involved in user intervention.
Journal ArticleDOI
Population-based norms for the mini-mental state examination by age and educational level
TL;DR: Results presented should prove to be useful to clinicians who wish to compare an individual patient's MMSE scores with a population reference group and to researchers making plans for new studies in which cognitive status is a variable of interest.
Related Papers (5)
The Alzheimer's Disease Neuroimaging Initiative (ADNI): MRI methods.
Clifford R. Jack,Matt A. Bernstein,Nick C. Fox,Paul M. Thompson,Gene E. Alexander,Danielle J Harvey,Bret J. Borowski,Paula J. Britson,Jennifer L. Whitwell,Chadwick P. Ward,Anders M. Dale,Joel P. Felmlee,Jeffrey L. Gunter,Derek L. G. Hill,Ronald J. Killiany,Norbert Schuff,Sabrina Fox-Bosetti,Chen Lin,Colin Studholme,Charles DeCarli,Gunnar Krueger,Heidi A. Ward,Gregory J. Metzger,Katherine T. Scott,Richard Philip Mallozzi,Daniel J. Blezek,Joshua Levy,Josef Phillip Debbins,Adam S. Fleisher,Marilyn S. Albert,Robert C. Green,George Bartzokis,Gary H. Glover,John P. Mugler,Michael W. Weiner +34 more