Efficient, Distributed and Interactive Neuroimaging Data Analysis using the LONI Pipeline

Dinov, Ivo D.; Horn, John D. Van; Lozev, Kamen; Magsipoc, Rico; Petrosyan, Petros; Liu, Zhizhong; MacKenzie-Graham, Allan; Eggert, Paul; Parker, D. Stott; Toga, Arthur W.

doi:10.3389/neuro.11.022.2009

Cited by 140 publications

(149 citation statements)

References 33 publications

Supporting

Mentioning

149

Contrasting

Order By: Relevance

“…The incidence of posttraumatic seizures has been debated over the past 2 decades. 11 These studies focused on clinical seizure activity and did not use cEEG monitoring to define seizures. In contrast, we reported a 22% incidence rate of seizures when detailed, prospective cEEG monitoring of patients with TBI in the ICU was used.…”

Section: Discussionmentioning

confidence: 99%

Nonconvulsive seizures after traumatic brain injury are associated with hippocampal atrophy

Vespa¹,

McArthur²,

Xu³

et al. 2010

Neurology

270

172

View full text Add to dashboard Cite

Objective: To determine if posttraumatic nonconvulsive electrographic seizures result in longterm brain atrophy. Methods:Prospective continuous EEG (cEEG) monitoring was done in 140 patients with moderate to severe traumatic brain injury (TBI) and in-depth study of 16 selected patients was done using serial volumetric MRI acutely and at 6 months after TBI. Fluorodeoxyglucose PET was done in the acute stage in 14/16 patients. These data were retrospectively analyzed after collection of data for 7 years.Results: cEEG detected seizures in 32/140 (23%) of the entire cohort. In the selected imaging subgroup, 6 patients with seizures were compared with a cohort of 10 age-and GCS-matched patients with TBI without seizures. In this subgroup, the seizures were repetitive and constituted status epilepticus in 4/6 patients. Patients with seizures had greater hippocampal atrophy as compared to those without seizures (21 Ϯ 9 vs 12 Ϯ 6%, p ϭ 0.017). Hippocampi ipsilateral to the electrographic seizure focus demonstrated a greater degree of volumetric atrophy as compared with nonseizure hippocampi (28 Ϯ 5 vs 13 Ϯ 9%, p ϭ 0.007). A single patient had an ictal PET scan which demonstrated increased hippocampal glucose uptake. Conclusion:Acute posttraumatic nonconvulsive seizures occur frequently after TBI and, in a selected subgroup, appear to be associated with disproportionate long-term hippocampal atrophy. These data suggest anatomic damage is potentially elicited by nonconvulsive seizures in the acute postinjury setting. Neurology ® 2010;75:792-798 GLOSSARY cEEG ϭ continuous EEG; FLAIR ϭ fluid-attenuated inversion recovery; GCS ϭ Glasgow Coma Scale score; GRE ϭ gradient recalled echo; ICU ϭ intensive care unit; TBI ϭ traumatic brain injury.Neurologic critical care of traumatic brain injury (TBI) focuses on avoiding secondary insults.

show abstract

Section: Discussionmentioning

confidence: 99%

Nonconvulsive seizures after traumatic brain injury are associated with hippocampal atrophy

Vespa¹,

McArthur²,

Xu³

et al. 2010

Neurology

270

172

View full text Add to dashboard Cite

show abstract

“…The LONI Pipeline is a workflow system developed by the Laboratory of Neuro Imaging (LONI) mainly for neuroimaging applications [3] [4]. It provides an efficient distributed computing solution to address common challenges in neuroimaging research, enabling investigators to share, integrate, collaborate and expand resources including data, computing platforms, and analytic algorithms.…”

Section: The Loni Pipelinementioning

confidence: 99%

“…This paper reports on a study on workflow reuse in labs that use a particular workflow system, the LONI Pipeline [3] [4]. The LONI Pipeline includes facilities for users to define subsets of workflows as "groupings" that may be reused by themselves and with others in new workflows.…”

Section: Introductionmentioning

confidence: 99%

Workflow Reuse in Practice: A Study of Neuroimaging Pipeline Users

Garijo

Corcho

Gil

et al. 2014

2014 IEEE 10th International Conference on E-Science

View full text Add to dashboard Cite

Abstract-Workflow reuse is a major benefit of workflow systems and shared workflow repositories, but there are barely any studies that quantify the degree of reuse of workflows or the practical barriers that may stand in the way of successful reuse. In our own work, we hypothesize that defining workflow fragments improves reuse, since end-to-end workflows may be very specific and only partially reusable by others. 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 to define and reuse workflow fragments. We present an overview of the benefits of workflows and workflow fragments reported by users in informal discussions. 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. This leads to quantifiable indicators of the reuse of workflows and workflow fragments in practice. Finally, we discuss barriers to further adoption of workflow fragments and workflow reuse that motivate further work.

show abstract

“…42.8b . Utilizing the Pipeline environment developed by the Laboratory of Neuroimaging at UCLA ( http://pipeline.loni.ucla.edu/ ; [ 80 ] ) we have found that even without age-matching, anatomical brain regions could be mapped accurately. Beside the already available brain atlases, case-specifi c atlases can be developed for particular studies to improve computational performance.…”

Section: Anatomy-specifi C Lesion and Stem Cell Quantifi Cationmentioning

confidence: 99%

Computational Analysis: A Bridge to Translational Stroke Treatment

Ghosh

Sun

Turenius

et al. 2012

Translational Stroke Research

View full text Add to dashboard Cite

Objective rapid quantifi cation of injury using computational methods can improve the assessment of the degree of stroke injury, aid in the selection of patients for early or specifi c treatments, and monitor the evolution of injury and recovery. In this chapter, we use neonatal ischemia as a case-study of the application of several computational methods that in fact are generic and applicable across the age and disease spectrum. We provide a summary of current computational approaches used for injury detection, including Gaussian mixture models (GMM), Markov random fi elds (MRFs), normalized graph cut, and K-means clustering. We also describe more recent automated approaches to segment the region(s) of ischemic injury including hierarchical region splitting, support vector machine, a brain symmetry/asymmetry integrated model, and a watershed method that are robust at different developmental stages. We conclude with our assessment of probable future research directions in the fi eld of computational noninvasive stroke analysis such as automated detection of the ischemic core and penumbra, monitoring of implanted neuronal stem cells in the ischemic brain, injury localization specifi c to different brain anatomical regions, and quantifi cation of stroke evolution, recovery and spatiotemporal interactions between injury volume/severity and treatment. Computational analysis is expected to open a new horizon in current clinical and translational stroke research by exploratory data mining that is not detectable using the standard "methods" of visual assessment of imaging data.

show abstract

Efficient, Distributed and Interactive Neuroimaging Data Analysis using the LONI Pipeline

Cited by 140 publications

References 33 publications

Nonconvulsive seizures after traumatic brain injury are associated with hippocampal atrophy

Nonconvulsive seizures after traumatic brain injury are associated with hippocampal atrophy

Workflow Reuse in Practice: A Study of Neuroimaging Pipeline Users

Computational Analysis: A Bridge to Translational Stroke Treatment

Contact Info

Product

Resources

About