Evidence map›Paper›PMID 37562146›Full record

ArticleEpilepsy research2023

Image data harmonization tools for the analysis of post-traumatic epilepsy development in preclinical multisite MRI studies.

Sweta Bhagavatula, Ryan Cabeen, Neil G Harris, Olli Gröhn, David K Wright, Rachael Garner, Alexis Bennett, Celina Alba, Aubrey Martinez, Xavier Ekolle Ndode-Ekane and 24 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Epilepsy research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

34 authors.

Sweta BhagavatulaUSC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA. Electronic address: swetab@usc.edu.
Ryan CabeenUSC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
Neil G HarrisDepartment of Neurology, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, USA.
Olli GröhnA.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
David K WrightDepartments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia.
Rachael GarnerUSC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
Alexis BennettUSC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
Celina AlbaUSC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
Aubrey MartinezUSC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
Xavier Ekolle Ndode-EkaneA.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
Pedro AndradeA.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
Tomi PaananenA.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
Robert CiszekA.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
Riikka ImmonenA.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
Eppu ManninenA.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
Noora PuhakkaA.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
Jussi TohkaA.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
Mette HeiskanenA.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
Idrish AliDepartments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia.
Sandy R ShultzDepartments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia.
Pablo M Casillas-EspinosaDepartments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia.
Glenn R YamakawaDepartments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia.
Nigel C JonesDepartments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia.
Matthew R HudsonDepartments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia.
Juliana C SilvaDepartments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia.
Emma L BraineDepartments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia.
Rhys D BradyDepartments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia.
Cesar E Santana-GomezDepartment of Neurology, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, USA.
Gregory D SmithDepartment of Neurology, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, USA.
Richard StabaDepartment of Neurology, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, USA.
Terence J O'BrienDepartments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia.
Asla PitkänenA.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
Dominique DuncanUSC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
EpiBioS4Rx investigators

Funding

The Epilepsy Bioinformatics Study for Antiepileptogenic Therapy (EpiBioS4Rx) Public Engagement CoreU54NS100064 · NINDS · UNIVERSITY OF SOUTHERN CALIFORNIA · PI VESPA, PAUL M · 2017 to 2021
$21.7M
Translational Platform for Epilepsy Therapy and Biomarker DiscoveryR01NS127524 · NINDS · ALBERT EINSTEIN COLLEGE OF MEDICINE · PI Denes V. Agoston, LISA D COLES · 2022 to 2026
$11.0M
SCH: INT: Collaborative Research: Multimodal Signal Analysis and Data Fusion for Post-traumatic EpilepsyR01NS111744 · NINDS · UNIVERSITY OF SOUTHERN CALIFORNIA · PI DUNCAN, DOMINIQUE, ERDOGMUS, DENIZ · 2019 to 2022
$981k
NINDS NIH HHS R01 NS111744NINDS NIH HHS R01 NS127524NINDS NIH HHS U54 NS100064
6 · The paper itself

Abstract

Preclinical MRI studies have been utilized for the discovery of biomarkers that predict post-traumatic epilepsy (PTE). However, these single site studies often lack statistical power due to limited and homogeneous datasets. Therefore, multisite studies, such as the Epilepsy Bioinformatics Study for Antiepileptogenic Therapy (EpiBioS4Rx), are developed to create large, heterogeneous datasets that can lead to more statistically significant results. EpiBioS4Rx collects preclinical data internationally across sites, including the United States, Finland, and Australia. However, in doing so, there are robust normalization and harmonization processes that are required to obtain statistically significant and generalizable results. This work describes the tools and procedures used to harmonize multisite, multimodal preclinical imaging data acquired by EpiBioS4Rx. There were four main harmonization processes that were utilized, including file format harmonization, naming convention harmonization, image coordinate system harmonization, and diffusion tensor imaging (DTI) metrics harmonization. By using Python tools and bash scripts, the file formats, file names, and image coordinate systems are harmonized across all the sites. To harmonize DTI metrics, values are estimated for each voxel in an image to generate a histogram representing the whole image. Then, the Quantitative Imaging Toolkit (QIT) modules are utilized to scale the mode to a value of one and depict the subsequent harmonized histogram. The standardization of file formats, naming conventions, coordinate systems, and DTI metrics are qualitatively assessed. The histograms of the DTI metrics were generated for all the individual rodents per site. For inter-site analysis, an average of the individual scans was calculated to create a histogram that represents each site. In order to ensure the analysis can be run at the level of individual animals, the sham and TBI cohort were analyzed separately, which depicted the same harmonization factor. The results demonstrate that these processes qualitatively standardize the file formats, naming conventions, coordinate systems, and DTI metrics of the data. This assists in the ability to share data across the study, as well as disseminate tools that can help other researchers to strengthen the statistical power of their studies and analyze data more cohesively.

Indexed as

EpilepsyEpilepsy, Post-TraumaticAnimalsBiomarkersBrainDiffusion Tensor ImagingMagnetic Resonance ImagingBiomarkersEpilepsyMRINeuroimagingPreclinical researchRat modelTBI

Identifiers

PMID37562146
PMCPMC10528111

What OpenQuestion holds

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LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.