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

Autor:	Bhagavatula S; USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA. Electronic address: swetab@usc.edu., Cabeen R; USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA., Harris NG; Department of Neurology, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, USA., Gröhn O; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland., Wright DK; Departments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia., Garner R; USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA., Bennett A; USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA., Alba C; USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA., Martinez A; USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA., Ndode-Ekane XE; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland., Andrade P; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland., Paananen T; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland., Ciszek R; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland., Immonen R; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland., Manninen E; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland., Puhakka N; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland., Tohka J; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland., Heiskanen M; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland., Ali I; Departments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia., Shultz SR; Departments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia., Casillas-Espinosa PM; Departments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia., Yamakawa GR; Departments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia., Jones NC; Departments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia., Hudson MR; Departments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia., Silva JC; Departments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia., Braine EL; Departments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia., Brady RD; Departments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia., Santana-Gomez CE; Department of Neurology, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, USA., Smith GD; Department of Neurology, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, USA., Staba R; Department of Neurology, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, USA., O'Brien TJ; Departments of Neuroscience and Neurology, Central Clinical School, Alfred Health, Monash University, Melbourne, Victoria, Australia., Pitkänen A; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland., Duncan D; USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
Jazyk:	angličtina
Zdroj:	Epilepsy research [Epilepsy Res] 2023 Sep; Vol. 195, pp. 107201. Date of Electronic Publication: 2023 Aug 02.
DOI:	10.1016/j.eplepsyres.2023.107201
Abstrakt:	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. (Copyright © 2023 Elsevier B.V. All rights reserved.)
Databáze:	MEDLINE
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