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A Comparative Analysis of MRI Automated Segmentation of Subcortical Brain Volumes in a Large Dataset of Elderly Subjects

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Abstract

In this study, we perform a comparative analysis of automated image segmentation of subcortical structures in the elderly brain. Manual segmentation is very time-consuming and automated methods are gaining importance as a clinical tool for diagnosis. The two most commonly used software libraries for brain segmentation -FreeSurfer and FSL- are put to work in a large dataset of 4,028 magnetic resonance imaging (MRI) scans collected for this study. We find a lack of linear correlation between the segmentation volume estimates obtained from FreeSurfer and FSL. On the other hand, FreeSurfer volume estimates tend to be larger thanFSL estimates of the areas putamen, thalamus, amygdala, caudate, pallidum, hippocampus, and accumbens. The characterization of the performance of brain segmentation algorithms in large datasets as the one presented here is a necessary step towards partially or fully automated end-to-end neuroimaging workflow both in clinical and research settings.

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Acknowledgements

The authors would like to thank the generous persons that volunteered to participate in the study and Fundación Reina Sofía for their support. The authors acknowledge funding from Ministerio de Ciencia, Innovación y Universidades (CONNECT-AD) RTI2018-098762-B-C31 and and Structural Funds ERDF (INTERREG V-A Spain-Portugal (POCTEP) Grant: 0348CIE6E).

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  1. Instituto de Salud Carlos III, Centro de Alzheimer Fundación Reina Sofía, Madrid, Spain

    Jaime Gomez-Ramirez, Javier Quilis-Sancho & Miguel A. Fernandez-Blazquez

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  1. Jaime Gomez-Ramirez
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  3. Miguel A. Fernandez-Blazquez
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Correspondence to Jaime Gomez-Ramirez.

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Code and all data used in this research are publicly available on the Github repository under an Apache 2.0 license at https://github.com/grjd/automaticsegmentation. Part of the pre-processing code depends on FSL and FreeSurfer. Both software libraries are only licensed for non-commercial use and are freely available.

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Gomez-Ramirez, J., Quilis-Sancho, J. & Fernandez-Blazquez, M.A. A Comparative Analysis of MRI Automated Segmentation of Subcortical Brain Volumes in a Large Dataset of Elderly Subjects. Neuroinform 20, 63–72 (2022). https://doi.org/10.1007/s12021-021-09520-z

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