A1 Refereed original research article in a scientific journal

Subcortical and hippocampal brain segmentation in 5-year-old children: Validation of FSL-FIRST and FreeSurfer against manual segmentation




AuthorsLidauer Kristian, Pulli Elmo P., Copeland Anni, Silver Eero, Kumpulainen Venla, Hashempour Niloofar, Merisaari Harri, Saunavaara Jani, Parkkola Riitta, Lähdesmäki Tuire, Saukko Ekaterina, Nolvi Saara, Kataja Eeva-Leena, Karlsson Linnea, Karlsson Hasse, Tuulari Jetro J.

PublisherWILEY

Publication year2022

JournalEuropean Journal of Neuroscience

Journal acronymEUR J NEUROSCI

Volume56

Issue5

First page 4619

Last page4641

Number of pages23

ISSN0953-816X

eISSN1460-9568

DOIhttps://doi.org/10.1111/ejn.15761

Web address https://onlinelibrary.wiley.com/doi/10.1111/ejn.15761

Self-archived copy’s web addresshttps://research.utu.fi/converis/portal/detail/Publication/176170660


Abstract

Developing accurate subcortical volumetric quantification tools is crucial for neurodevelopmental studies, as they could reduce the need for challenging and time-consuming manual segmentation. In this study, the accuracy of two automated segmentation tools, FSL-FIRST (with three different boundary correction settings) and FreeSurfer, were compared against manual segmentation of the hippocampus and subcortical nuclei, including the amygdala, thalamus, putamen, globus pallidus, caudate and nucleus accumbens, using volumetric and correlation analyses in 80 5-year-olds.

Both FSL-FIRST and FreeSurfer overestimated the volume on all structures except the caudate, and the accuracy varied depending on the structure. Small structures such as the amygdala and nucleus accumbens, which are visually difficult to distinguish, produced significant overestimations and weaker correlations with all automated methods. Larger and more readily distinguishable structures such as the caudate and putamen produced notably lower overestimations and stronger correlations. Overall, the segmentations performed by FSL-FIRST's default pipeline were the most accurate, whereas FreeSurfer's results were weaker across the structures.

In line with prior studies, the accuracy of automated segmentation tools was imperfect with respect to manually defined structures. However, apart from amygdala and nucleus accumbens, FSL-FIRST's agreement could be considered satisfactory (Pearson correlation > 0.74, intraclass correlation coefficient (ICC) > 0.68 and Dice score coefficient (DSC) > 0.87) with highest values for the striatal structures (putamen, globus pallidus, caudate) (Pearson correlation > 0.77, ICC > 0.87 and DSC > 0.88, respectively). Overall, automated segmentation tools do not always provide satisfactory results, and careful visual inspection of the automated segmentations is strongly advised.


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Last updated on 2024-26-11 at 21:18