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Automatic thalamus and hippocampus segmentation from MP2RAGE: comparison of publicly available methods and implications for DTI quantification.

Abstract：

PURPOSE:In both structural and functional MRI, there is a need for accurate and reliable automatic segmentation of brain regions. Inconsistent segmentation reduces sensitivity and may bias results in clinical studies. The current study compares the performance of publicly available segmentation tools and their impact on diffusion quantification, emphasizing the importance of using recently developed segmentation algorithms and imaging techniques. METHODS:Four publicly available, automatic segmentation methods (volBrain, FSL, FreeSurfer and SPM) are compared to manual segmentation of the thalamus and hippocampus imaged with a recently proposed T1-weighted MRI sequence (MP2RAGE). We evaluate morphometric accuracy on 22 healthy subjects and impact on diffusivity measurements obtained from aligned diffusion-weighted images on a subset of 10 subjects. RESULTS:Compared to manual segmentation, the highest Dice similarity index of the thalamus is obtained with volBrain using a local library ([Formula: see text], [Formula: see text]) followed by volBrain using an external library ([Formula: see text], [Formula: see text]), FSL ([Formula: see text], [Formula: see text]), FreeSurfer ([Formula: see text], [Formula: see text]) and SPM ([Formula: see text], [Formula: see text]). The same order is found for hippocampus with volBrain local ([Formula: see text], [Formula: see text]), volBrain external ([Formula: see text], [Formula: see text]), FSL ([Formula: see text], [Formula: see text]), FreeSurfer ([Formula: see text], [Formula: see text]) and SPM ([Formula: see text], [Formula: see text]). For diffusivity measurements, volBrain provides values closest to those obtained from manual segmentations. volBrain is the only method where FA values do not differ significantly from manual segmentation of the thalamus. CONCLUSIONS:Overall we find that volBrain is superior in thalamus and hippocampus segmentation compared to FSL, FreeSurfer and SPM. Furthermore, the choice of segmentation technique and training library affects quantitative results from diffusivity measures in thalamus and hippocampus.

journal_name

Int J Comput Assist Radiol Surg

journal_title

International journal of computer assisted radiology and surgery

authors

Næss-Schmidt E,Tietze A,Blicher JU,Petersen M,Mikkelsen IK,Coupé P,Manjón JV,Eskildsen SF

doi

10.1007/s11548-016-1433-0

subject

Has Abstract

pub_date

2016-11-01 00:00:00

pages

1979-1991

issue

eissn

1861-6410

issn

1861-6429

pii

10.1007/s11548-016-1433-0

journal_volume

pub_type

杂志文章

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Automatic thalamus and hippocampus segmentation from MP2RAGE: comparison of publicly available methods and implications for DTI quantification.