Elsevier

NeuroImage

Volume 54, Issue 2, 15 January 2011, Pages 963-973
NeuroImage

Lesion Explorer: A comprehensive segmentation and parcellation package to obtain regional volumetrics for subcortical hyperintensities and intracranial tissue

https://doi.org/10.1016/j.neuroimage.2010.09.013Get rights and content

Abstract

Subcortical hyperintensities (SH) are a commonly observed phenomenon on MRI of the aging brain (Kertesz et al., 1988). Conflicting behavioral, cognitive and pathological associations reported in the literature underline the need to develop an intracranial volumetric analysis technique to elucidate pathophysiological origins of SH in Alzheimer's disease (AD), vascular cognitive impairment (VCI) and normal aging (De Leeuw et al., 2001, Mayer and Kier, 1991, Pantoni and Garcia, 1997, Sachdev et al., 2008). The challenge is to develop processing tools that effectively and reliably quantify subcortical small vessel disease in the context of brain tissue compartments. Segmentation and brain region parcellation should account for SH subtypes which are often classified as: periventricular (pvSH) and deep white (dwSH), incidental white matter disease or lacunar infarcts and Virchow–Robin spaces. Lesion Explorer (LE) was developed as the final component of a comprehensive volumetric segmentation and parcellation image processing stream built upon previously published methods (Dade et al., 2004, Kovacevic et al., 2002). Inter-rater and inter-method reliability was accomplished both globally and regionally. Volumetric analysis showed high inter-rater reliability both globally (ICC = .99) and regionally (ICC = .98). Pixel-wise spatial congruence was also high (SI = .97). Whole brain pvSH volumes yielded high inter-rater reliability (ICC = .99). Volumetric analysis against an alternative kNN segmentation revealed high inter-method reliability (ICC = .97). Comparison with visual rating scales showed high significant correlations (ARWMC: r = .86; CHIPS: r = .87). The pipeline yields a comprehensive and reliable individualized volumetric profile for subcortical vasculopathy that includes regionalized (26 brain regions) measures for: GM, WM, sCSF, vCSF, lacunar and non-lacunar pvSH and dwSH.

Research highlights

►Lesion Explorer segmentation and parcellation of structural MRI show high reliability. ►LE allows for segmentation of periventricular, deep white, VR, and lacunar subtypes. ►LE provides comprehensive volumetric profiles to examine subcortical vasculopathy.

Introduction

Subcortical hyperintensities (SH) are frequently observed on T2-weighted MRI of the aging brain (Jack et al., 2001, Kertesz et al., 1988, Longstreth et al., 1996). Clinico-pathological correlations suggest vascular and degenerative origins including: ischemic tissue damage via arteriosclerosis (Babikian and Ropper, 1987, van Swieten et al., 1991); vasogenic edema from periventricular venous collagenosis (Black et al., 2009, Gao et al., 2008, Moody et al., 1995); multiple lacunar infarcts (Longstreth et al., 1996); état criblé or dilated perivascular spaces (Awad et al., 1986); demyelination and subependymal gliosis; amyloid angiopathy (Pantoni and Garcia, 1997); and clasmatodendrosis (Sahlas et al., 2002).

Although the pathophysiological origins are not fully understood, the current literature suggests that SH: are common after age 60 (Longstreth et al., 1996); share common cerebrovascular risk factors such as diabetes and hypertension (De Leeuw et al., 2001, Liao et al., 1996, Sachdev et al., 2008); and are associated with increased risk of cognitive decline, stroke, gait disorders and neuropsychiatric disorders (De Groot et al., 2001, Koga et al., 2009, Longstreth et al., 1996, Longstreth et al., 2005, Srikanth et al., 2009, Vermeer et al., 2003a, Vermeer et al., 2003b). To further assess the effects of vascular risk factors in overt and covert cerebrovascular disease and in dementia, consensus criteria were developed that underline the importance of accounting for SH in studies on aging (Hachinski et al., 2006).

Although visual scales can provide quick ratings of SH severity on MRI (Bocti et al., 2005, Fazekas et al., 1987, Scheltens et al., 1993, Wahlund et al., 2001), inconsistencies in methodological properties (Mantyla et al., 1997) have led some researchers to apply intensity-based segmentation techniques that provide a more accurate estimation of SH burden — as well as quantify their extent and location. However, typical T1-based tissue segmentation techniques that do not explicitly segment T2 hyperintensities can inflate other tissue volumes. Depending on the segmentation technique used, gray matter volumes can be overestimated by failing to segment the hyperintensities (Levy-Cooperman et al., 2008), see Fig. 7 for example.

Quantitative segmentation approaches have been applied to capture SH on T2, proton density (PD) and fluid-attenuated inversion recovery (FLAIR) images. Some of the recent approaches in the last decade include: fuzzy clustering models that include a lesion class (Admiraal-Behloul et al., 2005, Gosche et al., 1999); Gaussian curve fitting to determine lesion intensity cut-off points (Decarli et al., 2005a); modal intensity cut-offs applied to slice-by-slice intensity histograms (Jack et al., 2001); k-Nearest Neighbor (kNN) algorithmic combination approaches (Anbeek et al., 2004, Seghier et al., 2008, Swartz et al., 2002, Wen et al., 2008); and coregistration to normal templates comparing the voxel-wise SH probabilities from FLAIR images to a white matter probability map using a weighting function (Burton et al., 2004, Wen and Sachdev, 2004). These approaches range from fully automated to semi-automated labor intensive processes.

Fully automated techniques offer the advantage of high reliability and are preferable for processing large scale studies. They typically require FLAIR imaging, where SH are often more conspicuous relative to standard PD/T2 images. However, FLAIR imaging is less sensitive in detecting focal thalamic lesions (Bastos Leite et al., 2004, Jack et al., 2001) and was not included in the multi-center Alzheimer's Disease Neuroimaging Initiative (ADNI) acquisitions (Jack et al., 2008). Furthermore, FLAIR imaging alone cannot disambiguate the possible heterogeneity that is implicated in SH pathology.

In an attempt to address the hypothesis of pathological heterogeneity within SH, various subtypes have been suggested for further segmentation. One common, albeit controversial, distinction is between periventricular (pvSH) and deep white (dwSH) subcortical hyperintensities (Decarli et al., 2005a, Sachdev and Wen, 2005). Although dwSH and pvSH volumes are correlated (Decarli et al., 2005a), some studies have shown pvSH and dwSH to be differentially associated with: gray matter atrophy; ventricular dilatation; and cognitive, behavioral and motor/gait performance (Sachdev and Wen, 2005, Sachdev et al., 2005, Silbert et al., 2008).

Lack of a standardized methodology for the definition of pvSH may be the cause of inconsistent reports in the literature. The typical method to distinguish pvSH from dwSH is to create an arbitrary two-dimensional cut-off line lateral to the ventricles on axial slices in a slice-by-slice manner. This arbitrary line is sometimes calculated as a proportional distance from the ventricular border to the dura mater (Decarli et al., 2005a), or set using an arbitrary voxel distance from the ventricle out into the centrum semiovale. Some reviewers have suggested that there may be some neuroanatomic justification for classifying SH within a 13 mm rim around the ventricle as pvSH (Mayer and Kier, 1991, Sachdev et al., 2008). Various other methods arbitrarily delineate pvSH from dwSH using a linear distance calculation. However, a standardized, unbiased method that recognizes the 3-dimensional nature of SH would be preferable.

Other subtypes of SH include perivascular (Virchow–Robin) spaces and cystic fluid-filled lacunar-like infarcts. Virchow–Robin (VR) spaces are CSF-filled extensions of the subarachnoid space in the sheath surrounding blood vessels. They appear as hyperintense dots or lines on T2 images, are isointense on PD and typically 1 mm or less in diameter (Awad et al., 1986). Their size, shape, and differential appearance on T2 and PD allow them to be distinguished from other SH subtypes — including lacunes.

Automatic segmentation of lacunes is less common since this requires coregistration of T2/PD/FLAIR images to a T1-based segmentation, in order to identify CSF intensity within SH. Lacunes are associated with aging, hypertension, increased risk of stroke, and are found in 11–28% of elderly (Longstreth et al., 1998, Vermeer et al., 2003b, Vermeer et al., 2007). These so-called silent strokes or covert infarcts, are usually defined as 3–15 mm in diameter, are hypointense on T1, and hyperintense on both T2 and PD images. Their presence is associated with increased risk of dementia and have been correlated with decreased frontal lobe glucose metabolism with positron emission tomography (PET) imaging (Reed et al., 2004). However, without a coregistered T1-segmentation and PD-T2 contrast for comparison, lacunes and VR spaces are difficult to quantify through volumetric segmentation with FLAIR alone.

An additional benefit of a T1-based tissue segmentation combined with PD-T2-based SH segmentation is that it allows for relative volumetric tissue comparisons for gray matter (GM), white matter (WM), ventricular-CSF (vCSF) and sulcal-CSF (sCSF). However, whole brain global volumetrics alone provide limited information, and regionalized quantification, whether ROI-based or template-based, has become a standard expectation for any MRI-based segmentation procedure.

Hence, the need for a comprehensive, individualized MRI processing pipeline that reliably segments the brain into regionalized tissue compartments and includes the various SH subtypes has become increasingly important. Lesion Explorer (LE) is the final component of an MRI-based processing pipeline that was developed with these considerations. It was built upon updated versions of two previously published components: an automated T1-based tissue segmentation protocol (Kovacevic et al., 2002); and the Semi-Automated Brain Region Extraction (SABRE) parcellation procedure (Dade et al., 2004). The LE pipeline makes use of 3 processing components that effectively allow comprehensive analysis of individual brains through the segmentation of 8 tissue classes: GM, WM, sCSF, vCSF, lacunar and non-lacunar pvSH and dwSH — tissue volumes are then parcellated into 26 SABRE brain regions. Inter-rater and inter-method reliability data is presented with validation against an alternative kNN segmentation approach and 2 different visual rating scales.

Section snippets

Subjects

Images used for this study (n = 20) were selected from participants in the Sunnybrook Dementia Study — a large ongoing longitudinal observational study conducted in the LC Campbell Cognitive Neurology Research Unit and the Heart & Stroke Foundation Centre for Stroke Recovery (http://www.heartandstroke-centrestrokerecovery.ca) at Sunnybrook Health Sciences Centre, a University of Toronto academic healthcare institution. See Table 1 for additional details. Exclusion criteria for this sub-study

Whole brain results

Whole brain mean absolute volume differences between the two raters was 230 mm3 with the following results: ICC = .99, p < .0001, and mean SI = .97, indicating excellent inter-rater reliability for whole brain volumetric and pixel-wise spatial agreement (see Table 1 for raw data). Compared to volumes from a previously published semi-automated segmentation using a kNN algorithm, high reliability was also demonstrated (ICC = .97, p < .0001). Whole brain segmentation of pvSH volumes also yielded high

Discussion

Lesion Explorer is the final component of a comprehensive segmentation and parcellation package that provides an individualized volumetric profile from standard structural MRI. The overall MRI volumetrics package is a reliable application that may be used with confidence in aging populations for both cross-sectional, and longitudinal studies with a standard structural acquisition protocol.

The brain-extraction component, Brain-Sizer, provides an accurate measure of an individual's total

Acknowledgments

The authors gratefully acknowledge financial support from the following sources. The development and testing of this image analysis pipeline was supported by several grants, most notably from the Canadian Institutes of Health Research (MT#13129), the Alzheimer Society of Canada and Alzheimer Association (US), the Heart and Stroke Foundation Centre for Stroke Recovery, and the LC Campbell Foundation. JR receives salary support from the Alzheimer Society of Canada; BL from CIHR; NLC from U of T

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