Ardekani BA, Guckemus S, Bachman A, Hoptman MJ, Wojtaszek M, Nierenberg J. Quantitative comparison of inter-subject volumetric MRI registration methods. J Neurosci Methods 142: 67-76

Center for Advanced Brain Imaging, Nathan Kline Institute for Psychiatric Research, 140 Old Orangeburg Road, Orangeburg, NY 10962, USA.
Journal of Neuroscience Methods (Impact Factor: 2.05). 04/2005; 142(1):67-76. DOI: 10.1016/j.jneumeth.2004.07.014
Source: PubMed


The objective of inter-subject registration of three-dimensional volumetric brain scans is to reduce the anatomical variability between the images scanned from different individuals. This is a necessary step in many different applications such as voxelwise group analysis of imaging data obtained from different individuals. In this paper, the ability of three different image registration algorithms in reducing inter-subject anatomical variability is quantitatively compared using a set of common high-resolution volumetric magnetic resonance imaging scans from 17 subjects. The algorithms are from the automatic image registration (AIR; version 5), the statistical parametric mapping (SPM99), and the automatic registration toolbox (ART) packages. The latter includes the implementation of a non-linear image registration algorithm, details of which are presented in this paper. The accuracy of registration is quantified in terms of two independent measures: (1) post-registration spatial dispersion of sets of homologous landmarks manually identified on images before or after registration; and (2) voxelwise image standard deviation maps computed within the set of images registered by each algorithm. Both measures showed that the ART algorithm is clearly superior to both AIR and SPM99 in reducing inter-subject anatomical variability. The spatial dispersion measure was found to be more sensitive when the landmarks were placed after image registration. The standard deviation measure was found sensitive to intensity normalization or the method of image interpolation.

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    • "Using an automated method, data from large sample sizes can be analyzed using standardized analysis algorithms with minimal time and monetary cost. These algorithms utilize either volume-based [Ardekani et al., 2005; Gholipour et al., 2007; Klein et al., 2009; Tustison et al., 2014] or surface-based [Davatzikos et al., 1996; Fischl et al., 1999; Hinds et al., 2009; Khan et al., 2011; Liem et al., 2015; Storsve et al., 2014; Tosun and Prince, 2008] registrations. Volume-based registrations have been shown to result in high intersubject variability as their use of intensities to define cortical regions causes poor anatomical delineation [Ghosh et al., 2010]. "
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    ABSTRACT: In the last decade, many studies have used automated processes to analyze magnetic resonance imaging (MRI) data such as cortical thickness, which is one indicator of neuronal health. Due to the convenience of image processing software (e.g., FreeSurfer), standard practice is to rely on automated results without performing visual inspection of intermediate processing. In this work, structural MRIs of 40 healthy controls who were scanned twice were used to determine the test-retest reliability of FreeSurfer-derived cortical measures in four groups of subjects-those 25 that passed visual inspection (approved), those 15 that failed visual inspection (disapproved), a combined group, and a subset of 10 subjects (Travel) whose test and retest scans occurred at different sites. Test-retest correlation (TRC), intraclass correlation coefficient (ICC), and percent difference (PD) were used to measure the reliability in the Destrieux and Desikan-Killiany (DK) atlases. In the approved subjects, reliability of cortical thickness/surface area/volume (DK atlas only) were: TRC (0.82/0.88/0.88), ICC (0.81/0.87/0.88), PD (0.86/1.19/1.39), which represent a significant improvement over these measures when disapproved subjects are included. Travel subjects' results show that cortical thickness reliability is more sensitive to site differences than the cortical surface area and volume. To determine the effect of visual inspection on sample size required for studies of MRI-derived cortical thickness, the number of subjects required to show group differences was calculated. Significant differences observed across imaging sites, between visually approved/disapproved subjects, and across regions with different sizes suggest that these measures should be used with caution. Hum Brain Mapp, 2015. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.
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    • "The total volume of brain tissue affected by WMH was measured for each participant and then divided by the corresponding ICV. For each subject, the average T 1 -weighted MPRAGE data in FLAIR space were non-linearly registered to those of all other participants using the Automatic Registration Toolbox (ART) (Ardekani et al. 2005). The resulting ART transformations were averaged and applied to the map of WMH of the subject. "
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    ABSTRACT: Both presence of white matter hyperintensities (WMH) and smaller total gray matter volume on brain magnetic resonance imaging (MRI) are common findings in old age, and contribute to impaired cognition. We tested whether total WMH volume and gray matter volume had independent associations with cognition in community-dwelling individuals without dementia or mild cognitive impairment (MCI). We used data from participants of the Rush Memory and Aging Project. Brain MRI was available in 209 subjects without dementia or MCI (mean age 80; education = 15 years; 74 % women). WMH and gray matter were automatically segmented, and the total WMH and gray matter volumes were measured. Both MRI-derived measures were normalized by the intracranial volume. Cognitive data included composite measures of five different cognitive domains, based on 19 individual tests. Linear regression analyses, adjusted for age, sex, and education, were used to examine the relationship of logarithmically-transformed total WMH volume and of total gray matter volume to cognition. Larger total WMH volumes were associated with lower levels of perceptual speed (p < 0.001), but not with episodic memory, semantic memory, working memory, or visuospatial abilities (all p > 0.10). Smaller total gray matter volumes were associated with lower levels of perceptual speed (p = 0.013) and episodic memory (p = 0.001), but not with the other three cognitive domains (all p > 0.14). Larger total WMH volume was correlated with smaller total gray matter volume (p < 0.001). In a model with both MRI-derived measures included, the relation of WMH to perceptual speed remained significant (p < 0.001), while gray matter volumes were no longer related (p = 0.14). This study of older community-dwelling individuals without overt cognitive impairment suggests that the association of larger total WMH volume with lower perceptual speed is independent of total gray matter volume. These results help elucidate the pathological processes leading to lower cognitive function in aging.
    Full-text · Article · Apr 2015 · Brain Structure and Function
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    • "For parametric analysis, V T /f P was calculated at every voxel using Bayesian estimation in graphical analysis (Zanderigo et al., 2010), a fully automatic approach that incorporates LEGA V T estimation in a Bayesian framework. Voxel images were placed in standard space as follows: each subject's MRI was nonlinearly warped to a high-resolution MRI template (Holmes et al., 1998) using the Automatic Registration Toolbox (ART, Ardekani et al. 2005). Voxel maps (V T /f P ) were then warped to this space using the PET-to-MRI coregistration and the ARTderived nonlinear transformation. "
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    ABSTRACT: Background Interferon- (IFN-) therapy is frequently associated with disabling depression, fatigue, and related neuropsychiatric effects. Although depression in major depressive disorder is associated with low serotonin transporter binding, animal models suggest that IFN-associated mood effects are linked to increased presynaptic serotonin transporter binding. This study tested the hypotheses that IFN administration to human subjects increases presynaptic serotonin binding activity, and that this effect correlates with incident depression symptoms. Methods Positron emission tomography (PET) scans using [C-11]-DASB were obtained for nine hepatitis C patients before and after IFN- treatment for 8 weeks. Serotonin transporter binding was estimated using the likelihood estimation in graphical analysis (LEGA) model and measured as the volume of distribution (V-T) divided by the free fraction of ligand (f(P)). Depression was measured with the Structured Clinical Interview for DSM-IV Diagnosis (SCID) and the Hamilton Rating Scale for Depression (HAM-D). ResultsCompared to pre-IFN treatment values, changes in serotonin transporter binding and depression symptoms were not significant. There was no correlation between changes in serotonin transporter binding and depression symptoms. LimitationsThe study is limited by small sample size, minimal effect on observed mood symptoms within the sample, and brief duration of follow-up. Conclusion These findings do not support the hypothesis of an IFN-induced change in serotonin transporter function as the cause of incident depressive symptoms in patients treated with IFN-. Additional study of these possible relationships should be of longer duration and include more subjects with more pronounced changes in mood. Synapse 68:548-555, 2014. (c) 2014 Wiley Periodicals, Inc.
    Full-text · Article · Nov 2014 · Synapse
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