Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration

Klein, Arno; Andersson, Jesper; Ardekani, Babak A.; Ashburner, John; Avants, Brian B.; Chiang, Ming‐Chang; Christensen, Gary E.; Collins, D. Louis; Gee, James C.; Hellier, Pierre; Song, Joo‐Hyun; Jenkinson, Mark; Lepage, Claude; Rueckert, Daniel; Thompson, Paul M.; Vercauteren, Tom; Woods, Roger P.; Mann, J. John; Parsey, Ramin V.

doi:10.1016/j.neuroimage.2008.12.037

Cited by 2,027 publications

(1,830 citation statements)

References 69 publications

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“…For comparison across participants, we created a study‐specific FA‐template based on all available images using Advanced Normalization Tools (ANTs) algorithms (Avants et al., 2014; Lawson, Duda, Avants, Wu, & Farah, 2013), which showed the highest accuracy in software comparisons (Klein et al., 2009; Murphy et al., 2011; Tustison et al., 2014). Individual images were transformed to template space using non‐linear registration with symmetric diffeomorphic normalization as implemented in ANTs (Avants, Epstein, Grossman, & Gee, 2008).…”

Section: Methodsmentioning

confidence: 99%

Differences in brain morphology and working memory capacity across childhood

Bathelt

Gathercole

Johnson

et al. 2017

Developmental Science

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Working memory (WM) skills are closely associated with learning progress in key areas such as reading and mathematics across childhood. As yet, however, little is known about how the brain systems underpinning WM develop over this critical developmental period. The current study investigated whether and how structural brain correlates of components of the working memory system change over development. Verbal and visuospatial short‐term and working memory were assessed in 153 children between 5.58 and 15.92 years, and latent components of the working memory system were derived. Fractional anisotropy and cortical thickness maps were derived from T1‐weighted and diffusion‐weighted MRI and processed using eigenanatomy decomposition. There was a greater involvement of the corpus callosum and posterior temporal white matter in younger children for performance associated with the executive part of the working memory system. For older children, this was more closely linked with the thickness of the occipitotemporal cortex. These findings suggest that increasing specialization leads to shifts in the contribution of neural substrates over childhood, moving from an early dependence on a distributed system supported by long‐range connections to later reliance on specialized local circuitry. Our findings demonstrate that despite the component factor structure being stable across childhood, the underlying brain systems supporting working memory change. Taking the age of the child into account, and not just their overall score, is likely to be critical for understanding the nature of the limitations on their working memory capacity.

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Section: Methodsmentioning

confidence: 99%

Differences in brain morphology and working memory capacity across childhood

Bathelt

Gathercole

Johnson

et al. 2017

Developmental Science

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“…DARTEL is a fully deformable registration method that is effectively unconstrained by number of degrees of freedom. It has proven good segmentation and registration accuracy in comparison with other algorithms [19,20].…”

Section: Pre-processing and Segmentationmentioning

confidence: 98%

Global and focal brain volume in long-term breast cancer survivors exposed to adjuvant chemotherapy

Koppelmans

Ruiter

Lijn

et al. 2011

Breast Cancer Res Treat

150

113

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A limited number of studies have associated adjuvant chemotherapy with structural brain changes. These studies had small sample sizes and were conducted shortly after cessation of chemotherapy. Results of these studies indicate local gray matter volume decrease and an increase in white matter lesions. Up till now, it is unclear if non-CNS chemotherapy is associated with long-term structural brain changes. We compared focal and total brain volume (TBV) of a large set of non-CNS directed chemotherapy-exposed breast cancer survivors, on average 21 years post-treatment, to that of a population-based sample of women without a history of cancer. Structural MRI (1.5T) was performed in 184 chemotherapy-exposed breast cancer patients, mean age 64.0 (SD = 6.5) years, who had been diagnosed with cancer on average 21.1 (SD = 4.4) years before, and 368 age-matched cancer-free reference subjects from a population-based cohort study. Outcome measures were: TBV and total gray and white matter volume, and hippocampal volume. In addition, voxel based morphometry was performed to analyze differences in focal gray matter. The chemotherapy-exposed breast cancer survivors had significantly smaller TBV (-3.5 ml, P = 0.019) and gray matter volume (-2.9 ml, P = 0.003) than the reference subjects. No significant differences were observed in white matter volume, hippocampal volume, or local gray matter volume. This study shows that adjuvant chemotherapy for breast cancer is associated with long-term reductions in TBV and overall gray matter volume in the absence of focal reductions. The observed smaller gray matter volume in chemotherapy- 123Breast Cancer Res Treat (2012) 132:1099-1106 DOI 10.1007/s10549-011-1888-1 exposed survivors was comparable to the effect of almost 4 years of age on gray matter volume reduction. These volume differences might be associated with the slightly worse cognitive performance that we observed previously in this group of breast cancer survivors.

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“…Preprocessing consisted of realignment (FSL), artifact rejection (RapidArt) and spatiotemporal filtering to reduce physiological noise (Behzadi et al 2007). Further preprocessing steps included band-pass filtering (0.1-1.0 Hz), registration to an individual highresolution T1-weighted anatomical image and normalization into MNI stereotaxic space using ANTs (Klein et al 2009). The data were resampled to a 3-mm isotropic resolution and moderately smoothed using an isotropic 5-mm FWHM Gaussian kernel to improve signal to noise ratio.…”

Section: Preprocessingmentioning

confidence: 99%

Tinnitus- and Task-Related Differences in Resting-State Networks

Lanting

WoźAniak

Dijk

et al. 2016

Advances in Experimental Medicine and Biology

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We investigated tinnitus-related differences in functional networks in adults with tinnitus by means of a functional connectivity study. Previously it was found that various networks show differences in connectivity in patients with tinnitus compared to controls. How this relates to patients' ongoing tinnitus and whether the ecological sensory environment modulates connectivity remains unknown. Twenty healthy controls and twenty patients suffering from chronic tinnitus were enrolled in this study. Except for the presence of tinnitus in the patient group, all subjects were selected to have normal or near-normal hearing. fMRI data were obtained in two different functional states. In one set of runs, subjects freely viewed emotionally salient movie fragments ("fixed-state") while in the other they were not performing any task ("resting-state"). After data pre-processing, Principal Component Analysis was performed to obtain 25 components for all datasets. These were fed into an Independent Component Analysis (ICA), concatenating the data across both groups and both datasets, to obtain group-level networks of neural origin, each consisting of spatial maps with their respective time-courses. Subject-specific maps and their time-course were obtained by back-projection (Dual Regression). For each of the components a mixed-effects linear model was composed with factors group (tinnitus vs. controls), task (fixed-state vs. resting state) and their interaction. The neural components comprised the visual, sensorimotor, auditory, and limbic systems, the default mode, dorsal attention, executive-control, and frontoparietal networks, and the cerebellum. Most notably, the default mode network (DMN) was less extensive and shows significantly less connectivity in tinnitus patients than in controls. This group difference existed in both paradigms. At the same time, the DMN was stronger during resting-state than during fixed-state in the controls but not the patients. We attribute this pattern to the unremitting engaging effect of the tinnitus percept.

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Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration

Cited by 2,027 publications

References 69 publications

Differences in brain morphology and working memory capacity across childhood

Differences in brain morphology and working memory capacity across childhood

Global and focal brain volume in long-term breast cancer survivors exposed to adjuvant chemotherapy

Tinnitus- and Task-Related Differences in Resting-State Networks

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