The Insight ToolKit image registration framework

Avants, Brian B.; Tustison, Nicholas J.; Stauffer, Michael; Song, Gang; Wu, Bangyu; Gee, James C.

doi:10.3389/fninf.2014.00044

Cited by 551 publications

(435 citation statements)

References 36 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

View full text Add to dashboard Cite

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“…More precise comparisons between different tongue images, including the definition of a standard X-Y template, will require local warping and alignment of images that differ due to biological variation and the effects of sample preparation. Algorithms that warp and align images to match a template have been developed for brain histology and magnetic resonance imaging (Avants et al, 2014;Economo et al, 2016) and might be adaptable to tongue images. If these technical challenges can be met, it should be possible to generate LP vector maps at single LP resolution and to compare WT and mutant maps to reveal the magnitude and statistical significance of variation in LP orientation at every X-Y location.…”

Section: The Tongue Epithelium As a System For Quantitative Analysis mentioning

confidence: 99%

Patterning of papillae on the mouse tongue: A system for the quantitative assessment of planar cell polarity signaling

Wang

Williams

Rattner

et al. 2016

Developmental Biology

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The dorsal surface of the mouse tongue is covered by ~7000 papillae, asymmetric epithelial protrusions that are precisely oriented to create a stereotyped macroscopic pattern. Within the context of this large-scale pattern, neighboring papillae exhibit a high degree of local order that minimizes the differences in their orientations. We show here that the orientations of lingual papillae are under the control of the core planar cell polarity (PCP) genes Vangl1, Vangl2, and Celsr1. Using K14-Cre and Nkx2.5-Cre to induce conditional knockout of Vangl1 and/or Vangl2 in the tongue epithelium, we observe more severe disruptions to local order among papillae with inactivation of larger numbers of Vangl genes, a greater role for Vangl2 than Vangl1, and a more severe phenotype with the Vangl2 Looptail (Lp) allele than the Vangl2 null allele, consistent with a dominant negative mode of action of the Vangl2 allele. Interestingly, Celsr1 tongues show disruption of both local and global order, with many papillae in the anterior tongue showing a reversed orientation. To quantify each of these phenotypes, we have developed and applied three procedures for sampling the orientations of papillae and assessing the degree of order on different spatial scales. The experiments reported here establish the dorsal surface of the mouse tongue as a favorable system for studying PCP control of epithelial patterning.

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“…It is built on the widely used Insight ToolKit (ITK) [20], and is open source and freely available. Each of the cohort MDTs was constructed using the Advanced Normalization Tools (ANTs; stnava.github.io/ANTs/) software package and accompanying scripts (at commit: 88276f8).…”

Section: Template Creationmentioning

confidence: 99%

Comparison of template registration methods for multi-site meta-analysis of brain morphometry

et al. 2016

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Neuroimaging consortia such as ENIGMA can significantly improve power to discover factors that affect the human brain by pooling statistical inferences across cohorts to draw generalized conclusions from populations around the world. Voxelwise analyses such as tensor-based morphometry also allow an unbiased search for effects throughout the brain. Even so, such consortium-based analyses are limited by a lack of high-powered methods to harmonize voxelwise information across study populations and scanners. While the simplest approach may be to map all images to a single standard space, the benefits of cohort-specific templates have long been established. Here we studied methods to pool voxel-wise data across sites using templates customized for each cohort but providing a meaningful common space across all studies for voxelwise comparisons. As non-linear 3D MRI registrations represent mappings between images at millimeter resolution, we need to consider the reliability of these mappings. To evaluate these mappings, we calculated test-retest statistics on the volumetric maps of expansion and contraction. Further, we created study-specific brain templates for ten T1-weighted MRI datasets, and a common space from four study-specific templates. We evaluated the efficacy of using a two-step registration framework versus a single standard space. We found that the two-step framework more reliably mapped subjects to a common space.

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The Insight ToolKit image registration framework

Cited by 551 publications

References 36 publications

Differences in brain morphology and working memory capacity across childhood

Differences in brain morphology and working memory capacity across childhood

Patterning of papillae on the mouse tongue: A system for the quantitative assessment of planar cell polarity signaling

Comparison of template registration methods for multi-site meta-analysis of brain morphometry

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