Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements

Tustison, Nicholas J.; Cook, Philip A.; Klein, Arno; Song, Gang; Das, Sandhitsu R.; Duda, Jeffrey T.; Kandel, Benjamin M.; Strien, Niels van; Stone, James L.; Gee, James C.; Avants, Brian B.

doi:10.1016/j.neuroimage.2014.05.044

Cited by 602 publications

(579 citation statements)

References 60 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%

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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%

“…Details about the processing pipeline and thickness estimation are described in Tustison et al. (2014) and Das, Avants, Grossman, and Gee (2009). Tissue priors were taken from the OASIS‐TRT‐20 template (http://www.mindboggle.info/data.html#mindboggle-software-data).…”

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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“…BPF can be also obtained from Freesurfer and ANTs pipelines or any software providing brain four-tissue segmentation as FSL [43] or SPM [50]. Cortical thickness (CTh) can be calculated with different software tools as Freesurfer, which includes a surface-based method [51], or the more recent ANTs with its registration-based DiR-ECT algorithm [52,53].…”

Section: Mri Imaging Of Brain Atrophymentioning

confidence: 99%

Effects of disease modifying therapies on brain and grey matter atrophy in relapsing remitting multiple sclerosis

Favaretto

Lazzarotto

Margoni

et al. 2018

Mult Scler Demyelinating Disord

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Background: Progressive brain atrophy is a major feature of multiple sclerosis (MS) pathology and is actually considered a major determinant of the progressive accumulation of physical and cognitive disability in MS patients. Although brain atrophy may have different pathological substrates, several lines of evidence suggest that in disease modifying drug (DMD)-treated MS patients, the higher is the anti-inflammatory effect of the DMD the lower is the progression of brain volume loss, grey matter atrophy and the accumulation of disability. Areas covered: Magnetic resonance imaging (MRI)-based measurements of inflammation (focal white matter and grey matter lesions) and neurodegeneration (decrease in brain volume, cortical and deep grey matter atrophy) are currently included among the primary or secondary end-points of Phase II and III randomized clinical trials (RCT). This review summarizes literature data on the effects of DMDs on either whole brain or grey matter atrophy emerged from RCT and from post-marketing studies.

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“…Diffusionweighted images were acquired in a single-shot, spin-echo, 30-direction diffusion-weighted echo planar imaging sequence ( ) along 30 noncollinear directions. All T1 and DTI image preprocessing was performed with Advanced Normalization Tools, which provides a state-of-the-art pipeline as previously reported 18 and described in detail in appendix e-1 at Neurology.org. We report voxelwise analyses of cortical thickness for GM and fractional anisotropy (FA) for WM.…”

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confidence: 99%

Multimodal imaging evidence of pathology-mediated disease distribution in corticobasal syndrome

et al. 2016

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Objective: To use multimodal neuroimaging to evaluate the influence of heterogeneous underlying pathology in corticobasal syndrome (CBS) on the neuroanatomical distribution of disease.Methods: We performed a retrospective evaluation of 35 patients with CBS with T1-weighted MRI, diffusion tensor imaging, and neuropathologic, genetic, or CSF evidence of underlying pathology. Patients were assigned to 2 groups: those with evidence of Alzheimer pathology (CBS-AD) and those without Alzheimer pathology (CBS-non-AD). Group comparisons of CBS-AD and CBS-non-AD assessed clinical features, gray matter (GM) cortical thickness, and white matter (WM) fractional anisotropy.Results: CBS-AD was found in 34% (n 5 12) and CBS-non-AD in 66% (n 5 23) of CBS patients.Clinical evaluations revealed that CBS-non-AD had a higher frequency of asymmetric rigidity compared to CBS-AD, but groups otherwise did not differ in dementia severity, impairments in cognition, or rates of extrapyramidal symptoms. We found frontoparietal GM and WM disease in each group compared to healthy, demographically comparable controls, as well as multimodal neuroimaging evidence of a double dissociation: CBS-non-AD had WM disease in the corpus callosum, corticospinal tract, and superior longitudinal fasciculus relative to CBS-AD, and CBS-AD had reduced temporoparietal GM relative to CBS-non-AD, including the precuneus and posterior cingulate. Conclusions:Patients with CBS have a pathology-mediated dissociation of GM and WM disease.Multimodality neuroimaging may be useful for improving in vivo pathologic diagnosis of CBS. Corticobasal syndrome (CBS) is a neurodegenerative condition characterized by lateralized extrapyramidal features and cortically mediated cognitive dysfunction.1 The underlying pathology of CBS is heterogeneous, and clinical features appear to be insufficient to identify an individual's histopathologic abnormality during life.2,3 The most common neuropathologic causes of CBS include corticobasal degeneration, a 4-repeat form of tau pathology associated with frontotemporal lobar degeneration (FTLD), 4 and Alzheimer disease (AD). 2,5,6 Multimodal neuroimaging studies suggest that AD and FTLD can be dissociated on the basis of gray matter (GM) and white matter (WM) neuroimaging. 7,8 Specifically, GM atrophy was evident in both AD and FTLD in T1-weighted MRI studies, but diffusion tensor imaging (DTI) revealed more WM disease in FTLD than in AD. Additional neuroimaging evidence suggests that tau pathology, the most common form of underlying pathology in CBS, is associated with substantial WM imaging changes 9 and that these findings converge with neuropathologic evidence of WM disease burden in 4-repeat tauopathy.9,10 However, prior evidence of greater WM pathology in FTLD disorders has been based on clinically heterogeneous study samples; therefore, it is not clear whether a dissociation of GM and WM disease is

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Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements

Cited by 602 publications

References 60 publications

Differences in brain morphology and working memory capacity across childhood

Differences in brain morphology and working memory capacity across childhood

Effects of disease modifying therapies on brain and grey matter atrophy in relapsing remitting multiple sclerosis

Multimodal imaging evidence of pathology-mediated disease distribution in corticobasal syndrome

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