brainR: Interactive 3 and 4D Images of High Resolution Neuroimage Data

Muschelli, John; Sweeney, Elizabeth; Crainiceanu, Ciprian M.

doi:10.32614/rj-2014-004

Cited by 15 publications

(11 citation statements)

References 12 publications

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“…Interactive plots of diel patterns in 3DKUD (Fig. 3) were rendered using the 'brainR' package in R and code adapted from Muschelli et al [29]. The proportion of overlap in the space used between day and night was also calculated for 50%-3DKUD and 95%-3DKUD for both species using R code from Simpfendorfer et al [2].…”

Section: Discussionmentioning

confidence: 99%

Diel patterns in three-dimensional use of space by sea snakes

2015

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Background: The study of animal movement and use of space have traditionally focused on horizontal and vertical movements separately. However, this may limit the interpretation of results of such behaviours in a three-dimensional environment. Here we use passive acoustic telemetry to visualise and define the three-dimensional use of space by two species of sea snake [Hydrophis (Lapemis) curtus; and Hydrophis elegans] within a coastal embayment and identify changes in how they use space over a diel cycle.Results: Monitored snakes exhibited a clear diel pattern in their use of space, with individuals displaying restricted movements at greater depths during the day, and larger movements on the surface at night. Hydrophis curtus generally occupied space in deep water within the bay, while H. elegans were restricted to mud flats in inundated inter-tidal habitats. The overlap in space used between day and night showed that individuals used different core areas; however, the extent of areas used was similar.Conclusions: This study demonstrates that by incorporating the capacity to dive in analyses of space use by sea snakes, changes over a diel cycle can be identified. Three-dimensional use of space by sea snakes can identify spatial or temporal overlaps with anthropogenic threats (e.g. trawling, dredging) and help develop targeted management policies that mitigate any adverse effects to ensure healthy populations of sea snakes.

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Section: Discussionmentioning

confidence: 99%

Diel patterns in three-dimensional use of space by sea snakes

2015

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“…We performed all statistical modeling in the R environment (version 3.1.0, R Foundation for Statistical Computing, Vienna, Austria) utilizing the packages oasis, 18 ROCR, 19 data.table, 20 brainR, 21 oro.nifti, 22 and fslr. 23…”

Section: Methodsmentioning

confidence: 99%

MIMoSA: An Automated Method for Intermodal Segmentation Analysis of Multiple Sclerosis Brain Lesions

Valcarcel

Linn

Vandekar

et al. 2018

Journal of Neuroimaging

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“…It led to similar results, including the identification rate on FP was the highest (90.6 % ) (Table 5). The 20 identifying pairs within the FP network are visualized (see Figure 7) on the ICBM 152 template brain (Mazziotta et al, 2001) with the rgl and misc3d packages in R (Adler et al, 2018; Feng et al, 2008; Muschelli, Sweeney & Crainiceanu, 2014).…”

Section: Numerical Experimentsmentioning

confidence: 99%

On statistical tests of functional connectome fingerprinting

et al. 2021

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Fingerprinting of functional connectomes is an increasingly standard measure of reproducibility in functional magnetic resonance imaging connectomics. In such studies, one attempts to match a subject's first session image with their second, in a blinded fashion, in a group of subjects measured twice. The number or percentage of correct matches is usually reported as a statistic, which is then used in permutation tests. Despite the simplicity and increasing popularity of such procedures, the soundness of the statistical tests, the power, and the factors impacting the test are unstudied. In this article, we investigate the statistical tests of matching based on exchangeability assumption in the fingerprinting analysis. We show that a nearly universal Poisson(1) approximation applies for different matching schemes. We theoretically investigate the permutation tests and explore the issue that the test is overly sensitive to uninteresting directions in the alternative hypothesis, such as clustering due to familial status or demographics. We perform a numerical study on two functional magnetic resonance imaging (fMRI) resting-state datasets, the Human Connectome Project (HCP) and the Baltimore Longitudinal Study of Aging (BLSA). These datasets are instructive, as the HCP includes technical replications of long scans and includes monozygotic and dizygotic twins, as well as non-twin siblings. In contrast, the BLSA study incorporates more typical length resting-state scans in a longitudinal study. Finally, a study of single regional connections is performed on the HCP data. The

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brainR: Interactive 3 and 4D Images of High Resolution Neuroimage Data

Cited by 15 publications

References 12 publications

Diel patterns in three-dimensional use of space by sea snakes

Diel patterns in three-dimensional use of space by sea snakes

MIMoSA: An Automated Method for Intermodal Segmentation Analysis of Multiple Sclerosis Brain Lesions

On statistical tests of functional connectome fingerprinting

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