Vanderbilt University Institute of Imaging Science Center for Computational Imaging XNAT: A multimodal data archive and processing environment

Harrigan, Robert L.; Yvernault, Benjamin C.; Boyd, Brian D.; Damon, Stephen; Gibney, Kyla D.; Conrad, Benjamin; Phillips, Nicholas S.; Rogers, Baxter P.; Gao, Yurui; Landman, Bennett A.

doi:10.1016/j.neuroimage.2015.05.021

Cited by 41 publications

(34 citation statements)

References 29 publications

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“…This work was conducted in part using the resources of the Advanced Computing Center for Research and Education at Vanderbilt University, and XNAT[20, 21]. The project was also supported by the National Center for Research Resources, Grant UL1 RR024975-01, and is now at the National Center for Advancing Translational Sciences, Grant 2 UL1 TR000445-06.…”

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confidence: 99%

A 3D high resolution ex vivo white matter atlas of the common squirrel monkey (saimiri sciureus) based on diffusion tensor imaging

et al. 2016

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Modern magnetic resonance imaging (MRI) brain atlases are high quality 3-D volumes with specific structures labeled in the volume. Atlases are essential in providing a common space for interpretation of results across studies, for anatomical education, and providing quantitative image-based navigation. Extensive work has been devoted to atlas construction for humans, macaque, and several non-primate species (e.g., rat). One notable gap in the literature is the common squirrel monkey – for which the primary published atlases date from the 1960’s. The common squirrel monkey has been used extensively as surrogate for humans in biomedical studies, given its anatomical neuro-system similarities and practical considerations. This work describes the continued development of a multi-modal MRI atlas for the common squirrel monkey, for which a structural imaging space and gray matter parcels have been previously constructed. This study adds white matter tracts to the atlas. The new atlas includes 49 white matter (WM) tracts, defined using diffusion tensor imaging (DTI) in three animals and combines these data to define the anatomical locations of these tracks in a standardized coordinate system compatible with previous development. An anatomist reviewed the resulting tracts and the inter-animal reproducibility (i.e., the Dice index of each WM parcel across animals in common space) was assessed. The Dice indices range from 0.05 to 0.80 due to differences of local registration quality and the variation of WM tract position across individuals. However, the combined WM labels from the 3 animals represent the general locations of WM parcels, adding basic connectivity information to the atlas.

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A 3D high resolution ex vivo white matter atlas of the common squirrel monkey (saimiri sciureus) based on diffusion tensor imaging

et al. 2016

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“…The ON-CSF measurement code is primarily written in MATLAB (The MathWorks, Inc., Natick, Massachusetts, United States) and bundled into an automated program (i.e., “spider” [27]) that combines these tools using PyXNAT [28] and DAX[29] for XNAT [30] and is available through the NITRC project MASIMATLAB (http://www.nitrc.org/projects/masimatlab). …”

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confidence: 99%

Improved automatic optic nerve radius estimation from high resolution MRI

et al. 2017

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The optic nerve (ON) is a vital structure in the human visual system and transports all visual information from the retina to the cortex for higher order processing. Due to the lack of redundancy in the visual pathway, measures of ON damage have been shown to correlate well with visual deficits. These measures are typically taken at an arbitrary anatomically defined point along the nerve and do not characterize changes along the length of the ON. We propose a fully automated, three-dimensionally consistent technique building upon a previous independent slice-wise technique to estimate the radius of the ON and surrounding cerebrospinal fluid (CSF) on high-resolution heavily T2-weighted isotropic MRI. We show that by constraining results to be three-dimensionally consistent this technique produces more anatomically viable results. We compare this technique with the previously published slice-wise technique using a short-term reproducibility data set, 10 subjects, follow-up <1 month, and show that the new method is more reproducible in the center of the ON. The center of the ON contains the most accurate imaging because it lacks confounders such as motion and frontal lobe interference. Long-term reproducibility, 5 subjects, follow-up of approximately 11 months, is also investigated with this new technique and shown to be similar to short-term reproducibility, indicating that the ON does not change substantially within 11 months. The increased accuracy of this new technique provides increased power when searching for anatomical changes in ON size amongst patient populations.

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“…Images were post-processed with Vanderbilt University Institute for Imaging Science Center of Computational Imaging resources (Vanderbilt University, Nashville, TN) using an established pipeline previously described [43–46]. Standard tensor fitting methods were used to estimate the diffusion tensor and resulting tensor parameters fractional anisotropy (FA) and mean diffusivity (MD) [47].…”

Section: Methodsmentioning

confidence: 99%

The Vanderbilt Memory & Aging Project: Study Design and Baseline Cohort Overview

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Gifford

Acosta

et al. 2016

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Background Vascular health factors frequently co-occur with Alzheimer’s disease (AD). A better understanding of how systemic vascular and cerebrovascular health intersects with clinical and pathological AD may inform prevention and treatment opportunities. Objective To establish the Vanderbilt Memory & Aging Project, a case-control longitudinal study investigating vascular health and brain aging, and describe baseline methodology and participant characteristics. Methods From September 2012 to November 2014, 335 participants age 60–92 were enrolled, including 168 individuals with mild cognitive impairment (MCI, 73 ± 8 years, 41% female) and 167 age-, sex-, and race-matched cognitively normal controls (NC, 72 ± 7 years, 41% female). At baseline, participants completed a physical and frailty examination, fasting blood draw, neuropsychological assessment, echocardiogram, cardiac MRI, and brain MRI. A subset underwent 24-hour ambulatory blood pressure monitoring and lumbar puncture for cerebrospinal fluid (CSF) collection. Results As designed, participant groups were comparable for age (p = 0.31), sex (p = 0.95), and race (p = 0.65). MCI participants had greater Framingham Stroke Risk Profile scores (p = 0.008), systolic blood pressure values (p = 0.008), and history of left ventricular hypertrophy (p = 0.04) than NC participants. As expected, MCI participants performed worse on all neuropsychological measures (p-values<0.001), were more likely to be APOE ε4 carriers (p = 0.02), and had enhanced CSF biomarkers, including lower Aβ42 (p = 0.02), higher total tau (p = 0.004), and higher p-tau (p = 0.02) compared to NC participants. Conclusion Diverse sources of baseline and longitudinal data will provide rich opportunities to investigate pathways linking vascular and cerebrovascular health, clinical and pathological AD, and neurodegeneration contributing to novel strategies to delay or prevent cognitive decline.

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Vanderbilt University Institute of Imaging Science Center for Computational Imaging XNAT: A multimodal data archive and processing environment

Cited by 41 publications

References 29 publications

A 3D high resolution ex vivo white matter atlas of the common squirrel monkey (saimiri sciureus) based on diffusion tensor imaging

A 3D high resolution ex vivo white matter atlas of the common squirrel monkey (saimiri sciureus) based on diffusion tensor imaging

Improved automatic optic nerve radius estimation from high resolution MRI

The Vanderbilt Memory & Aging Project: Study Design and Baseline Cohort Overview

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