Bago Amirbekian

and 1 more

INTRODUCTION Diffusion weighted magnetic resonance imaging (MRI) is an imaging technique that has allowed unique insights into both the microstructural properties and the organization of cerebral white matter tissues. This technique measures the relative displacement of water molecules in the biological tissues and is highly sensitive to any microstructure which restricts this diffusion. Diffusion MRI is particularly useful in tissues with a high degree of organization, such as the white matter tissues of the brain. This organization means that the restricted diffusion is coherent and measuring the diffusion signal allows us to not only infer the presence or absence of diffusion restricting elements, but also how they’re organized and other tissue properties. For example, in the white matter of the brain, the diffusion characteristics of the tissue can give us insight into the organization of axons, the level of myelination of those axons and possible pathology in these tissues. The level of information contained in diffusion imaging makes this imaging technique both powerful and challenging to work with. Diffusion images cannot generally be read by human specialists, but instead must be modeled using computational techniques. These modeling techniques can produce either composite images or 3d renderings, which can then be used in clinic or for research, or quantitative measurements which can then be used as biomarkers of brain heath or disease progression. However, in order to maximize the utility of diffusion imaging one needs to pick the right imaging protocol and modeling approach for a given problem. The modeling of the diffusion signal can be approached both as a local problem, modeling the characteristics of a given brain region or voxel using the diffusion signal specific to that structure. The model can also be thought of as a whole brain model, trying not only the estimate local tissue properties, but also the organization of connections and pathways that contribute to the architecture of the whole brain. Fiber tracking, or tractography, describes the process of using local directional information from brain tissues to build reconstruct these tracts and pathways. These techniques are fairly new and actively being developed and have had some success in describing the organizational properties of the human brain, or the human connectome. In this work, I present some common diffusion modeling techniques that have been applied to diffusion MRI, focused specifically on modeling techniques that estimate directional information which can be used for fiber tacking. I present and compare several methods for estimating diffusion MRI noise and in the process discuss how noise estimates for diffusion MRI acquisitions can help identify model failures inform the choice of model for an acquisition type. I further present a framework for thinking about and implement fiber tract reconstruction from diffusion MRI data. Finally I present an application of these methods to a large, public data set for the purpose of understanding the impact of high body mass index on brain health.

Anisha Keshavan

and 2 more

REVIEWER 1 - I am pleased with the changes in the paper, however I would like a more direct answer to the previously stated question on repositioning consistency, since gradient-nonlinearity induced volume changes are dependent on positioning inside scanner. The previously stated question was: - It is mentioned in the Methods section that repositioning consistency of each site’s scanning procedure was captures, however there is no metric in the results section focusing explicitly on that (i.e consistency of the subject position). It would be important to compare it to the consistency of subject positioning in Caramanos 2010 , since it will affect assumption on ability to correct gradient-distortions caused variations with a scaling factor derived from different acquisition. We would like to thank Reviewer 1 for the feedback and will address this concern by reporting the consistency of Z-positioning in relation to . In , researchers found that variations in z-position affected the percent brain volume change (PBVC) measurements of a longitudinal SIENA pipeline significantly. Specifically, they compared results of “accurate as possible” repositioning with a 50mm displacement repositioning, and found significant differences between measurements. When comparing the “accurate as possible” repositioning to the phantom-corrected result, the absolute error was much lower than that of the 50mm displacement. They calculated an average Z-displacement of 4.3 mm (-9.0 to 21.1). We ran rigid-body-registration to calculate the Z-translations for each subject at each site in our dataset. Overall, our average absolute Z-displacement across all sites was 3.5mm ± 3.7mm, which falls within the range of the “as accurate as possible” repositioning from . Our average Z-shift, for each site separately is provided in the supplemental materials. The following text was added to the methods: _“By repositioning in our study, a realistic measure of test-retest variability, which includes the repositioning consistency of each site’s scanning procedure, was captured. Because gradient distortion effects correspond to differences in z-positioning , the average translation in the Z-direction between the two runs of each subject at each site was estimated with a rigid body registration.”_ And in the results we report: _“In addition, the average translation in the Z-direction across all sites was 3.5mm ± 3.7mm, which falls within the accuracy range reported by . The repositioning Z-translation measurements for each site separately is reported in the supplemental materials.”_

Anisha Keshavan

and 3 more

OVERVIEW There is a disconnect between clinical disability in multiple sclerosis (MS) and structural damage seen on MRI, called the clinico-radiological paradox . Even though focal white matter lesions seen on MRI largely characterize multiple-sclerosis, lesion volumes are not strongly correlated with clinical motor disability . Possible reasons for this paradox include lesion location and gray matter atrophy , however the correlations with disability are modest (r=0.3). Another hypothesis is that functional adaptation plays a role, where brains adapt to the damage caused by MS in order to minimize disability. My preliminary results have shown that changes in functional MRI network connections correlate with performance on a complex motor dexterity task, even after accounting for structural damage. However, poor performance on a complex motor task may not be attributable to motor network damage and reorganization alone. For example, damage to the visual pathway involved in a complex task may confound results. Therefore, I propose to study how performance on simpler motor tasks relate to functional network connectivity changes, and develop a functional biomarker to predict motor performance. I intend to measure the central motor conduction time (CMCT), which is sensitive to corticospinal tract damage, by measuring motor evoked potentials (MEP) using transcranial magnetic stimulation (TMS). Additionally, finger tapping speed (FT) will be collected on MS patients, which has been shown to be more impaired in MS patients compared to measures of manual dexterity. Functional biomarkers will be developed using a traditional, hypothesis driven approach, followed by a functional dynamic network analysis focused on the posteriomedial cortex (PMC). Features of the functional network will be extracted based on CMCT and FT. This will result in a biomarker that reflects the ability of a subject to functionally adapt to MS-related damage to the motor system, which could lead to personalized medical treatment of their disease. Specific Aim 1: Develop an fMRI metric that relates to CMCT and FT using a hypothesis driven analysis Specific Aim 2: Improve on the prediction of simple and complex motor tasks by developing an fMRI metric based on dynamic functional connectivity of the PMC
Mindcontrol meteor diagram1

Anisha Keshavan

and 6 more

Tissue classification plays a crucial role in the investigation of normal neural development, brain-behavior relationships, and the disease mechanisms of many psychiatric and neurological illnesses. Ensuring the accuracy of tissue classification is important for quality research and, in particular, the translation of imaging biomarkers to clinical practice. Assessment with the human eye is vital to correct various errors inherent to all currently available segmentation algorithms. Manual quality assurance becomes methodologically difficult at a large scale - a problem of increasing importance as the number of data sets is on the rise. To make this process more efficient, we have developed Mindcontrol, an open-source web application for the collaborative quality control of neuroimaging processing outputs. The Mindcontrol platform consists of a dashboard to organize data, descriptive visualizations to explore the data, an imaging viewer, and an in-browser annotation and editing toolbox for data curation and quality control. Mindcontrol is flexible and can be configured for the outputs of any software package in any data organization structure. Example configurations for three large, open-source datasets are presented: the 1000 Functional Connectomes Project (FCP), the Consortium for Reliability and Reproducibility (CoRR), and the Autism Brain Imaging Data Exchange (ABIDE) Collection. These demo applications link descriptive quality control metrics, regional brain volumes, and thickness scalars to a 3D imaging viewer and editing module, resulting in an easy-to-implement quality control protocol that can be scaled for any size and complexity of study.