Biology subjects

Madan, C. R.

Publications and source records attributed to Madan, C. R..

5 recordsLinked to original sources

bioRxiv2018

Extending FreeSurfer to estimate sulcal morphology

While it is well established that cortical morphology differs in relation to a variety of inter-individual factors, it is often characterized using estimates of volume, thickness, surface area, or gyrification. Here we developed a computational approach for estimating sulcal width and depth that relies on cortical surface reconstructions output by FreeSurfer. While other approaches for estimating sulcal morphology exist, studies often require the use of multiple brain morphology programs that have been shown to differ in their approaches to localize sulcal landmarks, yielding morphological estimates based on inconsistent boundaries. To demonstrate the approach, sulcal morphology was estimated in three large sample of adults across the lifespan, in relation to aging. A fourth sample is additionally used to estimate test-retest reliability of the approach. This toolbox is now made freely available as supplemental to this paper: https://cmadan.github.io/calcSulc/.

neuroscience↗

bioRxiv2018

Age differences in head motion and estimates of cortical morphology

Cortical morphology is known to differ with age, as measured by cortical thickness, fractal dimensionality, and gyrification. However, head motion during MRI scanning has been shown to influence estimates of cortical thickness as well as increase with age. Studies have also found task-related differences in head motion and relationships between body-mass index (BMI) and head motion. Here I replicated these prior findings, as well as several others, within a large, open-access dataset (Centre for Ageing and Neuroscience, CamCAN). This is a larger dataset than these results have been demonstrated previously, within a sample size of more than 600 adults across the adult lifespan. While replicating prior findings is important, demonstrating these key findings concurrently also provides an opportunity for additional related analyses: Critically, I test for the influence of head motion on cortical fractal dimensionality and gyrification; effects were statistically significant in some cases, but small in magnitude.

neuroscience↗

bioRxiv2017

Shape-related characteristics of age-related differences in subcortical structures

OBJECTIVESWith an increasing aging population, it is important to gain a better understanding of biological markers of aging. Subcortical volume is known to differ with age; additionally considering shape-related characteristics may provide a better index of age-related differences in subcortical structure. Recently fractal dimensionality has been shown to be more sensitive to age-related differences, but this measure is borne out of mathematical principles, rather than quantifying a neurobiologically relevant characteristic directly. We considered four distinct measures of shape and how they relate to aging and fractal dimensionality: surface-to-volume ratio, sphericity, long-axis curvature, and surface texture.\n\nMETHODSStructural MRIs from two samples, with a combined sample size of over 600 healthy adults across the adult lifespan, were used to measure age-related differences in the structure of the thalamus, putamen, caudate, and hippocampus. For each structure, volume and fractal dimensionality were calculated, as well as each of the four distinct shape measures. These measures were then examined in their utility in explaining age-related variability in brain structure.\n\nRESULTSThe four shape measures were able to account for 80-90% of the variance in fractal dimensionality, indicating that these measures were sensitive to the same shape characteristics. Of the distinct shape measures, surface-to-volume ratio was the most sensitive aging biomarker.\n\nCONCLUSIONThough volume is often used to characterize inter-individual differences in subcortical structures, our results demonstrate that additional measures can be useful complements to volumetry. Our results indicate that shape characteristics of subcortical structures are useful biological markers of healthy aging.

neuroscience↗

bioRxiv2017

Non-contact measurement of emotional and physiological changes in heart rate from a webcam

Heart rate, measured in beats per minute (BPM), can be used as an index of an individuals physiological state. Each time the heart beats, blood is expelled and travels through the body. This blood flow can be detected in the face using a standard webcam that is able to pick up subtle changes in color that cannot be seen by the naked eye. Due to the light absorption spectrum of blood, we are able to detect differences in the amount of light absorbed by the blood traveling just below the skin (i.e., photoplethysmography). By modulating emotional and physiological stress--i.e., viewing arousing images and sitting vs. standing, respectively--to elicit changes in heart rate, we explored the feasibility of using a webcam as a psychophysiological measurement of autonomic activity. We found a high level of agreement between established physiological measures, electrocardiogram (ECG), and blood pulse oximetry, and heart rate estimates obtained from the webcam. We thus suggest webcams can be used as a non-invasive and readily available method for measuring psychophysiological changes, easily integrated into existing stimulus presentation software and hardware setups.

physiology↗

bioRxiv2016

Mindcontrol: A Web Application for Brain Segmentation Quality Control

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.

bioinformatics↗