Biology subjects

Tahayori, B.

Publications and source records attributed to Tahayori, B..

4 recordsLinked to original sources

bioRxiv2025

Robust-tedana: An automated denoising pipeline for multi-echo fMRI data

Multi-echo functional Magnetic Resonance Imaging (fMRI) data are acquired by recording image volumes at multiple echo times and can be used to improve the separation of neural activity from noise. TE-Dependent ANAlysis (tedana) is an open-source software tailored to denoising of multi-echo fMRI data. The efficacy of denoising can however be inconsistent, often necessitating manual inspection that precludes its application in large-scale studies where processing is ideally fully automated. Here, we introduce Robusttedana, an optimised denoising pipeline that achieves adequate results at both single-subject and group level. Robust-tedana incorporates Marchenko-Pastur Principal Component Analysis (MPPCA) for effective thermal noise reduction, robust independent component analysis for stabilised signal decomposition, and a modified component classification process. We evaluated its performance on Multi-Band Multi-Echo (MBME) language-task fMRI data from the Australian Epilepsy Project (AEP) using objective measures, comparing to conventional fMRI analysis with and without multi-echo-based denoising. Experts manual evaluation was undertaken on a subset of these data to validate the objective measures. The proposed pipeline both mitigates the prevalence of erroneous attenuation of genuine task activation due to instability of single-subject analysis, and increases the magnitude of group-wise effects. Robust-tedana therefore facilitates advanced analysis of MBME fMRI data in an automated pipeline, including for clinical research assessment of individuals.

bioengineering↗

bioRxiv2025

Common pitfalls during model specification in psychophysiological interaction analysis

Psychophysiological interaction (PPI) analysis is a widely used regression method in functional neuroimaging for capturing task-dependent changes in connectivity from a seed region. The present work identifies, and provides corrections for, common methodological pitfalls in PPI analysis that compromise model validity. Firstly, if the seed time series is extracted with prewhitening, the temporal structure of the signal is altered and subsequent deconvolution of prewhitened data becomes suboptimal. Furthermore, prewhitening again during model fitting results in double prewhitening of the seed regressor. Secondly, a failure to mean-centre the task regressor when calculating the interaction term can also lead to model misspecification and potentially spurious inferences. By using simulations and empirical language fMRI data from the Australian Epilepsy Project, we demonstrate the adverse effects of these issues, and how they are resolved when corrected. A systematic review of current practices revealed widespread model misspecification, and underreporting of methods, in published PPI studies. We provide clearer reporting guidelines, and advocate for appropriate methods for handling of prewhitening and mean-centring to ensure the validity of PPI analyses.

neuroscience↗

bioRxiv2021

Postural perturbation induced by electrical stimulation; A new approach to examine the mechanism of falling

BackgroundFalling is a major cause of disability and death among elderly people. Therefore, a clear understanding of fall mechanism is necessary for providing preventative and treatment methods. Several fall simulation protocols have been introduced to study lost of balance in a laboratory setting. New MethodWe have explained and examined a new method to induce a sudden perturbation on standing posture to provide an insight into the mechanism of falling. The method comprises eliciting an H-reflex protocol while subjects are standing which produces a contraction in soleus and gastrocnemius muscles. We have also defined analytical techniques to provide biomarkers of balance control during perturbation. The method is easy to implement and interpret. The H-reflex or M-wave can be elicited unilaterally or bilaterally causing a forward or sideway perturbation. The vector analysis and the Equilibrium Point calculations defined here can quantify the amplitude, direction, and evolution of the perturbation. ResultsWe tested this method on a group of healthy individuals and observed clear patterns of loss of balance due to stimulation. Direction and magnitude of deviation was manifested through the reconstructed vectors, with bilateral stimulation causing the largest perturbation. Comparison and conclusionThe resultant plantarflexion torque is reminiscent of tripping over an obstacle and triggers corrective reactions to restore balance. Therefore, it is more similar to an internal perturbation. Mechanical perturbations to the torso cause a displacement in center of mass (COM) and trigger a cascade of mechanisms. Our method, does not trigger the perturbation by the displacement of COM initially and therefore, triggers fewer mechanisms for regaining balance.

neuroscience↗

bioRxiv2018

Minimizing activation of overlying axons with epiretinal stimulation: The role of fiber orientation and electrode configuration

AO_SCPCAPBSTRACTC_SCPCAPObjective. Currently, a challenge in electrical stimulation of the retina is to excite only the cells lying directly under the electrode in the ganglion cell layer, while avoiding excitation of the axons that pass over the surface of the retina in the nerve fiber layer. Since these passing fibers may originate from distant regions of the ganglion cell layer. Stimulation of both target retinal ganglion cells and overlying axons results in irregular visual percepts, significantly limiting perceptual efficacy. This research explores how differences in fiber orientation between the nerve fiber layer and ganglion cell layer leads to differences in the activation of the axon initial segment and axons of passage. Approach. Axons of passage of retinal ganglion cells in the nerve fiber layer are characterized by a narrow distribution of fiber orientations, causing highly anisotropic spread of applied current. In contrast, proximal axons in the ganglion cell layer have a wider distribution of orientations. A four-layer computational model of epiretinal extracellular stimulation that captures the effect of neurite orientation in anisotropic tissue has been developed using a modified version of the standard volume conductor model, known as the cellular composite model. Simulations are conducted to investigate the interaction of neural tissue orientation, stimulating electrode configuration, and stimulation pulse duration and amplitude. Main results. The dependence of fiber activation on the anisotropic nature of the nerve fiber layer is first established. Via a comprehensive search of key parameters, our model shows that the simultaneous stimulation with multiple electrodes aligned with the nerve fiber layer can be used to achieve selective activation of axon initial segments rather than passing fibers. This result can be achieved with only a slight increase in total stimulus current and modest increases in the spread of activation in the ganglion cell layer, and is shown to extend to the general case of arbitrary electrode array positioning and arbitrary target neural volume. Significance. These results elucidate a strategy for more targeted stimulation of retinal ganglion cells with experimentally-relevant multi-electrode geometries and readily achievable stimulation requirements.

biophysics↗