Biology subjects

Malik, S. J.

Publications and source records attributed to Malik, S. J..

3 recordsLinked to original sources

bioRxiv2025

7 Tesla fMRI characterisation of the cortical-depth-dependentBOLD response in early human development

Human cortical development leading up to and around birth is crucial for lifelong brain function. Cortical activity can be studied using BOLD fMRI, however, previously limited sensitivity and spatial specificity has constrained understanding of how its emergence relates to functional cortical circuitry and neurovascular development at the mesoscale. To resolve this, we used ultra-high-field 7 Tesla MRI to acquire sub-millimetre resolution BOLD-fMRI data from 40 newborns and 4 adults. In all subjects, passive right-hand movement elicited localised, positive BOLD responses in contralateral primary somatosensory cortex. In newborns, depth-specific BOLD responses were still evident in the thinner cortex, with developmental changes in response temporal features and amplitudes at different depths. This provides insight into key rapidly evolving factors in early cortical development including neuronal function, vascular architecture, and neurovascular coupling. Our framework and findings provide a foundation for future studies of emerging cortical circuitry and how disruption leads to adverse outcomes.

developmental biology↗

bioRxiv2019

Fetal whole-heart 4D flow cine MRI using multiple non-coplanar balanced SSFP stacks

PurposeTo develop an MRI framework for reconstruction of 4D velocity vector blood flow volumes for visualisation and quantification of circulation in the fetal heart and major vessels.\n\nMethodsA novel method of velocity-encoding using multiple non-coplanar stacks of bSSFP phase images was combined with a previous framework for reconstruction of motion-corrected 4D magnitude cine volumes to generate spatiotemporally-paired 4D flow cine volumes of the fetal circulatory system. The multiple stack velocity-encoding scheme was validated in a simulated flow phantom and compared with a gold-standard method for velocity-encoding in a physical flow phantom. The 4D flow cine framework was evaluated in seven fetal subjects. Reconstructed 4D flow volumes were evaluated by an expert fetal cardiologist and preliminary flow measurements were taken in various major vessels of the heart.\n\nResultsPhantom experiments showed that the multiple non-coplanar stack velocity-encoding scheme was accurate. The 4D flow cine reconstruction framework was robust in fetal subjects and generated multi-dimensional velocity vector maps of blood flow through the cardiac cycle. Directionality of blood flow was consistent with expected fetal circulatory hemodynamics. Relative blood flow rates in the major vessels were in line with previous observations, although absolute values were underestimated by a factor of approximately two due to limitations of spatial and temporal resolution.\n\nConclusion4D flow cine volumes can be reconstructed from multiple non-coplanar stacks of slices. The proposed framework was used to visualise and quantify flow through the whole fetal heart and great vessels, but is applicable to any imaging scenario where motion is a major challenge.

bioengineering↗

bioRxiv2019

Robust 3D Bloch-Siegert based B1+ mapping using Multi-Echo General Linear Modelling

PurposeQuantitative MRI applications, such as mapping the T1 time of tissue, puts high demands on the accuracy and precision of transmit field (B1+) estimation. A candidate approach to satisfy these requirements exploits the difference in phase induced by the Bloch-Siegert Shift (BSS) of two acquisitions with opposite off-resonance frequency RF pulses. Interleaving these RF pulses ensures robustness to motion and scanner drifts, however, here we demonstrate that doing so also introduces a bias in the B1+ estimates. MethodsWe show via simulation and experiments that the amplitude of the error depends on MR pulse sequence parameters, such as TR and RF spoiling increment, but more problematically, on the intrinsic properties, T1 and T2, of the investigated tissue. To solve these problems, we present a new approach to BSS-based B1+ estimation that uses a multi-echo acquisition and a general linear model (GLM) to estimate the correct BSS-induced phase. ResultsIn line with simulations, phantom and in-vivo experiments confirmed that the GLM-based method removed the dependency on tissue properties and pulse sequence settings. It also showed greater robustness to hardware imperfections. ConclusionThe GLM-based method is recommended as a more accurate approach to BSS-based B1+ mapping.

neuroscience↗