Biology subjects

Schira, M. M.

Publications and source records attributed to Schira, M. M..

4 recordsLinked to original sources

bioRxiv2025

Paediatric MRI: High-Resolution in vivo 3T Methods

Magnetic Resonance Imaging (MRI) is a powerful tool for investigating the brain in vivo but is limited by image resolution and scan artefact. In paediatric research, these limitations are compounded by reduced participant compliance, which in turn necessitates shorter scan times to minimise motion artefacts, resulting in less than satisfactory image resolution. We report here methods for MRI acquisition which afford high-resolution, low-noise, paediatric brain data in under nine-minute scans, and novel post-processing with our code freely available at https://osf.io/ckh5t/. Whole-brain in vivo single-participant images were generated at 0.5mm isotropic resolution. This resolution permitted accurate delineation of fine structures, including the hippocampal subfields. The ability to resolve intricate structures in paediatric data provides a tool for studying brain development and its disruption in neurologic and psychiatric disorders.

neuroscience↗

bioRxiv2022

HumanBrainAtlas: an in vivo MRI dataset for detailed segmentations

We introduce HumanBrainAtlas, an initiative to construct a highly detailed, open-access atlas of the living human brain that combines high-resolution in vivo MR imaging and detailed segmentations previously possible only in histological preparations. Here, we present and evaluate the first step of this initiative: a comprehensive dataset of two healthy male volunteers reconstructed to a 0.25 mm3 isotropic resolution for T1w, T2w and DWI contrasts. Multiple high-resolution acquisitions were collected for each contrast and each participant, followed by averaging using symmetric group-wise normalisation (Advanced Normalisation Tools). The resulting image quality permits structural parcellations rivalling histology-based atlases, while maintaining the advantages of in vivo MRI. For example, components of the thalamus, hypothalamus, and hippocampus - difficult or often impossible to identify using standard MRI protocols, can be identified within the present data. Our data are virtually distortion free, fully 3D, and compatible with existing in vivo Neuroimaging analysis tools. The dataset is suitable for teaching and is publicly available via our website (www.hba.neura.edu.au), which also provides data processing scripts. Instead of focusing on coordinates in an averaged brain space, our approach focuses on providing an example segmentation at great detail in the high quality individual brain, this serves as an illustration on what features contrasts and relations can be used to interpret MRI datasets, in research, clinical and education settings.

neuroscience↗

bioRxiv2019

Anatomy-guided Inverse-phase-encoding Registration Method for Correcting Susceptibility Artifacts in Sub-millimeter fMRI

Echo planar imaging (EPI) is a fast and non-invasive magnetic resonance imaging (MRI) technique that supports data acquisition at spatial and temporal resolutions suitable for brain function studies. However, susceptibility artifacts are unavoidable distortions in EPI. These distortions are especially strong in high spatial resolution images and can lead to misrepresentation of brain function in fMRI experiments. A common method for correcting susceptibility artifacts is based on a registration scheme which uses two EPI images acquired using identical sequences but with inverse phase-encoding (PE) directions. In this paper, we present a new method for correcting susceptibility artifacts by integrating a T1-weighted (T1w) image into the inverse-PE based registration, since the T1w structural image is considered as a ground-truth measurement of the brain. Furthermore, the T1w image is used as a criterion to select automatically the regularization parameters of the proposed image registration. Evaluations on two high-resolution EPI-fMRI datasets, acquired at 3T and 7T scanners, confirm that the proposed method provides more robust and sharper corrections and runs faster compared with two other state-of-the-art inverse-PE based susceptibility artifact correction methods, i.e. HySCO and TOPUP.

neuroscience↗

bioRxiv2018

Vascular effects on the BOLD response and the retinotopic mapping of hV4

Despite general acceptance that the retinotopic organisation of human V4 (hV4) takes the form of a single, uninterrupted ventral hemifield, measured retinotopic maps of this visual area are often incomplete. Here, we test hypotheses that artefact from draining veins close to hV4 cause inverted BOLD responses that may serve to obscure a portion of the lower visual quarterfield -- including the lower vertical meridian -- in some hemispheres. We further test whether correcting such responses can restore the missing retinotopic coverage in hV4. Subjects (N=11) viewed bowtie, ring, drifting bar and full field flash stimuli. Functional EPIs were acquired over approximately 1.5h and analysed to reveal retinotopic maps of early visual cortex, including hV4. Normalised mean maps (which show the average EPI signal amplitude) were constructed by voxel-wise averaging of the EPI time course and used to locate venous eclipses, which can be identified by a decrease in the EPI signal caused by deoxygenated blood. Inverted responses are shown to cluster in these regions, and correcting these responses improves maps of hV4 in some hemispheres, including restoring a complete hemifield map in one. A leftwards bias was found in which 11/11 hV4 maps in the left hemisphere were classified as incomplete, while this was the case in only 3/11 right hemisphere maps. Incomplete hV4 maps did not correspond with venous artefact in many instances, with incomplete maps being present in the absence of a venous eclipse and complete maps coexisting with a proximate venous eclipse. We also show that mean maps of upper surfaces (near the boundary between cortical grey matter and CSF) provide highly detailed maps of veins on the cortical surface. Results suggest that venous eclipses and inverted voxels can explain some incomplete hV4 maps, but cannot explain the remainder nor the leftwards bias in hV4 coverage reported here.

neuroscience↗