Biology subjects

Bajada, C. J.

Publications and source records attributed to Bajada, C. J..

8 recordsLinked to original sources

bioRxiv2026

Testing diffusion-derived orientation priors for streamline modelling of the MRI-visible glioblastoma core: the BRIAN framework

Glioblastoma spreads diffusely beyond the abnormality visible on conventional magnetic resonance imaging, and because tumour cells migrate preferentially along white-matter pathways, growth models that assume isotropic spread may misrepresent the geometry of invasion relevant to radiotherapy planning. This work introduces and evaluates BRIAN, a diffusion-informed simulator that biases tumour propagation along directions derived from diffusion MRI. Patient tumour masks from the UPENN-GBM cohort are transferred onto healthy host brains from the Human Connectome Project through the MNI152 template as a proxy, diffusion orientation distribution functions (dODFs) are reconstructed on each host, and stochastic streamline propagation with the MRtrix3 iFOD2 algorithm yields volumetric occupancy maps. Propagation parameters are fitted per tumour under a three-stage curriculum that tightens a constrained five-metric objective. Across 30 unifocal tumours, each propagated onto 65 validation hosts (1 950 tumour-host pairings), the simulator reached a per-tumour median Dice coefficient of 0.748 (0.745 pooled across all pairings) and a median bounded Hausdorff agreement of 0.776. Because parameters are calibrated against each tumours own reference mask and the train/validation split is over hosts, these figures quantify reproduction and host-transfer of a known lesion; prediction of unseen tumours is outside their scope. On a purposively selected ten-tumour subset, controlled comparisons tested both the contribution of directional information and whether a richer angular reconstruction improved performance. Relative to a direction-blind isotropic null, orientation-informed tracking improved all five evaluated metrics (dz = 0.4-1.2), although only surface Dice remained significant after Holm correction. A second comparison replaced the multi-shell SHORE dODF with a single-tensor dODF while keeping the tracking framework unchanged. No statistically detectable differences were observed between the two directional models on this subset, providing no evidence that resolving crossing fibres improved agreement with the visible tumour envelope. Directional sampling improved agreement with the MRI-visible tumour core, but the selected subset provided no evidence that the SHORE dODF outperformed the tensor dODF.

neuroscience↗

bioRxiv2026

The Signal Generating (SiGn) fMRI Phantom

Functional magnetic resonance imaging (fMRI) quality assurance has traditionally relied on static, geometrically regular phantoms that cannot generate the dynamic signal changes fMRI analysis pipelines are designed to detect. Here we present the Signal Generating (SiGn) anthropomorphic brain phantom, a 3D-printed cortical model derived from an individual participant's structural MRI, filled with tissue contrast-mimicking agar gels and coupled to a hemin-based infusion system that produces controlled, time-varying $T_2^*$-weighted signal changes. We validated the phantom across two scanning sessions on a 3\,T Siemens MAGNETOM Vida scanner, demonstrating that hemin infusion produced spatially localised activation detectable by standard general linear model analyses. Because the phantom's geometry is derived from real participant anatomy, its functional data can be coregistered and spatially normalised to standard brain templates through the same pipeline applied to human data, enabling end-to-end assessment of how each preprocessing step affects a known ground-truth signal. To support adoption and reproducibility, we openly release the full resource, including 3D-printable STL model files, tissue-mimicking gel recipes, the BIDS-formatted dataset, preprocessing and analysis scripts, and a containerised reproducibility workflow; the corresponding archival container image is also deposited on Zenodo. This framework is intended to lower the barrier for other groups to fabricate, scan, and analyse an equivalent device on their own hardware, adapt it to specific research questions, and iteratively improve the design, thereby supporting more rigorous and transparent fMRI quality assurance practices across the neuroimaging community.

neuroscience↗

bioRxiv2025

Impact of air pollution on Neurite Orientation Dispersion and Density metrics (NODDI) in 10-13-year-old children with and without ADHD diagnosis

Air pollution is a significant risk factor for adverse neurodevelopmental outcomes in children. While studies have linked pollutants to changes in brain structure, specific effects on white matter microstructure remain inconclusive. Neurite Orientation Dispersion and Density Imaging (NODDI) provide two nuanced, separate white matter measures that serve as proxies for neurite density and cell-body organization. We used NODDI to examine potential associations between prenatal, early life and current exposure to nitrogen dioxide (NO2) and particulate matter with diameter < 10 micrometers (PM10) and white matter microstructure in school-aged children. We also explored whether ADHD diagnosis moderated these associations. We observed several negative associations between both NO2 and PM10 exposure and neurite density across various white-matter fibers and exposure windows, but none of the associations were statistically significant after correcting for multiple comparisons. In this analysis, we did not find any statistically significant associations between long-term exposure to PM10 and NO2 and white matter microstructural integrity as measured by NODDI. Our results highlight the challenge of detecting modest environmental impacts on the brain and underscore the need for larger, more targeted studies to confirm these preliminary trends.

neuroscience↗

bioRxiv2025

Testing the Vogt-Bailey Index using task-based fMRI across pulse sequence protocols

Local connectivity analyses in fMRI such as the Vogt-Bailey Index, investigate the prevalence of co-fluctuations in the time-series of adjacent voxels. While there have been in silico assessments of the VB Index, this technique has not yet been assessed in vivo. This study has two aims: first, to assess the VB Index using a task paradigm with well established a priori expectations on the brain region predominantly responsible for executing this task to determine whether the VB Index highlights this area. Second, we investigate if, and how, the spatial resolution of the sequence protocols employed, with their inherent effects on the signal-to-noise ratio, affect the resultant VB maps. A cohort of 10 research volunteers underwent fMRI acquisitions utilising a block design finger tapping experiment. Each volunteer was scanned with three sequence protocols, with all parameters equivalent except for the volume of the voxels. The resulting parametric maps derived using the VB Index were compared with those obtained from the conventional General Linear Model approach. Particular emphasis was placed on the identification of the hand portion of the motor homunculus. Across sequence protocols, the VB Index consistently identified elevated local connectivity in, qualitatively, the same portion of the motor cortex as that yielded by the General Linear Model based on the task paradigm. However, the VB Index also detected elevated local connectivity outside the motor cortex while the General Linear Model results were mostly restricted to the motor cortex. The consistently high VB Index, across sequence protocols, in the cortical region associated with an fMRI task paradigm, despite the approachs agnosticism to that task, provides support for the biological relevance of such local connectivity measures.

neuroscience↗

bioRxiv2022

The Vogt-Bailey index: a local gradient analysis

In this work, we take a closer look at the Vogt-Bailey (VB) index, proposed in Ref. [1] as a tool for studying local functional homogeneity in the human cortex. We interpret the VB index in terms of the minimum ratio cut, a parameter that indicates whether a network can easily be disconnected into two parts having a comparable number of nodes. In our case, the nodes of the network consist of a brain vertex/voxel and its nearest neighbours, and a given edge is weighted according to the affinity of the nodes it connects (as reflected by the modified Pearson correlation between their fMRI time series). Consequently, the minimum ratio cut quantifies the degree of small-scale similarity in brain activity: the greater the similarity, the heavier the edges and the more difficult it is to disconnect the network, hence the higher the value of the minimum ratio cut. We compare the performance of the VB index with that of the Regional Homogeneity (ReHo) algorithm, commonly used to assess whether voxels in close proximity have synchronised fMRI signals, and find that the VB index is uniquely placed to detect sharp changes in the (local) functional organization of the human cortex.

neuroscience↗

bioRxiv2022

Feature similarity gradients detect alterations in the neonatal cortex associated with preterm birth

The early life environment programmes cortical architecture and cognition across the life course. A measure of cortical organisation that integrates information from multi-modal MRI and is unbound by arbitrary parcellations has proven elusive, which hampers efforts to uncover the perinatal origins of cortical health. Here, we use the Vogt-Bailey index to provide a fine-grained description of regional homogeneities and sharp variations in cortical microstructure based on feature gradients, and we investigate the impact of being born preterm on cortical development. Preterm infants have a homogeneous microstructure in temporal and occipital lobes, and the medial parietal, cingulate, and frontal cortices, compared with term infants. These observations replicated across two independent datasets and were robust to differences that remain in the data after matching samples and alignment of processing and quality control strategies. We conclude that cortical microstructural architecture is altered in preterm infants in a spatially distributed rather than localised fashion.

neuroscience↗

bioRxiv2020

A technical note on the geometric effects of volume to surface mapping of fMRI data

In this work, we identify a problem with the process of volume-to-surface mapping of functional Magnetic Resonance Imaging (fMRI) data when interested in investigating local connectivity. We show that neighborhood correlations on the surface of the brain vary spatially with anatomical patterns (gyral structure), even when the underlying volumetric data are uncorrelated noise. This could potentially have impacted studies focusing upon local neighborhood connectivity. We explore the effects of this anomaly across varying data resolutions and surface mesh densities, and propose an approach to mitigate these unwanted effects.

neuroscience↗

bioRxiv2020

Occipital Intralobar fasciculi and a novel description of three forgotten tracts

The continuously developing field of magnetic resonance imaging (MRI) has made a considerable contribution to the knowledge of brain architecture. It has given shape to a desire to construct a complete map of functional and structural connections. In particular, diffusion MRI paired with tractography has facilitated a non-invasive exploration of structural brain anatomy, which has helped build evidence for the existence of many association, projection and commissural fiber tracts. However, there is still a scarcity in research studies related to intralobar association fibers. The Dejerines (two of the most notable neurologists of 19th century France) gave an in-depth description of the intralobar fibers of the occipital lobe. Unfortunately, their exquisite work has since been sparsely referred to in the modern literature. This work gives the first modern description of many of the occipital intralobar lobe fibers described by the Dejerines. We perform a virtual dissection and reconstruct the tracts using diffusion MRI tractography. The virtual dissection is guided by the Dejerines treatise, Anatomie des Centres Nerveux. As an accompaniment to this article, the authors provided a French-to-English translation of the treatise portion concerning intra-occipital fiber bundles. This text provides the original description of five intralober occipital tracts, namely: the stratum calcarinum, the stratum proprium cunei, the vertical occipital fasciculus of Wernicke, the transverse fasciculus of the cuneus (TFC) and the transverse fasciculus of the lingual lobe of Vialet. It was possible to reconstruct all these tracts except for the TFC - possibly because its trajectory intermingles with a large amount of other fiber bundles. For completeness, the recently described sledge runner fasciculus, although not one of the Dejerine tracts, was identified and successfully reconstructed.

neuroscience↗