Biology subjects

Kowalczyk, O. S.

Publications and source records attributed to Kowalczyk, O. S..

5 recordsLinked to original sources

bioRxiv2025

Susceptibility-matched padding improves the quality of cervical and lumbar spinal fMRI

Spinal cord functional magnetic resonance imaging (fMRI) has advanced significantly in recent years, revealing insights into the function of somatosensory and motor systems. However, the complex environment of the spinal cord induces unique sources of noise, limiting the quality of spinal fMRI recordings. Various hardware and software solutions have been proposed to address these challenges. Among them, susceptibility-matched padding has gained popularity due its low cost, ease of use, and effectiveness in reducing static B0 field inhomogeneities, which are a major source of artefacts in spinal fMRI. Despite anecdotal evidence, the impact of susceptibility-matched padding on the quality of spinal cord fMRI has not been assessed systematically. We investigated the effects of non-protonated perfluorocarbon liquid-filled padding (SatPad) on B0 field homogeneity and functional echo-planar imaging (EPI) in cervical and lumbar spinal cord in 10 healthy volunteers. Participants underwent two resting-state fMRI scanning sessions, one per cord section. Within each session they were scanned with and without SatPad in a pseudo-randomised order. The use of SatPad increased B0 field homogeneity and improved functional image quality metrics, including temporal signal-to-noise ratio, timeseries coefficient of variation, DVARS, and ghosting artefacts. While both cervical and lumbar cord data benefited from the use of SatPad, greater effects were observed in the cervical cord. These findings provide a compelling basis for integrating susceptibility-matched padding into routine spinal fMRI protocols.

neuroscience↗

bioRxiv2025

Test-retest reliability of sensorimotor activity measured with spinal cord fMRI

Establishing the reliability of spinal cord functional magnetic resonance imaging (fMRI) is critical before employing it to assess experimental or clinical interventions. Previous studies have mapped human motor activity primarily to the ipsilateral ventral horn, aligning with myotomal and dermatomal projections. Despite these insights, the test-retest reliability of spinal fMRI remains under-investigated. Here we assessed spinal cord activation during a sensorimotor paradigm involving right-hand grasping and grip force estimation in 30 healthy volunteers. Participants completed two identical scanning visits, each time performing the same task twice, enabling the investigation of test-retest reliability both within a single experimental visit and between visits performed on different days. Aggregating all task runs, motor-evoked activation was observed in ipsilateral ventro-dorsal regions of spinal segmental levels C5-T1, as well as in medial regions of levels C2-C3. Despite highly reliable task performance (grip force) and fMRI signal quality (temporal signal-to-noise ratio), the reliability of motor activation was predominantly poor-to-fair both within and between visits, with notable variability in spatial distribution observed across task runs. Increasing the number of task runs per individual improved the robustness of group-level activation, as indexed by higher activated voxel count, larger cluster spatial extent, and attenuated t-statistic distribution. Although we demonstrated that motor-evoked activation corresponds to the known neuroanatomical organisation of motor circuits, its low test-retest reliability presents a challenge for wider applications of spinal fMRI. Understanding the drivers of low reliability in functional imaging is warranted, but we suggest that looking beyond measurement error is required, including careful consideration of inherent within-individual variability underpinned by neurophysiological and psychological factors.

neuroscience↗

bioRxiv2025

EPISeg: Automated segmentation of the spinal cord on echo planar images using open-access multi-center data

Functional magnetic resonance imaging (fMRI) of the spinal cord is relevant for studying sensation, movement, and autonomic function. Preprocessing of spinal cord fMRI data involves segmentation of the spinal cord on gradient-echo echo planar imaging (EPI) images. Current automated segmentation methods do not work well on these data, due to the low spatial resolution, susceptibility artifacts causing distortions and signal drop-out, ghosting, and motion-related artifacts. Consequently, this segmentation task demands a considerable amount of manual effort which takes time and is prone to user bias. In this work, we (i) gathered a multi-center dataset of spinal cord gradient-echo EPI with ground-truth segmentations and shared it on OpenNeuro https://openneuro.org/datasets/ds005143/versions/1.3.0, and (ii) developed a deep learning-based model, EPISeg, for the automatic segmentation of the spinal cord on gradient-echo EPI data. We observe a significant improvement in terms of segmentation quality compared to other available spinal cord segmentation models. Our model is resilient to different acquisition protocols as well as commonly observed artifacts in fMRI data. The training code is available at https://github.com/sct-pipeline/fmri-segmentation/, and the model has been integrated into the Spinal Cord Toolbox as a command-line tool.

neuroscience↗

bioRxiv2023

A novel implementation of spinal fMRI demonstrates segmental organisation of functionally connected networks in the cervical spinal cord: A test-retest reliability study

Resting fMRI studies have identified intrinsic spinal cord activity, which forms organised motor (ventral) and sensory (dorsal) resting-state networks. However, to facilitate the use of spinal fMRI in, for example, clinical studies, it is crucial to first assess the reliability of the method, particularly given the unique anatomical, physiological, and methodological challenges associated with acquiring the data. Here we demonstrate a novel implementation for acquiring BOLD-sensitive resting-state spinal fMRI, which was used to characterise functional connectivity relationships in the cervical cord and assess their test-retest reliability in 23 young healthy volunteers. Resting-state networks were estimated in two ways: (1) by extracting the mean timeseries from anatomically constrained seed masks and estimating voxelwise connectivity maps and (2) by calculating seed-to-seed correlations between extracted mean timeseries. Seed regions corresponded to the four grey matter horns (ventral/dorsal and left/right) of C5-C8 segmental levels. Test-retest reliability was assessed using the intraclass correlation coefficient (ICC) in the following ways: for each voxel in the cervical spine; each voxel within an activated cluster; the mean signal as a summary estimate within an activated cluster; and correlation strength in the seed-to-seed analysis. Spatial overlap of clusters derived from voxelwise analysis between sessions was examined using Dice coefficients. Following voxelwise analysis, we observed distinct unilateral dorsal and ventral organisation of cervical spinal resting-state networks that was largely confined in the rostro-caudal extent to each spinal segmental level, with more sparse connections observed between segments (Bonferroni corrected p < 0.003, threshold-free cluster enhancement with 5000 permutations). Additionally, strongest correlations were observed between within-segment ipsilateral dorso-ventral connections, followed by within-segment dorso-dorsal and ventro-ventral connections. Test-retest reliability of these networks was mixed. Reliability was poor when assessed on a voxelwise level, with more promising indications of reliability when examining the average signal within clusters. Reliability of correlation strength between seeds was highly variable, with highest reliability achieved in ipsilateral dorso-ventral and dorso-dorsal/ventro-ventral connectivity. However, the spatial overlap of networks between sessions was excellent. We demonstrate that while test-retest reliability of cervical spinal resting-state networks is mixed, their spatial extent is similar across sessions, suggesting that these networks are characterised by a consistent spatial representation over time.

neuroscience↗

bioRxiv2017

The effect of smoking on the brain revealed by using electronic cigarettes with concurrent fMRI

Cigarette addiction is driven partly by the physiological effects of nicotine, but also by the distinctive sensory and behavioural aspects of smoking, and understanding the neural effects of such processes is vital. There are many practical difficulties associated with subjects smoking in the modern neuroscientific laboratory environment, however electronic cigarettes obviate many of these issues, and provide a close simulation of smoking tobacco cigarettes. We have examined the neural effects of smoking electronic cigarettes with concurrent functional Magnetic Resonance Imaging (fMRI). The results demonstrate the feasibility of using these devices in the MRI environment, and show brain activation in a network of cortical (motor cortex, insula, cingulate, amygdala) and sub-cortical (putamen, thalamus, globus pallidus, cerebellum) regions. Concomitant relative deactivations were seen in the ventral striatum and orbitofrontal cortex. These results reveal the brain processes involved in (simulated) smoking for the first time, and validate a novel approach to the study of smoking, and addiction more generally.

neuroscience↗