arXiv subjects

Penny Gowland

Publications and source records attributed to Penny Gowland.

7 recordsLinked to original sources

arXiv2026

Accelerating MRI Colon Volume Measurements and Reducing Inter-Observer Variation through Automatic Segmentation and Human-in-the-Loop Correction

The movement distribution, and volume of both chyme and gas in the colon, are important metrics to understand colonic function in health, disease, and the effects of treatments and different foodstuffs. Current methods available for assessment of these colonic contents using MRI consist mainly of manual segmentation or semi-automatic segmentation. However, these methods of segmentation are very labour intensive and too slow for clinical applications, require expert knowledge and some semi-automatic methods require use of bowel preparation. MRI scans were acquired in 2 breath holds using mDIXON sequences. We used the 'No New U-Net' (nnU-Net) ML model to automatically segment the colon, including colonic regions (ascending, transverse, descending and sigmoid-rectal). The ML-generated masks were corrected manually and the time taken for correction was recorded. ML segmentations were compared to both manual segmentations and observer corrected ML (CorrML) segmentations. Observer repeatability was also evaluated for both manual and CorrML methods to create a benchmark for the allowable error in the automatic segmentations. Analysis time was significantly reduced (p<0.0001) from 56 mins (+-11 mins (SD)) for manual masks to 11 mins (+-5 mins (SD)) for CorrML masks. Both DICE and ICC values showed excellent agreement between manual, ML and CorrML segmentations for whole colonic volume (ICC = 0.96) whilst regional volumes were good-excellent (ICC = 0.80-0.95). Inter-observer repeatability was improved when using CorrML methods over manual segmentation (ICC manual > 0.89, CorrML > 0.93). Analysis time was reduced by over 80% when using CorrML methods and whole colonic volumes measured by ML would be suitable for use with minimal checks. Hence the methods proposed here would be clinically useful.

physics.med-ph↗

arXiv2026

T$_2$* and Susceptibility Mapping as Indicators of Placental Health

Objective(s): T$_2$* and susceptibility ($χ$) MRI mapping provide complimentary measures of the haemodynamic environment in the placenta. The aims of this work were to use these simultaneously obtained measures to investigate the role of oxygen distribution on the well-established reduction of T$_2$* with gestational age found in healthy pregnancies and explore differences in both measures in compromised placentas. Methods: T$_2$* and $χ$ were measured simultaneously from a double echo, echo planar scan of the whole placenta, across a range of gestational ages and pregnancy complications. Regional variations across the placenta were investigated. Results: Whole placental mean T$_2$* was more correlated with standard deviation of $χ$ than mean $χ$ indicating it is more driven by increasing local inhomogeneities rather than bulk deoxygenation with healthy gestation. Compromised placentas also showed increased standard deviation of $χ$ as well as lower mean T$_2$* suggesting flow/uptake mismatch and reduced oxygenation. Regionally, the susceptibility was lowest (most oxygenated) and least variable in the central region of the placenta indicating good mixing and refreshment of blood in this area. The susceptibility was highest (most deoxygenated) and most variable at the fetal side, suggesting less effective perfusion in this region. Compromised cases showed the greatest difference on the fetal side for both mean and standard deviation of $χ$. T$_2$* was lowest at the fetal side for healthy and compromised cases but the maternal and central regions better distinguished between the two groups. Conclusion(s): T$_2$* and susceptibility can be mapped simultaneously from a single MRI scan and provide complimentary information about the function of the placenta across healthy gestational development, and as a potential indicator of placental compromise.

physics.med-ph↗

arXiv2026

Placental contractions in uncomplicated pregnancies

In 2020 we first described placental contractions, and we have now undertaken a study to characterise them and seek features that might automatically separate them from uterine contractions. We recruited 36 healthy pregnant women to undergo magnetic resonance imaging (MRI) between 29 and 42 weeks of pregnancy in a single-centre, prospective, observational study. Participants had fetal ultrasound to confirm normal growth. Dynamic MRI was acquired for between 15 and 32 minutes using respiratory triggered, multi-slice, single shot, gradient echo, echo planar imaging covering the whole uterus. All participants had a live birth of a healthy baby weighing over the 10th centile for gestational age and none developed any associated conditions of placental dysfunction e.g. pre-eclampsia, or severe maternal or fetal villous malperfusion on placental histopathology. Any visible contractions were recorded for all participants who completed their MRI scan and placental contractions occurred in at least 60% of our healthy pregnant population with a median frequency of approximately 2 per hour, and a median duration of 2.4 minutes. Contractions involving a decrease in placental volume of >10% were classified as either placental or uterine by visual observation. Placental contractions occurred more frequently than uterine contractions (p=0.0061), were associated with a larger increase in the surface area of the uterine wall not covered by the placenta (p=0.0015), placental sphericity (p<0.0001) and longer duration (p=0.0151). All contractions led to an increase in the MRI parameter R2* in the placenta. There was large variation both between participants and between contractions from the same individual, in terms of time course and contractions features, with no apparent change across the gestational age range studied, although the largest fractional volume changes were detected at early gestation.

physics.med-ph↗

arXiv2026

Charting the velocity of brain growth and development

Brain charts have emerged as a highly useful approach for understanding brain development and aging on the basis of brain imaging and have shown substantial utility in describing typical and atypical brain development with respect to a given reference model. However, all existing models are fundamentally cross-sectional and cannot capture change over time at the individual level. We address this using velocity centiles, which directly map change over time and can be overlaid onto cross-sectionally derived population centiles. We demonstrate this by modelling rates of change for 24062 scans from 10795 healthy individuals with up to 8 longitudinal measurements across the lifespan. We provide a method to detect individual deviations from a stable trajectory, generalising the notion of thrive lines, which are used in pediatric medicine to declare failure to thrive. Using this approach, we predict transition from mild cognitive impairment to dementia more accurately than by using either time point alone, replicated across two datasets. Last, by taking into account multiple time points, we improve the sensitivity of velocity models for predicting the future trajectory of brain change. This highlights the value of predicting change over time and makes a fundamental step towards precision medicine.

q-bio.NC↗

arXiv2025

An Attentive Representative Sample Selection Strategy Combined with Balanced Batch Training for Skin Lesion Segmentation

An often overlooked problem in medical image segmentation research is the effective selection of training subsets to annotate from a complete set of unlabelled data. Many studies select their training sets at random, which may lead to suboptimal model performance, especially in the minimal supervision setting where each training image has a profound effect on performance outcomes. This work aims to address this issue. We use prototypical contrasting learning and clustering to extract representative and diverse samples for annotation. We improve upon prior works with a bespoke cluster-based image selection process. Additionally, we introduce the concept of unsupervised balanced batch dataloading to medical image segmentation, which aims to improve model learning with minimally annotated data. We evaluated our method on a public skin lesion dataset (ISIC 2018) and compared it to another state-of-the-art data sampling method. Our method achieved superior performance in a low annotation budget scenario.

cs.CV↗

arXiv2025

Automatic rating of incomplete hippocampal inversions evaluated across multiple cohorts

Incomplete Hippocampal Inversion (IHI), sometimes called hippocampal malrotation, is an atypical anatomical pattern of the hippocampus found in about 20% of the general population. IHI can be visually assessed on coronal slices of T1 weighted MR images, using a composite score that combines four anatomical criteria. IHI has been associated with several brain disorders (epilepsy, schizophrenia). However, these studies were based on small samples. Furthermore, the factors (genetic or environmental) that contribute to the genesis of IHI are largely unknown. Large-scale studies are thus needed to further understand IHI and their potential relationships to neurological and psychiatric disorders. However, visual evaluation is long and tedious, justifying the need for an automatic method. In this paper, we propose, for the first time, to automatically rate IHI. We proceed by predicting four anatomical criteria, which are then summed up to form the IHI score, providing the advantage of an interpretable score. We provided an extensive experimental investigation of different machine learning methods and training strategies. We performed automatic rating using a variety of deep learning models (conv5-FC3, ResNet and SECNN) as well as a ridge regression. We studied the generalization of our models using different cohorts and performed multi-cohort learning. We relied on a large population of 2,008 participants from the IMAGEN study, 993 and 403 participants from the QTIM/QTAB studies as well as 985 subjects from the UKBiobank. We showed that deep learning models outperformed a ridge regression. We demonstrated that the performances of the conv5-FC3 network were at least as good as more complex networks while maintaining a low complexity and computation time. We showed that training on a single cohort may lack in variability while training on several cohorts improves generalization.

eess.IV↗

arXiv2015

Nonlinear functional mapping of the human brain

The field of neuroimaging has truly become data rich, and novel analytical methods capable of gleaning meaningful information from large stores of imaging data are in high demand. Those methods that might also be applicable on the level of individual subjects, and thus potentially useful clinically, are of special interest. In the present study, we introduce just such a method, called nonlinear functional mapping (NFM), and demonstrate its application in the analysis of resting state fMRI from a 242-subject subset of the IMAGEN project, a European study of adolescents that includes longitudinal phenotypic, behavioral, genetic, and neuroimaging data. NFM employs a computational technique inspired by biological evolution to discover and mathematically characterize interactions among ROI (regions of interest), without making linear or univariate assumptions. We show that statistics of the resulting interaction relationships comport with recent independent work, constituting a preliminary cross-validation. Furthermore, nonlinear terms are ubiquitous in the models generated by NFM, suggesting that some of the interactions characterized here are not discoverable by standard linear methods of analysis. We discuss one such nonlinear interaction in the context of a direct comparison with a procedure involving pairwise correlation, designed to be an analogous linear version of functional mapping. We find another such interaction that suggests a novel distinction in brain function between drinking and non-drinking adolescents: a tighter coupling of ROI associated with emotion, reward, and interoceptive processes such as thirst, among drinkers. Finally, we outline many improvements and extensions of the methodology to reduce computational expense, complement other analytical tools like graph-theoretic analysis, and allow for voxel level NFM to eliminate the necessity of ROI selection.

q-bio.NC↗