Biology subjects

van der Werf, Y. D.

Publications and source records attributed to van der Werf, Y. D..

8 recordsLinked to original sources

bioRxiv2026

The ENIGMA-PD-WML Pipeline: A Containerized, User-Friendly Approach for Accurate, Standardized Segmentation of White Matter Lesions in Multi-Site MRI Data

Understanding vascular contributions to disease is a major unmet need. White matter lesions (WML) are an accepted imaging marker of cerebral small vessel disease, giving insights into its related pathologies. A unified approach for WML analyses in large multi-site data is lacking despite the need for pooling of data to overcome the limitations of often small heterogenous MRI studies which make subtyping and identifying patterns within disease groups difficult. Our ENIGMA-PD-WML pipeline is an open-source containerized pipeline containing all the code and packages required for pre-processing, processing and post-processing of T1-weighted and FLAIR data, outputting accurate and reproducible binary WML maps using a UNet approach. The pipeline provides a standardized image analysis approach for WML and outputs data in both native and MNI space to allow for sharing and pooling of data from multiple sites for large-data analysis. In addition to a reliable standardized approach for WML segmentation, key priorities when developing the pipeline included: usability, i.e., requiring minimal manual input and technical expertise to use, and suitability to run on various MRI scanners and acquisition parameters as is common in multi-site data. This paper describes the pipeline in detail, with rationale for each step, providing transparency and facilitating its usage to overcome reproducibility issues in large-scale WML analyses.

neuroscience↗

bioRxiv2026

Comparison of Automated White Matter Lesion Segmentation Approaches for Use in Large, Multi-Site Data Analyses in Parkinson's Disease

BackgroundParkinsons disease (PD) is the second most common neurodegenerative disorder. PD currently lacks effective disease-modifying treatments, likely due to its diverse clinical features and underlying neuropathology. The vascular role in PD is emerging, with vascular mechanisms increasingly implicated, yet the literature remains conflicted, motivating large-data analyses with greater statistical power. White matter lesions (WML) are an accepted imaging marker of small vessel disease. Accurate automated WML segmentation techniques are crucial for large-scale studies in PD due to the impracticality of manual segmentation for extensive datasets and to ensure consistency. Evaluation of the optimum approach in PD for large-scale analysis is lacking. This study aimed to evaluate various automated WML segmentation algorithms to determine the most accurate and reliable method, among those selected, for assessing WML for multi-site large data analysis in PD. MethodsWe assessed whole-brain volumetric T1-weighted and FLAIR images from 201 PD patients (mean age, 66.6 {+/-} 7.86 years) and 64 healthy controls (HC; mean age, 66.3 {+/-} 8.67) across three datasets: the Parkinsons Progression Markers Initiative (PPMI), the University of Pennsylvania (UPenn) and the Montreal Neurological Institute Biobank: Clinical Biological Imaging and Genetic Repository (C-BIG). The sample included different scanners, imaging parameters and lesion loads, as would be expected for multi-site data. WML were manually segmented to provide the gold standard, and four freely available automated algorithms were evaluated: FSLs BIANCA, FreeSurfer, SPMs LST-LPA and U-Net-pgs using the performance metrics: Dice score, Hausdorff distance, recall, precision, F1 score, log absolute volume difference (LOGAVD) and intraclass correlation coefficient (ICC). Subgroup analyses were performed based on lesion load and lobar regions. The associations of data from these automated approaches with age, and with Fazekas and Wahlund visual rating scales, were assessed through partial correlation analysis. ResultsU-Net-pgs performed best overall, with the highest Dice score (PD: 0.46 {+/-} 0.21; HC: 0.39 {+/-} 0.21), recall (PD: 0.76 {+/-} 0.25; HC: 0.62 {+/-} 0.31), precision (PD: 0.49 {+/-} 0.25; HC: 0.63 {+/-} 0.27), F1 score (PD: 0.54 {+/-} 0.22; HC: 0.56 {+/-} 0.22) and ICC (PD: 0.965; HC: 0.967) and lowest Hausdorff distance (PD: 8.89 {+/-} 3.96; HC: 6.33 {+/-} 2.91). U-Net-pgs achieved the lowest LOGAVD in the PD group (0.31 {+/-} 0.31) whereas BIANCA-LOO with a threshold of 0.9 was lowest in HC (0.27 {+/-} 0.30). U-Net also showed superior performances in all lesion loads for PD and overall across various brain regions in both PD and HC. ConclusionOverall, U-Net-pgs emerged as the best performing automated method, of those we evaluated, for WML segmentation in PD and HC within a dataset collected with various scanner and image acquisition parameters. U-Net-pgs consistently outperformed other automated approaches across lesion loads and brain regions, for most metrics. The accuracy and reliability of U-Net-pgs make it a promising tool for large-scale analyses, facilitating future research investigating WML in PD.

neuroscience↗

bioRxiv2026

Nipoppy: A framework for standardizing neuroimaging studies to facilitate international derived-data sharing

Neuroimaging data management and processing are tedious and error-prone, prompting reproducibility concerns. Globally, studies with heterogeneous infrastructure and governance policies lead to eclectic data processing and sharing, necessitating standardization of data workflows to ensure reusability and comparability of multi-centric datasets. The Nipoppy neuroinformatics framework facilitates such standardization by combining specification, protocol, and software to manage study-level data workflows. With its adoption, researchers can share standardized, derived datasets enabling efficient, reproducible, and inclusive research.

bioinformatics↗

bioRxiv2026

Open neuroinformatics infrastructure ecosystem for federated multisite studies

Despite growing understanding of the benefits of having Findable, Accessible, Interoperable, and Reusable (FAIR) data, many datasets still cannot be shared. Federated analysis methods can enable multisite studies that do not require the sharing of participant-level information. However, there are many practical hurdles that prevent the large-scale adoption of federated methods. We discuss challenges related to cross-site data preparation for federated learning, present solutions offered by recent neuroinformatics projects, and showcase an example of tool integration applied to neurodegenerative disease data.

neuroscience↗

bioRxiv2025

Executive control in Obsessive-Compulsive Disorder: A worldwide mega-analysis of task-based functional neuroimaging data of the ENIGMA-OCD consortium

ObjectiveObsessive-compulsive disorder (OCD) is associated with impaired executive function and altered activity in associated neural circuits, contributing to reduced goal-directed behavior. To investigate neural activation during executive control, we conducted a mega-analysis in the ENIGMA-OCD consortium pooling individual participant data from 475 individuals with OCD and 345 healthy controls across 15 fMRI tasks collected worldwide. MethodsIndividual participant data was uniformly processed using HALFpipe to construct voxelwise statistical images of executive control and task load contrasts. Parameter estimates extracted from regions of interest were entered into multilevel Bayesian models to examine regional and whole-brain effects of diagnosis, and, within OCD, the influence of medication status, symptom severity, and age of onset on task activation. ResultsWe observed a robust task activation pattern across individuals with OCD and control participants in executive control regions across tasks. Relative to controls, individuals with OCD showed moderate to very strong evidence of weaker activation of the dorsolateral prefrontal cortex, precuneus, frontal eye fields, and inferior parietal lobule during executive control (all positive posterior probabilities [P+]<0.1). Individuals with OCD also showed stronger activation in regions of the default mode network during executive function relative to controls. We found little evidence for differential activation during executive control in task- positive regions related to disease onset, severity and medication status. ConclusionIn the first mega-analysis of fMRI studies of executive function in OCD, we found strong evidence of weaker frontoparietal activation during executive control tasks. Our findings also suggest a failure of default mode network regions to appropriately disengage during task performance in OCD.

neuroscience↗

bioRxiv2019

Resting-state and task-based centrality of dorsolateral prefrontal cortex predict resilience to inhibitory repetitive transcranial magnetic stimulation

BackgroundRepetitive transcranial magnetic stimulation (rTMS) is used to investigate normal brain function in healthy participants and as a treatment for brain disorders. Various subject factors can influence individual response to rTMS, including brain network properties.\n\nObjective/HypothesisA previous study by our group showed that virtually lesioning the left dorsolateral prefrontal cortex (dlPFC; important for cognitive flexibility) using inhibitory rTMS reduced performance on a set-shifting task. We aimed to determine whether this behavioural response was related to topological features of pre-TMS resting-state and task-based functional networks.\n\nMethodsInhibitory (1Hz) rTMS was applied to the left dlPFC in 16 healthy participants, and to the vertex in 17 participants as a control condition. Participants performed a set-shifting task during fMRI at baseline and directly after a single rTMS session 1-2 weeks later. Functional network topology measures were calculated from resting-state and task-based fMRI scans using graph theoretical analysis.\n\nResultsThe dlPFC-stimulated group, but not the vertex group, showed reduced set shifting performance after rTMS associated with lower task-based betweenness centrality of the dlPFC at baseline (p=.030) and a smaller reduction in task-based betweenness centrality after rTMS (p=.024). Reduced repeat trial accuracy after rTMS was associated with higher baseline resting state node strength of the dlPFC (p=.017).\n\nConclusionsOur results suggest that behavioural response to inhibitory rTMS to the dlPFC is dependent on baseline functional network features. Individuals with more globally integrated stimulated regions show greater resilience to inhibitory rTMS, while individuals with more locally well-connected regions show greater vulnerability.\n\nHighlightsO_LIFunctional brain network properties predict behavioural response to 1Hz DLPFC rTMS\nC_LIO_LIGlobally integrated stimulated regions are resilient to effects of inhibitory rTMS\nC_LIO_LISegregated, locally well-connected regions are vulnerable to inhibitory rTMS\nC_LIO_LIChange in performance after rTMS correlates with change in network properties\nC_LI

neuroscience↗

bioRxiv2019

Resting-state network topology and planning ability in healthy adults

Functional magnetic resonance imaging (fMRI) studies have been used extensively to investigate the brain areas that are recruited during the Tower of London (ToL) task. Nevertheless, little research has been devoted to study the neural correlates of the ToL task using a network approach. Here we investigated the association between functional connectivity and network topology during resting-state fMRI and ToL task performance, that was performed outside the scanner. Sixty-two (62) healthy subjects (21-74 years) underwent eyes-closed rsfMRI and performed the task on a laptop. We studied global (whole-brain) and within subnetwork resting-state topology as well as functional connectivity between subnetworks, with a focus on the default-mode, fronto-parietal and dorsal and ventral attention networks. Efficiency and clustering coefficient were calculated to measure network integration and segregation, respectively, at both the global and subnetwork level. Our main finding was that higher global efficiency was associated with slower performance ({beta} = .22, Pbca = .04) and this association seemed mainly driven by inter-individual differences in default-mode network connectivity. The reported results were independent from age, sex, education-level and motion. Although this finding is contrary to earlier findings on general cognition, we tentatively hypothesize that the reported association may indicate that individuals with a more integrated brain during the resting-state are less able to further increase network efficiency when transitioning from a rest to task state, leading to slower responses. This study also adds to a growing body of literature supporting a central role for the default-mode network in individual differences in cognitive performance.

neuroscience↗

bioRxiv2018

Functional connectivity alterations in Parkinson’s disease during the stop-signal task

Although deficits in response inhibition are common in Parkinsons disease (PD), studies on their neural correlates are relatively scarce. In our previous study, medication-naive PD patients showed, among others, lower activation of the inhibition-related bilateral inferior frontal gyrus (IFG) compared with healthy controls while performing the stop-signal task. Here we report on a follow-up study in the same cohort.\n\nFourteen medicated PD patients and 16 healthy controls performed the same stop-signal task during MRI; 3.1{+/-}1.0 years after our previous study. During that time, all PD patients had started to use dopaminergic medication. We analyzed task-related functional activity and connectivity in the bilateral IFG and anterior insula, brain regions that are important response inhibition. Task-related functional connectivity was analyzed with generalized psychophysiological interaction.\n\nPD patients were significantly slower on response initiation (GO reaction time) and response inhibition (stop-signal reaction time) than healthy controls. There were no between-group differences in functional activity. On the other hand, functional connectivity of the IFG and anterior insula was significantly lower in PD compared with healthy controls. Mainly the inferior parietal lobule and dorsolateral prefrontal cortex were less connected with these seed regions.\n\nThese results show that early-stage medicated PD patients show lower task-related functional connectivity but not activity of brain regions that are important for response inhibition; the IFG and anterior insula. We tentatively speculate that the use of dopaminergic medication upheld task-related activity but not connectivity.

neuroscience↗