Autistic vs. Control Differences in MRI Scan Quality Across ABIDE-II Sites.

Overview

1. Imaging Department, University of Algarve-Centre for Health Studies, 8005-139 Faro, Portugal
2. Faculty of Psychology, University of Aveiro, 3800-193 Aveiro, Portugal
3. Algarve Private Hospital Group, 8005-226 Faro, Portugal
4. Faculty of Biomedical Sciences and Medicine, University of Algarve, 8005-139 Faro, Portugal
5. Psychiatry Department, Hospital of Viana do Castelo, 4900-408 Viana do Castelo, Portugal

Abstract

Background: Head motion and variability in scan quality remain major methodological challenges in autism neuroimaging. Large multi-site datasets such as ABIDE-II provide a unique opportunity to systematically quantify diagnostic differences in MRI data quality and assess the influence of site-level heterogeneity. Methods: Functional MRI Quality Assessment Protocol (QAP) metrics were combined with phenotypic data from ABIDE-II. Participants were classified as autistic (ASD) or typically developing (TD). Key quality metrics—including mean framewise displacement (mFD), proportion of volumes exceeding 0.20 mm (FD > 0.20), signal-to-noise ratio (SNR), and entropy focus criterion (EFC)—were analyzed alongside age, sex, IQ, and site. Group differences were evaluated using non-parametric tests and linear mixed-effects models with site as a random factor. Additional analyses examined site-level heterogeneity and the impact of quality-control (QC) thresholds on sample composition. Results: The final sample included 1277 participants (579 ASD; 698 TD) across 14 sites. ASD participants exhibited significantly greater head motion (median mFD = 0.101 vs. 0.081 mm; p < 1 × 10−10) and modest reductions in signal quality (lower SNR, higher EFC). Elevated motion in ASD was observed in 12 of 14 sites, although effect sizes varied substantially. Mixed-effects models confirmed that diagnosis remained a significant predictor of motion after adjusting for covariates. In contrast, signal-quality differences were small and largely explained by site effects. Simulated QC procedures disproportionately excluded ASD participants, with exclusion rates up to 31% compared to 18% in TD. Conclusions: ASD participants show consistently higher head motion, while signal-quality differences are minimal and largely site-driven. Standard QC procedures disproportionately exclude ASD individuals, highlighting the need for improved motion handling and more balanced quality-control strategies in multi-site studies.

Reproduced under the paper's license (CC BY), from the paper cited above.

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Data

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Data Availability Statement

The data analyzed in this study are publicly available through the Autism Brain Imaging Data Exchange II (ABIDE-II) initiative. fMRI quality metrics (Quality Assessment Protocol; QAP) and phenotypic datasets were obtained from the ABIDE-II repository, accessible via the International Neuroimaging Data-sharing Initiative (INDI) platform (http://fcon_1000.projects.nitrc.org/indi/abide/abide_II.html, accessed on 27 January 2026). Access to ABIDE-II data requires registration and agreement to the data usage terms established by the data contributors. No new raw imaging data were generated as part of this study. All analyses were conducted using previously released, de-identified datasets. Derived analysis code and statistical scripts used to generate the results reported in this manuscript are available from the corresponding author upon reasonable request.

Reproduced under the paper's license (CC BY), from the paper cited above.

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Version 2, 28 September 2026

• Funding: added National Institute of Mental Health: R21 MH107045

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 5 keywords, 24 references.

Cite

This paper

Pinheiro, J., Afonso, B., de Seiça, E. C., Gonçalves, R., Ribeiro, L., & Reis, J. (2026). Autistic vs. Control Differences in MRI Scan Quality Across ABIDE-II Sites. Diagnostics (Basel, Switzerland), 16(10), 1478. https://doi.org/10.3390/diagnostics16101478

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