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Despite the high performances reported in numerous studies, developing CNN models with good generalization abilities is still a challenging task due to possible data leakage introduced during cross-validation (CV). In this study, we quantitatively assessed the effect of a data leakage caused by 3D MRI data splitting based on a 2D slice-level using three 2D CNN models to classify patients with Alzheimer\u2019s disease (AD) and Parkinson\u2019s disease (PD). Our experiments showed that slice-level CV erroneously boosted the average slice level accuracy on the test set by 30% on Open Access Series of Imaging Studies (OASIS), 29% on Alzheimer\u2019s Disease Neuroimaging Initiative (ADNI), 48% on Parkinson\u2019s Progression Markers Initiative (PPMI) and 55% on\u00a0a local de-novo PD Versilia dataset. Further tests on a randomly labeled OASIS-derived dataset produced about 96% of (erroneous) accuracy (slice-level split) and 50% accuracy (subject-level split), as expected from a randomized experiment. Overall, the extent of the effect of an erroneous slice-based CV is severe, especially for small datasets.<\/jats:p>","DOI":"10.1038\/s41598-021-01681-w","type":"journal-article","created":{"date-parts":[[2021,11,19]],"date-time":"2021-11-19T06:02:53Z","timestamp":1637301773000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":169,"title":["Effect of data leakage in brain MRI classification using 2D convolutional neural networks"],"prefix":"10.1038","volume":"11","author":[{"given":"Ekin","family":"Yagis","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Selamawet Workalemahu","family":"Atnafu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alba","family":"Garc\u00eda Seco de Herrera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chiara","family":"Marzi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Riccardo","family":"Scheda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Giannelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlo","family":"Tessa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Citi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefano","family":"Diciotti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,11,19]]},"reference":[{"key":"1681_CR1","doi-asserted-by":"crossref","first-page":"24411","DOI":"10.1109\/ACCESS.2018.2830661","volume":"6","author":"WG Hatcher","year":"2018","unstructured":"Hatcher, W. 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