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As projects grow in scale with hundreds, even thousands, of individual participants and scans collected, quantification of brain structures by automated algorithms is becoming the only truly tractable approach. Here, we assessed the spatial and numerical reliability for newly deployed automated segmentation of hippocampal subfields and amygdala nuclei in FreeSurfer 7. In a sample of participants with repeated structural imaging scans (\n                    <jats:italic>N<\/jats:italic>\n                    \u2009=\u2009\n                    <jats:italic>928<\/jats:italic>\n                    ), we found numerical reliability (as assessed by intraclass correlations, ICCs) was reasonable. Approximately 95% of hippocampal subfields had \u201cexcellent\u201d numerical reliability (ICCs\u2009\u2265\u20090.90), while only 67% of amygdala subnuclei met this same threshold. In terms of spatial reliability, 58% of hippocampal subfields and 44% of amygdala subnuclei had Dice coefficients\u2009\u2265\u20090.70. Notably, multiple regions had poor numerical and\/or spatial reliability. We also examined correlations between spatial reliability and person-level factors (e.g., participant age; T1 image quality). Both sex and image scan quality were related to variations in spatial reliability metrics. Examined collectively, our work suggests caution should be exercised for a few hippocampal subfields and amygdala nuclei with more variable reliability.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Graphical Abstract<\/jats:bold>\n                  <\/jats:p>","DOI":"10.1186\/s40708-023-00189-5","type":"journal-article","created":{"date-parts":[[2023,4,7]],"date-time":"2023-04-07T14:02:42Z","timestamp":1680876162000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Quantifying numerical and spatial reliability of hippocampal and amygdala subdivisions in FreeSurfer"],"prefix":"10.1186","volume":"10","author":[{"given":"Isabella","family":"Kahhale","sequence":"first","affiliation":[]},{"given":"Nicholas J.","family":"Buser","sequence":"additional","affiliation":[]},{"given":"Christopher R.","family":"Madan","sequence":"additional","affiliation":[]},{"given":"Jamie L.","family":"Hanson","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,4,7]]},"reference":[{"issue":"9","key":"189_CR1","doi-asserted-by":"publisher","first-page":"558","DOI":"10.1007\/s002340050644","volume":"40","author":"E Achten","year":"1998","unstructured":"Achten E, Deblaere K, De Wagter C, Van Damme F, Boon P, De Reuck J, Kunnen M (1998) Intra- and interobserver variability of MRI-based volume measurements of the hippocampus and amygdala using the manual ray-tracing method. 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