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Inconsistencies highlighted in previous studies on brainstem in the population with ASD may in part be a result of poor agreement in the extraction of structural features between different methods. A sample of 76 children with ASD and 76 age\u2010, gender\u2010, and intelligence\u2010matched controls was considered. Volumetric analyses were performed using common tools for brain structures segmentation, namely FSL\u2010FIRST, FreeSurfer (FS), and Advanced Normalization Tools (ANTs). For shape analysis SPHARM\u2010MAT was employed. Intermethod agreement was quantified in terms of Pearson correlations between pairs of volumes obtained by the different methods. The degree of overlap between segmented masks was quantified in terms of the Dice index. Both Pearson correlations and Dice indices, showed poor agreement between FSL\u2010FIRST and the other methods (ANTs and FS), which by contrast, yielded Pearson correlations greater than 0.93 and average Dice indices greater than 0.76 when compared with each other. As with volume, shape analyses exhibited discrepancies between segmentation methods, with particular differences noted between FSL\u2010FIRST and the others (ANT and FS), with under\u2010 and over\u2010segmentation in specific brainstem regions. These data suggest that research on brain structure alterations should cross\u2010validate findings across multiple methods. We consistently detected an enlargement of brainstem volume in the whole sample and in the male cohort across multiple segmentation methods, a feature particularly driven by the subgroup of children with idiopathic intellectual disability associated with ASD.<\/jats:p>","DOI":"10.1002\/hbm.24351","type":"journal-article","created":{"date-parts":[[2018,9,5]],"date-time":"2018-09-05T10:11:38Z","timestamp":1536142298000},"page":"7-19","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Brainstem enlargement in preschool children with autism: Results from an intermethod agreement study of segmentation algorithms"],"prefix":"10.1002","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4724-9423","authenticated-orcid":false,"given":"Paolo","family":"Bosco","sequence":"first","affiliation":[{"name":"Pisa Division INFN \u2010 National Institute for Nuclear Physics  Pisa Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alessia","family":"Giuliano","sequence":"additional","affiliation":[{"name":"Pisa Division INFN \u2010 National Institute for Nuclear Physics  Pisa Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Delafield\u2010Butt","sequence":"additional","affiliation":[{"name":"Faculty of Humanities and Social Science University of Strathclyde  Glasgow United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Filippo","family":"Muratori","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine University of Pisa  Pisa Italy"},{"name":"IRCCS Stella Maris Foundation  Pisa Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Calderoni","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine University of Pisa  Pisa Italy"},{"name":"IRCCS Stella Maris Foundation  Pisa Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5135-4472","authenticated-orcid":false,"given":"Alessandra","family":"Retico","sequence":"additional","affiliation":[{"name":"Pisa Division INFN \u2010 National Institute for Nuclear Physics  Pisa Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2018,9,5]]},"reference":[{"key":"e_1_2_7_2_1","unstructured":"American Psychiatric Association Task Force on DSM\u2010IV.2013. 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