Event Abstract Back to Event Comparison of FSL-FIRST with Manual Segmentation of Subcortical Brain Structures Janis Breeze1*, Brian Patenaude2, Mark Jenkinson2, Stephen Smith2, Jeanne Frazier3 and David Kennedy4 1 Harvard Medical School (CHA), United States 2 Oxford University, United Kingdom 3 Cambridge Health Alliance, United States 4 Mass. General Hospital, United States Introduction: FSL 4.0 includes FIRST, a tool for automatic segmentation and labeling of 17 subcortical structures (brainstem and bilateral amygdala, caudate nucleus, hippocampus, lateral ventricles, nucleus accumbens, putamen, pallidum, and thalamus). FIRST was trained on trained on 317 manually labeled T1-weighted MRIs of the brain, of which 120 were from children aged 4-19 with and without mental illness. The manual labeling was performed at the Center for Morphometric Analysis (CMA) at Massachusetts General Hospital (MGH). Methods:MRI scans from 24 children were analyzed using both the CMA and FIRST segmentation routines (these scans were not included as training data). Briefly, the volumetric labels produced by FIRST are parameterized by deforming a 3D-mesh representation of the most typical structure to each subject. For these data, all structures were segmented simultaneously (i.e., using first_all). Volumes were then produced using the optimized z-threshold for these structures based on the training data (z=2 for all structures except brain stem, caudate, and thalamus: z=2.5). The reliability of volumetric measurements between the two methods was then compared via intraclass correlation coefficients (ICCs) for consistency. Results: The subject population consisted of 11 males and 13 females, and was on average 11.1 ± 3.9 (range 3.9-17.6) years old. It included 3 subjects with bipolar disorder, 2 with ADHD, 6 with schizophrenia-spectrum illness, 4 children at genetic risk for bipolar disorder, and 9 healthy controls. The volumes generated by FIRST were significantly correlated (p<0.05) with the CMA results for all structures with the exception of left hippocampus (r=0.32, p>0.1), and bilateral nucleus accumbens (right: r=0.25, p>0.1; left: r=0.40, p=0.054) and amygdala (right: r=0.24, p>0.1; left: r=0.20, p>0.1). ICCs for consistency averaged 0.69 ± 0.12, and ranged from 0.32 (left amygdala) and 0.96 (left lateral ventricles). Conclusions: The subcortical volumetric results from FIRST are comparable with those obtained through semi-automated manual segmentation. Considering the CMA volumes as the gold-standard, structures with the highest reliability were the lateral ventricles and brainstem; FIRST showed weakest reliability when measuring some limbic and basal ganglia structures, particularly hippocampus, amygdala, and nucleus accumbens. These structures are difficult to segment even with user-defined or semi-automated methods and further development should improve the reliability of these measurements in FIRST. Conference: Neuroinformatics 2008, Stockholm, Sweden, 7 Sep - 9 Sep, 2008. Presentation Type: Poster Presentation Topic: Neuroimaging Citation: Breeze J, Patenaude B, Jenkinson M, Smith S, Frazier J and Kennedy D (2008). Comparison of FSL-FIRST with Manual Segmentation of Subcortical Brain Structures. Front. Neuroinform. Conference Abstract: Neuroinformatics 2008. doi: 10.3389/conf.neuro.11.2008.01.071 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 28 Jul 2008; Published Online: 28 Jul 2008. * Correspondence: Janis Breeze, Harvard Medical School (CHA), Boston, United States, jlb.spm@gmail.com Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Janis Breeze Brian Patenaude Mark Jenkinson Stephen Smith Jeanne Frazier David Kennedy Google Janis Breeze Brian Patenaude Mark Jenkinson Stephen Smith Jeanne Frazier David Kennedy Google Scholar Janis Breeze Brian Patenaude Mark Jenkinson Stephen Smith Jeanne Frazier David Kennedy PubMed Janis Breeze Brian Patenaude Mark Jenkinson Stephen Smith Jeanne Frazier David Kennedy Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.