title: Automated segmentation of multifocal basal ganglia T2*-weighted MRI hypointensities.
abstract: Multifocal basal ganglia T2*-weighted (T2*w) hypointensities, which are believed to arise mainly from vascular mineralization, were recently proposed as a novel MRI biomarker for small vessel disease and ageing. These T2*w hypointensities are typically segmented semi-automatically, which is time consuming, associated with a high intra-rater variability and low inter-rater agreement. To address these limitations, we developed a fully automated, unsupervised segmentation method for basal ganglia T2*w hypointensities. This method requires conventional, co-registered T2*w and T1-weighted (T1w) volumes, as well as region-of-interest (ROI) masks for the basal ganglia and adjacent internal capsule generated automatically from T1w MRI. The basal ganglia T2*w hypointensities were then segmented with thresholds derived with an adaptive outlier detection method from respective bivariate T2*w/T1w intensity distributions in each ROI. Artefacts were reduced by filtering connected components in the initial masks based on their standardised T2*w intensity variance. The segmentation method was validated using a custom-built phantom containing mineral deposit models, i.e. gel beads doped with 3 different contrast agents in 7 different concentrations, as well as with MRI data from 98 community-dwelling older subjects in their seventies with a wide range of basal ganglia T2*w hypointensities. The method produced basal ganglia T2*w hypointensity masks that were in substantial volumetric and spatial agreement with those generated by an experienced rater (Jaccard index = 0.62 ± 0.40). These promising results suggest that this method may have use in automatic segmentation of basal ganglia T2*w hypointensities in studies of small vessel disease and ageing.
authors.affiliation: Brain Research Imaging Centre, Neuroimaging Sciences, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; SINAPSE Collaboration, Brain Research Imaging Centre, Neuroimaging Sciences, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
authors.forename: Andreas
authors.initials: A
authors.lastname: Glatz
authors.affiliation: Brain Research Imaging Centre, Neuroimaging Sciences, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; SINAPSE Collaboration, Brain Research Imaging Centre, Neuroimaging Sciences, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK; Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK. Electronic address: Mark.Bastin@ed.ac.uk.
authors.forename: Mark E
authors.initials: ME
authors.lastname: Bastin
authors.affiliation: Brain Research Imaging Centre, Neuroimaging Sciences, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Kiker
authors.affiliation: Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK.
authors.forename: Ian J
authors.initials: IJ
authors.lastname: Deary
authors.affiliation: Brain Research Imaging Centre, Neuroimaging Sciences, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; SINAPSE Collaboration, Brain Research Imaging Centre, Neuroimaging Sciences, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK; Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK.
authors.forename: Joanna M
authors.initials: JM
authors.lastname: Wardlaw
authors.affiliation: Brain Research Imaging Centre, Neuroimaging Sciences, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; SINAPSE Collaboration, Brain Research Imaging Centre, Neuroimaging Sciences, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK; Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK.
authors.forename: Maria C
authors.initials: MC
authors.lastname: Valdés Hernández
mesh_terms: D000368:Aged; D000375:Aging / Q000473:pathology*; D001479:Basal Ganglia / Q000473:pathology*; D015331:Cohort Studies; D005260:Female; D006801:Humans; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods*; D008297:Male
keywords: Ageing; Automated segmentation; Basal ganglia; Focal T2*-weighted MRI hypointensities; Magnetic resonance imaging (MRI); Mineralization; Outlier detection