title: Assessment of the impact of the scanner-related factors on brain morphometry analysis with Brainvisa.
abstract: BACKGROUND
  Brain morphometry is extensively used in cross-sectional studies. However, the difference in the estimated values of the morphometric measures between patients and healthy subjects may be small and hence overshadowed by the scanner-related variability, especially with multicentre and longitudinal studies. It is important therefore to investigate the variability and reliability of morphometric measurements between different scanners and different sessions of the same scanner.
  
  
  METHODS
  We assessed the variability and reliability for the grey matter, white matter, cerebrospinal fluid and cerebral hemisphere volumes as well as the global sulcal index, sulcal surface and mean geodesic depth using Brainvisa. We used datasets obtained across multiple MR scanners at 1.5 T and 3 T from the same groups of 13 and 11 healthy volunteers, respectively. For each morphometric measure, we conducted ANOVA analysis and verified whether the estimated values were significantly different across different scanners or different sessions of the same scanner. The between-centre and between-visit reliabilities were estimated from their contribution to the total variance, using a random-effects ANOVA model. To estimate the main processes responsible for low reliability, the results of brain segmentation were compared to those obtained using FAST within FSL.
  
  
  RESULTS
  In a considerable number of cases, the main effects of both centre and visit factors were found to be significant. Moreover, both between-centre and between-visit reliabilities ranged from poor to excellent for most morphometric measures. A comparison between segmentation using Brainvisa and FAST revealed that FAST improved the reliabilities for most cases, suggesting that morphometry could benefit from improving the bias correction. However, the results were still significantly different across different scanners or different visits.
  
  
  CONCLUSIONS
  Our results confirm that for morphometry analysis with the current version of Brainvisa using data from multicentre or longitudinal studies, the scanner-related variability must be taken into account and where possible should be corrected for. We also suggest providing some flexibility to Brainvisa for a step-by-step analysis of the robustness of this package in terms of reproducibility of the results by allowing the bias corrected images to be imported from other packages and bias correction step be skipped, for example.
authors.affiliation: Department of Clinical Physics and Psychological Medicine, College of Medicine, Veterinary and Life Sciences, University of Glasgow, UK. m.shokouhi.1@research.gla.ac.uk
authors.forename: Mahsa
authors.initials: M
authors.lastname: Shokouhi
authors.forename: Anna
authors.initials: A
authors.lastname: Barnes
authors.forename: John
authors.initials: J
authors.lastname: Suckling
authors.forename: Thomas Wj
authors.initials: TW
authors.lastname: Moorhead
authors.forename: David
authors.initials: D
authors.lastname: Brennan
authors.forename: Dominic
authors.initials: D
authors.lastname: Job
authors.forename: Katherine
authors.initials: K
authors.lastname: Lymer
authors.forename: Paola
authors.initials: P
authors.lastname: Dazzan
authors.forename: Tiago
authors.initials: T
authors.lastname: Reis Marques
authors.forename: Clare
authors.initials: C
authors.lastname: Mackay
authors.forename: Shane
authors.initials: S
authors.lastname: McKie
authors.forename: Steven Cr
authors.initials: SC
authors.lastname: Williams
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Lawrie
authors.forename: Bill
authors.initials: B
authors.lastname: Deakin
authors.forename: Steve R
authors.initials: SR
authors.lastname: Williams
authors.forename: Barrie
authors.initials: B
authors.lastname: Condon
mesh_terms: D000328:Adult; D001921:Brain / Q000033:anatomy & histology*; D006801:Humans; D007091:Image Processing, Computer-Assisted; D008279:Magnetic Resonance Imaging / Q000379:methods; D008297:Male; D008875:Middle Aged; D015203:Reproducibility of Results; D055815:Young Adult