title: A New MRI Masking Technique Based on Multi-Atlas Brain Segmentation in Controls and Schizophrenia: A Rapid and Viable Alternative to Manual Masking.
abstract: Brain masking of MRI images separates brain from surrounding tissue and its accuracy is important for further imaging analyses. We implemented a new brain masking technique based on multi-atlas brain segmentation (MABS) and compared MABS to masks generated using FreeSurfer (FS; version 5.3), Brain Extraction Tool (BET), and Brainwash, using manually defined masks (MM) as the gold standard. We further determined the effect of different masking techniques on cortical and subcortical volumes generated by FreeSurfer.
  
  
  METHODS
  Images were acquired on a 3-Tesla MR Echospeed system General Electric scanner on five control and five schizophrenia subjects matched on age, sex, and IQ. Automated masks were generated from MABS, FS, BET, and Brainwash, and compared to MM using these metrics: a) volume difference from MM; b) Dice coefficients; and c) intraclass correlation coefficients.
  
  
  RESULTS
  Mean volume difference between MM and MABS masks was significantly less than the difference between MM and FS or BET masks. Dice coefficient between MM and MABS was significantly higher than Dice coefficients between MM and FS, BET, or Brainwash. For subcortical and left cortical regions, MABS volumes were closer to MM volumes than were BET or FS volumes. For right cortical regions, MABS volumes were closer to MM volumes than were BET volumes.
  
  
  CONCLUSIONS
  Brain masks generated using FreeSurfer, BET, and Brainwash are rapidly obtained, but are less accurate than manually defined masks. Masks generated using MABS, in contrast, resemble more closely the gold standard of manual masking, thereby offering a rapid and viable alternative.
authors.affiliation: VA Boston Healthcare System, Brockton, MA.|Department of Psychiatry, Harvard Medical School, Boston, MA.
authors.forename: Elisabetta C
authors.initials: EC
authors.lastname: Del Re
authors.affiliation: Department of Psychiatry, Harvard Medical School, Boston, MA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Gao
authors.affiliation: Department of Psychiatry, Harvard Medical School, Boston, MA.
authors.forename: Ryan
authors.initials: R
authors.lastname: Eckbo
authors.affiliation: Department of Psychiatry, Harvard Medical School, Boston, MA.
authors.forename: Tracey L
authors.initials: TL
authors.lastname: Petryshen
authors.affiliation: Department of Psychiatry, Harvard Medical School, Boston, MA.
authors.forename: Gabriëlla A M
authors.initials: GA
authors.lastname: Blokland
authors.affiliation: Department of Psychiatry, Harvard Medical School, Boston, MA.
authors.forename: Larry J
authors.initials: LJ
authors.lastname: Seidman
authors.affiliation: VA Boston Healthcare System, Brockton, MA.|Department of Psychiatry, Harvard Medical School, Boston, MA.
authors.forename: Jun
authors.initials: J
authors.lastname: Konishi
authors.affiliation: Department of Psychiatry, Harvard Medical School, Boston, MA.
authors.forename: Jill M
authors.initials: JM
authors.lastname: Goldstein
authors.affiliation: VA Boston Healthcare System, Brockton, MA.|Department of Psychiatry, Harvard Medical School, Boston, MA.
authors.forename: Robert W
authors.initials: RW
authors.lastname: McCarley
authors.affiliation: VA Boston Healthcare System, Brockton, MA.|Department of Psychiatry, Harvard Medical School, Boston, MA.|Department of Radiology, Harvard Medical School, Boston, MA.
authors.forename: Martha E
authors.initials: ME
authors.lastname: Shenton
authors.affiliation: Department of Psychiatry, Harvard Medical School, Boston, MA.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Bouix
mesh_terms: D000293:Adolescent; D000328:Adult; D001921:Brain / Q000000981:diagnostic imaging*; D005260:Female; D006801:Humans; D007090:Image Interpretation, Computer-Assisted / Q000379:methods; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods*; D008297:Male; D008875:Middle Aged; D012559:Schizophrenia / Q000000981:diagnostic imaging*
keywords: BET; Brainwash; Dice coefficient; FreeSurfer; MABS; Schizophrenia