title: Automated Hippocampal Subfield Segmentation at 7T MRI.
abstract: High resolution 7T MRI is increasingly used to investigate hippocampal subfields in vivo, but most studies rely on manual segmentation which is labor intensive. We aimed to evaluate an automated technique to segment hippocampal subfields and the entorhinal cortex at 7T MRI.
  
  
  
  The cornu ammonis (CA)1, CA2, CA3, dentate gyrus, subiculum, and entorhinal cortex were manually segmented, covering most of the long axis of the hippocampus on 0.70-mm(3) T2-weighted 7T images of 26 participants (59 ± 9 years, 46% men). The automated segmentation of hippocampal subfields approach was applied and evaluated by using leave-one-out cross-validation.
  
  
  
  Comparison of automated segmentations with corresponding manual segmentations yielded a Dice similarity coefficient of >0.75 for CA1, the dentate gyrus, subiculum, and entorhinal cortex and >0.54 for CA2 and CA3. Intraclass correlation coefficients were >0.74 for CA1, the dentate gyrus, and subiculum; and >0.43 for CA2, CA3, and the entorhinal cortex. Restricting the comparison of the entorhinal cortex segmentation to a smaller range along the anteroposterior axis improved both intraclass correlation coefficients (left: 0.71; right: 0.82) and Dice similarity coefficients (left: 0.78; right: 0.77). The accuracy of the automated segmentation versus a manual rater was lower, though only slightly for most subfields, than the intrarater reliability of an expert manual rater, but it was similar to or slightly higher than the accuracy of an expert-versus-manual rater with ∼170 hours of training for almost all subfields.
  
  
  
  This work demonstrates the feasibility of using a computational technique to automatically label hippocampal subfields and the entorhinal cortex at 7T MRI, with a high accuracy for most subfields that is competitive with the labor-intensive manual segmentation. The software and atlas are publicly available: http://www.nitrc.org/projects/ashs/.
authors: From the Penn Image Computing and Science Laboratory, Department of Radiology (L.E.M.W., J.B.P., S.R.D., P.A.Y.) Laura.Wisse@uphs.upenn.edu.
authors: L E M
authors: 0000-0001-7504-3943
authors: LE
authors: Wisse
authors: Image Sciences Institute (H.J.K.).
authors: H J
authors: 0000-0001-6997-9059
authors: HJ
authors: Kuijf
authors: Julius Center for Health Sciences and Primary Care (A.M.H., M.I.G.).
authors: A M
authors: 0000-0003-4047-1520
authors: AM
authors: Honingh
authors: Almaden Research Center (H.W.), IBM Research, Almaden, California.
authors: H
authors: 0000-0001-8299-1247
authors: H
authors: Wang
authors: From the Penn Image Computing and Science Laboratory, Department of Radiology (L.E.M.W., J.B.P., S.R.D., P.A.Y.) Penn Memory Center, Department of Neurology (J.B.P., D.A.W.), University of Pennsylvania, Philadelphia, Pennsylvania.
authors: J B
authors: 0000-0002-8941-6242
authors: JB
authors: Pluta
authors: From the Penn Image Computing and Science Laboratory, Department of Radiology (L.E.M.W., J.B.P., S.R.D., P.A.Y.).
authors: S R
authors: 0000-0003-0530-2887
authors: SR
authors: Das
authors: Penn Memory Center, Department of Neurology (J.B.P., D.A.W.), University of Pennsylvania, Philadelphia, Pennsylvania.
authors: D A
authors: 0000-0002-3554-3481
authors: DA
authors: Wolk
authors: Department of Radiology (J.J.M.Z.), UMC Utrecht, Utrecht, the Netherlands.
authors: J J M
authors: 0000-0002-4282-5719
authors: JJ
authors: Zwanenburg
authors: From the Penn Image Computing and Science Laboratory, Department of Radiology (L.E.M.W., J.B.P., S.R.D., P.A.Y.).
authors: P A
authors: 0000-0001-8543-4016
authors: PA
authors: Yushkevich
authors: Julius Center for Health Sciences and Primary Care (A.M.H., M.I.G.).
authors: M I
authors: 0000-0002-4037-036X
authors: MI
authors: Geerlings
mesh_terms: D000368:Aged; D001331:Automation; D056547:CA1 Region, Hippocampal / Q000000981:diagnostic imaging; D056651:CA2 Region, Hippocampal / Q000000981:diagnostic imaging; D056654:CA3 Region, Hippocampal / Q000000981:diagnostic imaging; D018891:Dentate Gyrus / Q000000981:diagnostic imaging; D018728:Entorhinal Cortex / Q000000981:diagnostic imaging; D005260:Female; D006624:Hippocampus / Q000000981:diagnostic imaging*; D006801:Humans; D007091:Image Processing, Computer-Assisted; D008279:Magnetic Resonance Imaging / Q000379:methods*; D008297:Male; D008875:Middle Aged; D015588:Observer Variation; D015203:Reproducibility of Results