Automatic multispectral MRI segmentation of human hippocampal subfields: an evaluation of multicentric test–retest reproducibility

Andrea Chiappiniello, Roberto Tarducci, Cristina Muscio, Maria Grazia Bruzzone, Marco Bozzali, Pietro Tiraboschi, Anna Nigri, Claudia Ambrosi, Elena Chipi, Stefania Ferraro, Cristina Festari, Roberto Gasparotti, Ruben Gianeri, Giovanni Giulietti, Lorella Mascaro, Chiara Montanucci, Valentina Nicolosi, Cristina Rosazza, Laura Serra, Giovanni B. FrisoniDaniela Perani, Fabrizio Tagliavini, Jorge Jovicich

Research output: Contribution to journalArticlepeer-review


Accurate and reproducible automated segmentation of human hippocampal subfields is of interest to study their roles in cognitive functions and disease processes. Multispectral structural MRI methods have been proposed to improve automated hippocampal subfield segmentation accuracy, but the reproducibility in a multicentric setting is, to date, not well characterized. Here, we assessed test–retest reproducibility of FreeSurfer 6.0 hippocampal subfield segmentations using multispectral MRI analysis pipelines (22 healthy subjects scanned twice, a week apart, at four 3T MRI sites). The harmonized MRI protocol included two 3D-T1, a 3D-FLAIR, and a high-resolution 2D-T2. After within-session T1 averaging, subfield volumes were segmented using three pipelines with different multispectral data: two longitudinal (“long_T1s” and “long_T1s_FLAIR”) and one cross-sectional (“long_T1s_FLAIR_crossT2”). Volume reproducibility was quantified in magnitude (reproducibility error—RE) and space (DICE coefficient). RE was lower in all hippocampal subfields, except for hippocampal fissure, using the longitudinal pipelines compared to long_T1s_FLAIR_crossT2 (average RE reduction of 0.4–3.6%). Similarly, the longitudinal pipelines showed a higher spatial reproducibility (1.1–7.8% of DICE improvement) in all hippocampal structures compared to long_T1s_FLAIR_crossT2. Moreover, long_T1s_FLAIR provided a small but significant RE improvement in comparison to long_T1s (p = 0.015), whereas no significant DICE differences were found. In addition, structures with volumes larger than 200 mm3 had better RE (1–2%) and DICE (0.7–0.95) than smaller structures. In summary, our study suggests that the most reproducible hippocampal subfield FreeSurfer segmentations are derived from a longitudinal pipeline using 3D-T1s and 3D-FLAIR. Adapting a longitudinal pipeline to include high-resolution 2D-T2 may lead to further improvements.

Original languageEnglish
JournalBrain Structure and Function
Publication statusE-pub ahead of print - Nov 2020


  • Automated segmentation
  • FreeSurfer
  • Hippocampal subfields
  • Human brain morphometry
  • Multispectral MRI
  • Test–retest reproducibility

ASJC Scopus subject areas

  • Anatomy
  • Neuroscience(all)
  • Histology


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