High resolution automated labeling of the hippocampus and amygdala using a 3D convolutional neural network trained on whole brain 700 μm isotropic 7T MP2RAGE MRI

Heath R. Pardoe, Arun Raj Antony, Hoby Hetherington, Anto I. Bagić, Timothy M. Shepherd, Daniel Friedman, Orrin Devinsky, Jullie Pan

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2 Citations (Scopus)


Image labeling using convolutional neural networks (CNNs) are a template-free alternative to traditional morphometric techniques. We trained a 3D deep CNN to label the hippocampus and amygdala on whole brain 700 μm isotropic 3D MP2RAGE MRI acquired at 7T. Manual labels of the hippocampus and amygdala were used to (i) train the predictive model and (ii) evaluate performance of the model when applied to new scans. Healthy controls and individuals with epilepsy were included in our analyses. Twenty-one healthy controls and sixteen individuals with epilepsy were included in the study. We utilized the recently developed DeepMedic software to train a CNN to label the hippocampus and amygdala based on manual labels. Performance was evaluated by measuring the dice similarity coefficient (DSC) between CNN-based and manual labels. A leave-one-out cross validation scheme was used. CNN-based and manual volume estimates were compared for the left and right hippocampus and amygdala in healthy controls and epilepsy cases. The CNN-based technique successfully labeled the hippocampus and amygdala in all cases. Mean DSC = 0.88 ± 0.03 for the hippocampus and 0.8 ± 0.06 for the amygdala. CNN-based labeling was independent of epilepsy diagnosis in our sample (p =.91). CNN-based volume estimates were highly correlated with manual volume estimates in epilepsy cases and controls. CNNs can label the hippocampus and amygdala on native sub-mm resolution MP2RAGE 7T MRI. Our findings suggest deep learning techniques can advance development of morphometric analysis techniques for high field strength, high spatial resolution brain MRI.

Original languageEnglish
Pages (from-to)2089-2098
Number of pages10
JournalHuman Brain Mapping
Issue number7
Publication statusPublished - May 2021
Externally publishedYes


  • artificial intelligence
  • deep learning
  • high field MRI
  • segmentation

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