Deep Learning-based Hierarchical Brain Segmentation with Preliminary Analysis of the Repeatability and Reproducibility

Abstract

Purpose: We developed new deep learning-based hierarchical brain segmentation (DLHBS) method that can segment T1-weighted MR images (T1WI) into 107 brain subregions and calculate the volume of each subregion. This study aimed to evaluate the repeatability and reproducibility of volume estimation using DLHBS and compare them with those of representative brain segmentation tools such as statistical parametric mapping (SPM) and FreeSurfer (FS).

Methods: Hierarchical segmentation using multiple deep learning models was employed to segment brain subregions within a clinically feasible processing time. The T1WI and brain mask pairs in 486 subjects were used as training data for training of the deep learning segmentation models. Training data were generated using a multi-atlas registration-based method. The high quality of training data was confirmed through visual evaluation and manual correction by neuroradiologists. The brain 3D-T1WI scan–rescan data of the 11 healthy subjects were obtained using three MRI scanners for evaluating the repeatability and reproducibility. The volumes of the eight ROIs—including gray matter, white matter, cerebrospinal fluid, hippocampus, orbital gyrus, cerebellum posterior lobe, putamen, and thalamus—obtained using DLHBS, SPM 12 with default settings, and FS with the “recon-all” pipeline. These volumes were then used for evaluation of repeatability and reproducibility.

Results: In the volume measurements, the bilateral thalamus showed higher repeatability with DLHBS compared with SPM. Furthermore, DLHBS demonstrated higher repeatability than FS in across all eight ROIs. Additionally, higher reproducibility was observed with DLHBS in both hemispheres of six ROIs when compared with SPM and in five ROIs compared with FS. The lower repeatability and reproducibility in DLHBS were not observed in any comparisons.

Conclusion: Our results showed that the best performance in both repeatability and reproducibility was found in DLHBS compared with SPM and FS.