Nearly automatic segmentation of hippocampal subfields in in vivo focal T2-weighted MRI

We present and evaluate a new method for automatically labeling the subfields of the hippocampal formation in focal 0.4×0.5×2.0mm3 resolution T2-weighted magnetic resonance images that can be acquired in the routine clinical setting with under 5min scan time. The method combines multi-atlas segmentation, similarity-weighted voting, and a novel learning-based bias correction technique to achieve excellent agreement with manual segmentation. Initial partitioning of MRI slices into hippocampal ’head’, ’body’ and ’tail’ slices is the only input required from the user, necessitated by the nature of the underlying segmentation protocol. Dice overlap between manual and automatic segmentation is above 0.87 for the larger subfields, CA1 and dentate gyrus, and is competitive with the best results for whole-hippocampus segmentation in the literature. Intraclass correlation of volume measurements in CA1 and dentate gyrus is above 0.89. Overlap in smaller hippocampal subfields is lower in magnitude (0.54 for CA2, 0.62 for CA3, 0.77 for subiculum and 0.79 for entorhinal cortex) but comparable to overlap between manual segmentations by trained human raters. These results support the feasibility of subfield-specific hippocampal morphometry in clinical studies of memory and neurodegenerative disease. ►Automated segmentation of hippocampal subfields in T2-W MRI with excellent accuracy Dice overlap between automatic and manual segmentation >0.87 for CA1, dentate gyrus Applicable to MR images that can be acquired in the clinical setting (under 5min) Small amount of manual input (tagging slices as head/body/tail) is required