Nearly isotropic segmentation for medial temporal lobe subregions in multi-modality MRI

Morphometry of medial temporal lobe (MTL) subregions in brain MRI is sensitive biomarker to Alzheimers Disease and other related conditions. While T2-weighted (T2w) MRI with high in-plane resolution is widely used to segment hippocampal subfields due to its higher contrast in hippocampus, its lower out-of-plane resolution reduces the accuracy of subregion thickness measurements. To address this issue, we developed a nearly isotropic segmentation pipeline that incorporates image and label upsampling and high-resolution segmentation in T2w MRI. First, a high-resolution atlas was created based on an existing anisotropic atlas derived from 29 individuals. Both T1-weighted and T2w images in the atlas were upsampled from their original resolution to a nearly isotropic resolution 0.4x0.4x0.52mm3 using a non-local means approach. Manual segmentations within the atlas were also upsampled to match this resolution using a UNet-based neural network, which was trained on a cohort consisting of both high-resolution ex vivo and low-resolution anisotropic in vivo MRI with manual segmentations. Second, a multi-modality deep learning-based segmentation model was trained within this nearly isotropic atlas. Finally, experiments showed the nearly isotropic subregion segmentation improved the accuracy of cortical thickness as an imaging biomarker for neurodegeneration in T2w MRI.