High-resolution segmentations of the hypothalamus and its subregions for training of segmentation models

Segmentation of brain structures on magnetic resonance imaging (MRI) is a highly relevant neuroimaging topic, as it is a prerequisite for different analyses such as volumetry or shape analysis. Automated segmentation facilitates the study of brain structures in larger cohorts when compared with manual segmentation, which is time-consuming. However, the development of most automated methods relies on large and manually annotated datasets, which limits the generalizability of these methods. Recently, new techniques using synthetic images have emerged, reducing the need for manual annotation. Here we provide HELM, Hypothalamic ex vivo Label Maps, a dataset composed of label maps built from publicly available ultra-high resolution ex vivo MRI from 10 whole hemispheres, which can be used to develop segmentation methods using synthetic data. The label maps are obtained with a combination of manual labels for the hypothalamic regions and automated segmentations for the rest of the brain, and mirrored to simulate entire brains. We also provide the pre-processed ex vivo scans, as this dataset can support future projects to include other structures after these are manually segmented.

H-SynEx: Using synthetic images and ultra-high resolution ex vivo MRI for hypothalamus subregion segmentation

Purpose: To develop a method for automated segmentation of hypothalamus subregions informed by ultra-high resolution ex vivo magnetic resonance images (MRI), which generalizes across MRI sequences and resolutions without retraining. Materials and Methods: We trained our deep learning method, H-synEx, with synthetic images derived from label maps built from ultra-high resolution ex vivo MRI scans, which enables finer-grained manual segmentation when compared with 1mm isometric in vivo images. We validated this retrospective study using 1535 in vivo images from six datasets and six MRI sequences. The quantitative evaluation used the Dice Coefficient (DC) and Average Hausdorff distance (AVD). Statistical analysis compared hypothalamic subregion volumes in controls, Alzheimer's disease (AD), and behavioral variant frontotemporal dementia (bvFTD) subjects using the area under the curve (AUC) and Wilcoxon rank sum test. Results: H-SynEx can segment the hypothalamus across various MRI sequences, encompassing FLAIR sequences with significant slice spacing (5mm). Using hypothalamic volumes on T1w images to distinguish control from AD and bvFTD patients, we observed AUC values of 0.74 and 0.79 respectively. Additionally, AUC=0.66 was found for volume variation on FLAIR scans when comparing control and non-patients. Conclusion: Our results show that H-SynEx successfully leverages information from ultra-high resolution scans to segment in vivo from different MRI sequences such as T1w, T2w, PD, qT1, FA, and FLAIR. We also found that our automated segmentation was able to discriminate controls versus patients on FLAIR images with 5mm spacing. H-SynEx is openly available at https://github.com/liviamarodrigues/hsynex.