ASHS-OAP atlas for automatic entorhinal cortex segmentation

Early stages of Alzheimer’s disease (AD) are associated with volume reductions in specific subregions of the medial temporal lobe (MTL). Using a manual segmentation method—the Olsen-Amaral-Palombo (OAP) protocol— previous work in healthy older adults showed that reductions in grey matter volumes in MTL subregions were associated with lower scores on the Montreal Cognitive Assessment (MoCA), suggesting atrophy may occur prior to diagnosis of mild cognitive impairment, a condition that often progresses to AD. However, current manual segmentation methods are labour intensive and time consuming. Here, we examined the utility of Automatic Segmentation of Hippocampal Subfields (ASHS) to detect volumetric differences in MTL subregions of healthy older adults who varied in cognitive status as determined by the MoCA. We trained ASHS on the OAP protocol to create the ASHS-OAP atlas, and then examined how well automated segmentation replicated the ground truth of manual segmentation. Volumetric me..., Forty community-dwelling healthy older adults (as described in Olsen, Yeung et al., 2017; age range = 59-81 years; mean age = 71.4; mean education = 16.3 years; range = 12-23; 30 female) were recruited from participant databases at the Rotman Research Institute and the University of Toronto.
Neuroimaging was completed on a 3-Tesla Siemens Trio scanner using a 12-channel head coil. All participants received a T1-weighted, magnetization-prepared, rapid acquisition with gradient echo image (MP-RAGE) whole-brain anatomical scan (TE/TR=2.63ms/2000ms, 160 axial slices perpendicular to the AC-PC line, voxel size=1x1x1mm, FOV=256mm). The T1-weighted MP-RAGE was used for slice placement during the acquisition of a subsequent high in-plane resolution T2-weighted scan in an oblique-coronal plane, perpendicular to the hippocampal long axis (TE/TR=68/3000ms, 20-28 slices depending on head size, 512x512 acquisition matrix, voxel size=0.43x0.43x3mm, no skip, FOV=220mm). For the T2-weighted scan, the f..., , # ASHS-OAP atlas for automatic entorhinal cortex segmentation

[10.5061/dryad.6djh9w17h](10.5061/dryad.6djh9w17h∴)

[ASHS](https://sites.google.com/view/ashs-dox/local-ashs) is an open-source tool designed for the Automated Segmentation of Hippocampal Subfields from MRI images of the brain. Several atlases for the hippocampus are provided with ASHS. While it was developed for the segmentation of hippocampal subfields, the tools provided with ASHS can potentially be used for multi-atlas segmentation of any region if an appropriate set of expert-derived atlas segmentations is provided. Here, we extend ASHS by providing an atlas to segment subregions of the adjacent entorhinal cortex.

ASHS allows users to run the segmentation algorithm with a custom atlas (via the `-a ATLASDIR` parameter). Here, we provide all of the files required for ASHS to operate on the entorhial cortex. These were derived from expert manual segmentation of the regions and by using ASHS to create and cross-validate a...