Automated protocols for delineating human hippocampal subfields from 3T and 7T MRI data

Researchers who study the human hippocampus are naturally interested in how its subfields function. Unfortunately, many researchers are precluded from examining subfields because their manual delineation from MRI scans (still the gold standard approach) is time consuming and requires significant expertise. Here we present two protocols, one for 3T MRI and the other for 7T MRI, that permit automated subfield segmentation into dentate gyrus/CA4, CA2/3, CA1, subiculum, pre/parasubiculum and uncus along the entire length of the hippocampus. These protocols are particularly notable in that they were trained and tested using large numbers of healthy adults (N=140 at 3T, N=40 at 7T) whose hippocampi were manually segmented by experts. Using inter-rater reliability analyses, we showed that the quality of automated segmentations using these protocols was high. We provide full open access to the protocols, and anticipate they will save hippocampus researchers a significant amount of time. They could also facilitate increased numbers of subfield experiments which in turn could help to address the paucity of these potentially important studies in the field of hippocampus neuroscience.