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I would like to manually adjust the hippocampal segmentations created by the hippocampal/amygdala sub-field segmentation pipeline. The hippocampal head boundary with the amygdala was poorly defined in my subjects (1mm isotropic images), and I would like to manually adjust this boundary.

1) I used the longitudinal pipeline (subjects had three visits each). Ideally, I would like to do this once per subject (i.e., on the subject average), but am not sure if that is possible, or if the subject average boundaries would maintain their accuracy once applied to each individual visit. If this is not possible, I would like to adjust only a single image per subject/visit (outline of the whole hippocampus) and apply it to two of to the three available segmentation (HBT, CA), or more importantly, extract the volumes in a similar manner to the FS provided sub-field output.

2) I would like to know how the alveus is assigned in the CA and HBT segmentations. It appears to be included in the hippocampus in my images, and I am curious if this is an error. Should it be excluded?

Best, Kathy Reding