The manual protocol was made by doctors.They traced the hippocampus segmentation based on their knowledge of anatomical structures.
For automatic segmentation I've used the following command:
recon-all -i input_suject_name -autorecon1 -autorecon2 -s output_subject_name
and after this simulation I've been working with the values given in the terminal X11 for left-hippocampus and right-hippocampus.
Am I doing anything wrong? Or am I missing something?