Hi, you can use this command to perform the whole analysis:

recon-all -i input_file -s subject_name

The input file may be a nifti or dicom file. The subject name whatever you want, but not spaces within.

Then, you type:

recon-all -autorecon-all -s subject_name

It will perform all the analysis for your subject. In the stats folder (freesurfer/subjects/your_subject/stats), you will get a file called aseg.stats, there you can obtain the hippocampal volumes and the total intracranial volumes.
You should check the segmentation outputs before doing this.

You can also make a segmentation of the hippocampal subfields with :

recon-all -s subject_name -hippo-subfields ( if you use freesurfer v5.3 ).
more info here https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation

By the way, FreeSurfes has its own wiki, you can solve all your doubts there (http://www.freesurfer.net/).

If you need something, I can help you a little bit more jforejuela@gmail.com