I am a very new user to Freesurfer and I have a few questions.   1.) Are the sub cortical volumes and thicknesses that Freesurfer generates in the stats output during the recon-all  raw volumes (actual volumes) or are they somehow normalized by the time the stats are generated?   If they are raw, what sort of transformations must I do to compare them (in order to account for different total head sizes etc.) For instance, if I wanted to compare hippocampal volumes from one subject to another.   If they are already normalized is it appropriate to compare subject to subject without any other transformations?   2.)  Before using qdec, you must complete a smoothing process for subjects .   My understanding is that you have the option of comparing this smoothing to the pre-installed “average subject” or you can do the smoothing process in conjunction with an “average subject” that you create yourself.  Is is necessary to create your own “average subject” for each set of studies you do in qdec?     Do the cortical thickness comparison change if you are using the already installed “average subject” or if you create your own average subject?   Thank you so much.   Sincerely, Mark Fletcher eldermarky1@yahoo.com