Freesurfer is not necessarily the most user-friendly software around, but it was designed for exactly this kind of analysis, and the support community is active and responsive.

It works with T1-weighted scans to reconstruct a 3D model of the inner and outer cortical surfaces (that is, the grey matter/pia boundary and the grey matter/white matter boundary), letting you then calculate the volume between the two.

I agree, Freesurfer is not easy to manage but it is the state-of-the art in the estimation of cortical thickness. It is important to have 3-D T1 Images without GAP. You obtain the volume and thickness of different cortical areas. The main advantage is that it is free. 

FreeSurfer or SurfRelax

FreeSurfer has great tutorials online, and data you can download to practice!

http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials

CAT is more user friendly and less time consuming than FreeSurfer but requires matlab. High res T1 images are required

Dear Fabrizio 

CAT is a toolbox of SPM in matlab right?

and High res T1 you mean  a 3 tesla MRI scan impreg image?

Yes, CAT is a spm12 tool.

For high res images i mean an image with a voxel size of 1x1x1 mm . 3 or 1.5 tesla doesn't really matter

Indeed, FreeSurfer was designed for this type of analysis in one simple command.

For a step-by-step tutorial on how to use it, please see my ebook:

http://jeromemallershandbookofstructuralbrainmrianalysis.yolasite.com/ 

Regards,

Jerome