Hello,
 This is Rashmi. I am very new to neurobiology and computing and my very first project involves measuring cortical thickness from the reconstructed surfaces generated by FreeSurfer. I have recently started to self teach myself FreeSurfer, but with a background in immunology and almost no background in neurobiology I know I have  a long way to go and need a lot of help.
I have learnt to run FreeSurfer and am currently using Version 5.1.0. I am  also referring the FreeSurfer Lectures and Tutorial available online for free to learn usage of Tktools.  Despite that I don't have access to your tutorial data, I have found this tutorial helpful in learning how to use Tktools to view volumes and surfaces. 
At present I have few basic (naïve) questions that I need your help with, excuse me if you find my question ignorant.


A)My first question is about the cortical parcellation stats files.
After running the recon all on my MPRAGE data, I did get the ?.aparc.stats file in the stats folder. I also see ?.aparc.a2009S.stats files. I read and kind of understood the difference between these two files in how differently they calculate the gray matter. 
My question is which of these two files should be considered for measurement as generated by the automated calculation of the cortical thickness.

B) Besides the cortical thickness parameters the ?.aparc file has information on the white surface area and the mean thickness.
Is the mean thickens represents the average cortical thickness of the respective hemisphere? If not what does it represents and how can I calculate the hemisphere based cortical thickness?

C) How would I calculate the average cortical thickness of the whole brain?

D) In research articles related to measurement of cortical thickness, authors have reported mapping of the thickness measured on the inflated or semi-inflated surface . How is it done and what is the significance of doing it.

E)Once I have the measure of all the cortical thickness how do I compare all the Subjects measurements participating in my study?

F) Do you in your tutorial have some reference images for  labelled subcortical regions that are generated in aseg.mgz files.

Thanks for your response in advance.
Hope to hear from you soon.
Regards,
Rashm.



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