Thanks for taking a look at the file I sent! I think I have figured out the issue for the most part. While it shows that there is data in the recon-all log for the various cortical regions and eTIV, the data I extracted using aparcstats2table gives me zeros. Part of the problem seems to be that in the table aparcstats2table produces using the Destrieux atlas, some variables are listed twice, but in a different format. For example, frontomarginal thickness is listed as both rh_G_and_S_frontomargin_thickness and as rh_G_&_S_frontomargin_thickness. Some subjects have data for one variable and some for the other variable. This happened for 13 variables. I've attached an excel file with data from 2 subjects that shows the variables that are listed twice and how some subjects have data for some variables and others have data for other variables. Please let me if you have any ideas of why this may have happened. 

Thanks!

Morgan