I can see that the command line is not set up to create the mean cortical thickness, but I don't know why the arguments for the command are not being set up properly. Did you run mris_anatomical_stats yourself or did you just run recon-all again? If you ran recon-all, can you send me your recon-all script?

doug

On 01/07/2013 01:25 PM, Deirdre O Shea wrote:

Thanks Doug,

I have attached two files. You will see in 'aparc.stats' that there is no mean for cortical thickness and in the aparc.stats2 file there is.

thanks Deirdre

On Mon, Jan 7, 2013 at 12:48 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Can you send the aparc.stats file in question?
doug
On 01/07/2013 11:44 AM, Deirdre O Shea wrote:
> Dear FreeSurfers,
>
> My query relates to the aparc stats file in FreeSurfer. Upon the
> editing and reconstruction of my subjects I have noticed that
the Mean
> Thickness for the cortex was missing, i.e., no value was provided
> despite it being there before I ran another reconstruction.
While this
> has only occurred in a couple of my subjects (out of many) I'm
> wondering what may be the cause and how I may I now go about getting
> this value?
>
>
> Best,
> Deirdre
>
>
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