Oh, I see now, you are including -noaseg and that is causing the problem. Why are you including that? You can rerun like

recon-all -parcstats -parcstats2 -s subject

and it should regenerate the stats with the mean cortical thickness

doug

On 01/07/2013 02:32 PM, Deirdre O Shea wrote:

sure, here it is

On Mon, Jan 7, 2013 at 2:24 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

hmmm, that is bizarre. Can you send me the recon-all.log file for
this subject?


On 01/07/2013 02:23 PM, Deirdre O Shea wrote:

    I just ran ran recon-all myself. I have attached the script i
    have been using for all my subjects.

    thanks,
    deirdre

    On Mon, Jan 7, 2013 at 1:45 PM, Douglas N Greve
    <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>> wrote:


        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>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
            <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>

            <mailto: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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