sorry, it fell through the cracks. Please feel free to resend if I don't get back in a reasonable amount of time... Try this command instead

mri_segstats --annot subjectname lh aparc --sum lh.sulc.sum --i surf/lh.sulc

the output will be lh.sulc.sum

doug

On 08/16/2012 07:02 PM, Hugh Pemberton wrote:

Hi Doug, did you get a chance to see my last e mail by the way? The one below. Thanks very much indeed, Hugh

On 15 August 2012 10:32, Hugh Pemberton <hughpemberton1@gmail.com mailto:hughpemberton1@gmail.com> wrote:

HI Doug,

I tried the mris_anatomical_stats and may well be doing it wrong
but got this as the result:

hughp@naoshi-WS:~/freesurfer/subjects$ mris_anatomical_stats -a
ABM/surf/lh.sulc -b ABM lh
computing statistics for each annotation in ABM/surf/lh.sulc.
reading volume /home/hughp/freesurfer/subjects/ABM/mri/wm.mgz...
reading input surface
/home/hughp/freesurfer/subjects/ABM/surf/lh.white...
reading input pial surface
/home/hughp/freesurfer/subjects/ABM/surf/lh.pial...
reading input white surface
/home/hughp/freesurfer/subjects/ABM/surf/lh.white...
CTABfindAnnotation: ct was NULL
No such file or directory
Segmentation fault (core dumped)

Not sure how to rectify this, any ideas?

Many thanks again,
Hugh


On 15 August 2012 01:42, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    Hi Hugh, you can run mris_anatomical_stats passing it the sulc
    file as input. This will give you averages within aparc. I'm
    not sure what you mean by "measuring cortical folding". What
    measure would you accept? There's the sulcal depth and then
    there's curvature (?h.curv). There are two types of
    "normalization". One is intensity normalization which is a
    preprocessing step before the segmentation. "Normalization" is
    also refers to intersubject registration. Probably you mean
    the latter.
    doug



    On 08/13/2012 09:56 PM, Hugh Pemberton wrote:

        Hi Doug,

        Thanks so much for getting back to my original question
        (have included below) and apologies if my question seems
        trivial but I'm a bit of a novice with freesurfer.. I've
        found the ?h.sulc file but how do I go about extracting
        the sulcal depth measurements? Is there a command like
        aparcsstats2table?

        Also, is there a way of measuring cortical folding with
        freesurfer? And I've read about the noramlization step but
        am still not completely clear on it, is this part of the
        segmentation of white/gray surface and pial surface?

        Thanks so much for your help,
        Best,
        Hugh

        Message: 5
        Date: Sun, 12 Aug 2012 22:25:02 -0400
        From: Douglas Greve <greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>
        <mailto:greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>>>

        Subject: Re: [Freesurfer] (no subject)
        To: freesurfer@nmr.mgh.harvard.edu
        <mailto:freesurfer@nmr.mgh.harvard.edu>
        <mailto:freesurfer@nmr.mgh.harvard.edu
        <mailto:freesurfer@nmr.mgh.harvard.edu>>
        Message-ID: <5028657E.8070908@nmr.mgh.harvard.edu
        <mailto:5028657E.8070908@nmr.mgh.harvard.edu>
        <mailto:5028657E.8070908@nmr.mgh.harvard.edu
        <mailto:5028657E.8070908@nmr.mgh.harvard.edu>>>

        Content-Type: text/plain; charset="iso-8859-1"

        The values are in the ?h.sulc file
        doug

        On 8/12/12 10:12 PM, Hugh Pemberton wrote:
        > Hi,
        >
        > How can I get sulcal depth measurements from Freesurfer?
        >
        > Cheers,
        > Hugh


    -- 
    Douglas N. Greve, Ph.D.
    MGH-NMR Center
    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    Phone Number: 617-724-2358 <tel:617-724-2358>
    Fax: 617-726-7422 <tel:617-726-7422>

    Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
    FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>



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