Re: [Freesurfer] Re global lgi values

I think it would be

--parc aparc.pial_lgi

doug

On 11/14/2013 11:27 AM, Anna Jonsson wrote:

Thank you. Can I then use aparcstats2table --subjects XXXX --hemi lh --meas thickness --parc lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get all the values in 1 tablefile or should I use other command?

On Wed, Nov 13, 2013 at 6:59 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

yes and yes


On 11/13/2013 12:04 PM, Anna Jonsson wrote:

    Thank you very much. By second I assume you mean second row?
    And out of the values on the second row it must be the value
    2.9472? Is it headed by Area_mm2 or Mean? And what are the units?

    Thanks again



    On Wed, Nov 13, 2013 at 4:56 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:


        that looks correct. It is the 2nd number you want. The
    first is
        for the
        medial wall (not interesting). You can have it report only for
        cortex by
        adding --id 1

        doug


        On 11/13/2013 11:45 AM, Anna Jonsson wrote:
        > Dear list,
        >
        > I have a question about extracting global lgi
    values/hemisphere. I
        > think I have managed to do it correctly using :
        >
        >   mri_segstats --slabel subj lh
        $SUBJECTS_DIR/subj/label/lh.cortex --i
        $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum
    lh.aparc.pial_lgi.stats
        >
        > (Please let me know if this is not correct)
        >
        >
        > I then get this output ( for each individual)
        >
        >   ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
        StdDev Min Max Range
        >    1   0      7953     5220.0  Seg0000 2.4055 0.4052
    <tel:2.4055%20%20%200.4052>        1.5796     2.9763     1.3967
        >
        >    2   1    156737   101379.9  Seg0001 2.9472   0.9038  
         1.7030     6.0007     4.2977
        >
        > I assume one of these values (if above command has worked
        correctly) contains the mean lgi value for the left
    hemisphere.
        Can somebody please tell me which of the above values is the
        correct lgi value? Additionally, what units are lgi
    measured in,
        and are values between 1-5 what is considered normal?
        >
        >
        > Thank you very much
        >
        > Anna
        >
        >
        > _______________________________________________
        > Freesurfer mailing list
        > Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
        <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>>

        > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

        Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
        <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
        FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
    www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
        <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

        Outgoing:
    ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

        _______________________________________________
        Freesurfer mailing list
    Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
    <mailto:Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>>

    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


        The information in this e-mail is intended only for the
    person to
        whom it is
        addressed. If you believe this e-mail was sent to you in
    error and
        the e-mail
        contains patient information, please contact the Partners
        Compliance HelpLine at
    http://www.partners.org/complianceline . If the e-mail was sent to
        you in error
        but does not contain patient information, please contact the
        sender and properly
        dispose of the e-mail.



-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/