Re: [Freesurfer] mean gyrification index

On 9/10/2020 12:08 PM, vittal korann wrote:

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Finally, it worked. Thank you, Douglas.

My question is regarding the mean gyrification similar to what we get for thickness as a whole-brain mean thickness.

I'm not sure what you are asking here. gyrification and thickness are different

If there is a way to calculate, please let me know.

What?

Here is a command that I executed and got the mean gyrification value for the left/right hemisphere.

mri_segstats --slabel CSRI004  rh
 $SUBJECTS_DIR/CSRI004/label/rh.cortex --i
$SUBJECTS_DIR/CSRI004/surf/rh.pial_lgi  --sum
h.aparc.pial_lgi-csri004.stats

*/ /*

On Thu, Sep 10, 2020 at 7:22 PM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:

Can you send the actual command you ran and all the terminal output?

On 9/10/2020 12:58 AM, vittal korann wrote:

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Yes, I did replace question marks with left and right.

Thank you so much, Douglas.

With regards
Vittal
*/
/*


On Thu, Sep 10, 2020 at 1:11 AM Douglas N. Greve
<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote:

    Are you using actual question marks or are you replacing them
    with l or r? (you have to replace)

    On 9/9/2020 2:26 PM, vittal korann wrote:

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    I did that, but the error remains the same.

        mri_segstats --slabel CSRI001 ?h
         $SUBJECTS_DIR/CSRI001/label/?h.cortex --i
        $SUBJECTS_DIR/CSRI001/surf/?h.pial_lgi --sum
        h.aparc.pial_lgi-csri001.stats


    */
    /*


    On Wed, Sep 9, 2020 at 11:32 PM Douglas N. Greve
    <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote:

        You need to include the hemisphere in the --slabel
        arguments (maybe the 2nd one)

        On 9/9/2020 2:10 PM, vittal korann wrote:

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        Dear Douglas

        Thank you for your help!

        I got an error while executing the mris_segstats command.

            Command:
            mri_segstats --slabel CSRI001?h
             $SUBJECTS_DIR/CSRI001/label/?h.cortex.label --i
            $SUBJECTS_DIR/CSRI001/surf/?h.pial_lgi --sum
            h.aparc.pial_lgi-csri001.stats



            ERROR: Option
            /usr/local/freesurfer//subjects/CSRI001/surf/rh.pial_lgi
            unknown


        Please correct me if something wrong in the command line.
        Sorry for troubling you again.
        With regards
        Vittal
        */
        /*


        On Wed, Sep 9, 2020 at 10:23 PM Douglas N. Greve
        <dgreve@mgh.harvard.edu
        <mailto:dgreve@mgh.harvard.edu>> wrote:

            You can use mri_segstats with the --slabel option,
            specifying the ?h.cortex.label and using the
            gyrification as input

            On 9/9/2020 12:54 PM, vittal korann wrote:

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            Thank you so much, Douglas.

            Could you please guide me to obtain the global
            mean gyrification index for each subject?

            With regards
            korann
            */
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