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Thank you very much for your e-mail.

I tried, but this '' --o '' is unknown showing in terminal and the '' --id '' flag is subject name?

Could you please help me?

For example, I found the change in frontoinsula region between 2 groups in my dataset and I want to extract the values of this region.

On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

It might be easier to use mri_segstats, eg,

mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id 1 --o sum.dat

The mean value will be in the "Mean" column of the sum.dat

On 1/14/2020 7:08 PM, Tien Pham wrote:

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Dear FreeSurfer Experts,

I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI changes in my data set with two time points using longitudinal pipeline. Now I would like to extract the regional LGI and gray matter volume in my longitudinal results using QDEC to draw the ROIs which is showed significant differences, label it and map to all subjects. Then I get the LGI value of the ROI I saved before using the command below:

cd $SUBJECTS_DIR
mris_anatomical_stats -l lh.untitled.label \
 -t lh.pial_lgi \
 -b \

 -f subject_id/stats/lh.untitled.stats subject_id lh 

And this is the result:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% mris_anatomical_stats -l lh.frontoinsula.label \

? -t lh.pial_lgi \

? -b \

? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh

limiting computations to label lh.frontoinsula.label.

using thickness file lh.pial_lgi.

reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...

reading input surface /applications/freesurfer/subjects/VC019_1/surf/lh.white...

reading input pial surface /applications/freesurfer/subjects/VC019_1/surf/lh.pial...

reading input white surface /applications/freesurfer/subjects/VC019_1/surf/lh.white...

 

table columns are:

    number of vertices

    total surface area (mm^2)

    total gray matter volume (mm^3)

    average cortical thickness +- standard deviation (mm)

    integrated rectified mean curvature

    integrated rectified Gaussian curvature

    folding index

    intrinsic curvature index

    structure name

 

 6595   4368  15935  3.311 0.895     0.158     0.077      135    19.7  lh.frontoinsula.label

As I saw there was no columns showing the LGI value, I did similar with gray matter volume, the result displayed the different in some values of the columns.
Could you please help me to explain about this?

Thank you very much.

Best regards,

Tien Pham

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