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:
External Email - Use Caution
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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