External Email - Use Caution 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. < [email protected]> 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: > > 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 > > _______________________________________________ > Freesurfer mailing > [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
