External Email - Use Caution
Thank you for your e-mail. It seems I got another error. This is what it showed in terminal:
[toyama-no-iMac:/applications/freesurfer/subjects] toyama% mri_segstats --i lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label --id 1 --sum sum.dat
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --i lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label --id 1 --sum sum.dat
sysname Darwin
hostname toyama-no-iMac.local
machine x86_64
user toyama
UseRobust 0
Constructing seg from label
Segmentation fault
Could you help me please?
On Fri, Jan 17, 2020 at 11:56 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Sorry, it should have been --sum instead of --o the subject name is subject_id --id 1 just means to take the vertices in the label (--id 0 would mean to take the background)
On 1/16/2020 7:07 PM, Tien Pham wrote:
External Email - Use CautionThank 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:
External Email - Use CautionDear 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 name6595 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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