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Try this for the left hem. This command includes the excludeid = 0
mri_segstats --slabel subject_ID lh
$SUBJECTS_DIR/subject_ID/label/lh.cortex.label --i
$SUBJECTS_DIR/subject_ID/surf/lh.pial_lgi --excludeid 0 --sum
lh.aparc.pial_lgi_lh.stats
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of vittal korann
Sent: Wednesday, September 09, 2020 1:26 PM
To: Douglas N. Greve <dgr...@mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mean gyrification index
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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
<dgr...@mgh.harvard.edu<mailto:dgr...@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
<dgr...@mgh.harvard.edu<mailto:dgr...@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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