External Email - Use Caution        

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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of vittal korann
Sent: Wednesday, September 09, 2020 1:26 PM
To: Douglas N. Greve <dgreve@mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mean gyrification index

 

* External Email - Caution *

        External Email - Use Caution        

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 <dgreve@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:

        External Email - Use Caution        

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 <dgreve@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:

        External Email - Use Caution        

Thank you so much, Douglas.

 

Could you please guide me to obtain the global mean gyrification index for each subject?

 

With regards

korann

 

 

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

 

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

 

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.