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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
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 */ /*
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I have used this for mean GI per hemisphere:
mri_segstats --i lh.lgi.mgz --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex.label --excludeid 0 --o lh.lgi.sum
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Wednesday, September 09, 2020 11:54 AM To: vittal korann vittalkorann@gmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mean gyrification index
* External Email - Caution * 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 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.
I think that should work
On 9/9/2020 12:59 PM, Alexopoulos, Dimitrios wrote:
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I have used this for mean GI per hemisphere:
mri_segstats --i lh.lgi.mgz --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex.label --excludeid 0 --o lh.lgi.sum
Jim
*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Wednesday, September 09, 2020 11:54 AM *To:* vittal korann vittalkorann@gmail.com; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mean gyrification index
** External Email - Caution **
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 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 Douglas N. Greve Sent: Wednesday, September 09, 2020 12:13 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mean gyrification index
* External Email - Caution * I think that should work On 9/9/2020 12:59 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution I have used this for mean GI per hemisphere:
mri_segstats --i lh.lgi.mgz --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex.label --excludeid 0 --o lh.lgi.sum
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Wednesday, September 09, 2020 11:54 AM To: vittal korann vittalkorann@gmail.commailto:vittalkorann@gmail.com; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mean gyrification index
* External Email - Caution * 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 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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________ 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.
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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 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 CautionThank 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.
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 unknownPlease 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 mailto: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.
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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 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 CautionDear 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 CautionThank 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.
Are you using actual question marks or are you replacing them with l or r? (you have to replace)
On 9/9/2020 2:26 PM, vittal korann wrote:
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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 <dgreve@mgh.harvard.edu mailto: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 <mailto: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.
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Yes, I did replace question marks with left and right.
Thank you so much, Douglas.
With regards Vittal
On Thu, Sep 10, 2020 at 1:11 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Are you using actual question marks or are you replacing them with l or r? (you have to replace)
On 9/9/2020 2:26 PM, vittal korann wrote:
External Email - Use CautionI 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 CautionDear 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 CautionThank 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 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.
Can you send the actual command you ran and all the terminal output?
On 9/10/2020 12:58 AM, vittal korann wrote:
External Email - Use Caution
Yes, I did replace question marks with left and right.
Thank you so much, Douglas.
With regards Vittal */ /*
On Thu, Sep 10, 2020 at 1:11 AM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
Are you using actual question marks or are you replacing them with l or r? (you have to replace) On 9/9/2020 2:26 PM, vittal korann wrote: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 <mailto: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 <mailto: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 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.
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Finally, it worked. Thank you, Douglas.
My question is regarding the mean gyrification similar to what we get for thickness as a whole-brain mean thickness. If there is a way to calculate, please let me know. Here is a command that I executed and got the mean gyrification value for the left/right hemisphere.
mri_segstats --slabel CSRI004 rh $SUBJECTS_DIR/CSRI004/label/rh.cortex
--i $SUBJECTS_DIR/CSRI004/surf/rh.pial_lgi --sum h.aparc.pial_lgi-csri004.stats
On Thu, Sep 10, 2020 at 7:22 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Can you send the actual command you ran and all the terminal output?
On 9/10/2020 12:58 AM, vittal korann wrote:
External Email - Use CautionYes, I did replace question marks with left and right.
Thank you so much, Douglas.
With regards Vittal
On Thu, Sep 10, 2020 at 1:11 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Are you using actual question marks or are you replacing them with l or r? (you have to replace)
On 9/9/2020 2:26 PM, vittal korann wrote:
External Email - Use CautionI 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 CautionDear 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 CautionThank 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 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.
On 9/10/2020 12:08 PM, vittal korann wrote:
External Email - Use Caution
Finally, it worked. Thank you, Douglas.
My question is regarding the mean gyrification similar to what we get for thickness as a whole-brain mean thickness.
I'm not sure what you are asking here. gyrification and thickness are different
If there is a way to calculate, please let me know.
What?
Here is a command that I executed and got the mean gyrification value for the left/right hemisphere.
mri_segstats --slabel CSRI004 rh $SUBJECTS_DIR/CSRI004/label/rh.cortex --i $SUBJECTS_DIR/CSRI004/surf/rh.pial_lgi --sum h.aparc.pial_lgi-csri004.stats*/ /*
On Thu, Sep 10, 2020 at 7:22 PM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
Can you send the actual command you ran and all the terminal output? On 9/10/2020 12:58 AM, vittal korann wrote:External Email - Use Caution Yes, I did replace question marks with left and right. Thank you so much, Douglas. With regards Vittal */ /* On Thu, Sep 10, 2020 at 1:11 AM Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: Are you using actual question marks or are you replacing them with l or r? (you have to replace) On 9/9/2020 2:26 PM, vittal korann wrote: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 <mailto: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 <mailto: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 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.
External Email - Use Caution
Sorry, Douglas, I might have confused you.
Freesurfer will provide mean thickness for the whole-brain. similarly, can I have mean gyrification for the whole brain (not individual values for left and right hemisphere)?
*Finally, it worked. Thank you, Douglas.* So far I was able to get mean gyrification values for each hemisphere separately.
*What?* I want to club the left and right hemisphere values into a single value.
On Thu, Sep 10, 2020 at 9:50 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
On 9/10/2020 12:08 PM, vittal korann wrote:
External Email - Use CautionFinally, it worked. Thank you, Douglas.
My question is regarding the mean gyrification similar to what we get for thickness as a whole-brain mean thickness.
I'm not sure what you are asking here. gyrification and thickness are different
If there is a way to calculate, please let me know.
What?
Here is a command that I executed and got the mean gyrification value for the left/right hemisphere.
mri_segstats --slabel CSRI004 rh $SUBJECTS_DIR/CSRI004/label/rh.cortex
--i $SUBJECTS_DIR/CSRI004/surf/rh.pial_lgi --sum h.aparc.pial_lgi-csri004.stats
On Thu, Sep 10, 2020 at 7:22 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Can you send the actual command you ran and all the terminal output?
On 9/10/2020 12:58 AM, vittal korann wrote:
External Email - Use CautionYes, I did replace question marks with left and right.
Thank you so much, Douglas.
With regards Vittal
On Thu, Sep 10, 2020 at 1:11 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Are you using actual question marks or are you replacing them with l or r? (you have to replace)
On 9/9/2020 2:26 PM, vittal korann wrote:
External Email - Use CautionI 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 CautionDear 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 CautionThank 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 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 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.
Can't you just average the lh and rh values? You can weight by the surface area or number of vertices
On 9/10/2020 12:53 PM, vittal korann wrote:
External Email - Use Caution
Sorry, Douglas, I might have confused you.
Freesurfer will provide mean thickness for the whole-brain. similarly, can I have mean gyrification for the whole brain (not individual values for left and right hemisphere)?
*Finally, it worked. Thank you, Douglas.* So far I was able to get mean gyrification values for each hemisphere separately.
*What?* I want to club the left and right hemisphere values into a single value.
*/ /*
On Thu, Sep 10, 2020 at 9:50 PM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
On 9/10/2020 12:08 PM, vittal korann wrote:External Email - Use Caution Finally, it worked. Thank you, Douglas. My question is regarding the mean gyrification similar to what we get for thickness as a whole-brain mean thickness.I'm not sure what you are asking here. gyrification and thickness are differentIf there is a way to calculate, please let me know.What?Here is a command that I executed and got the mean gyrification value for the left/right hemisphere. mri_segstats --slabel CSRI004 rh $SUBJECTS_DIR/CSRI004/label/rh.cortex --i $SUBJECTS_DIR/CSRI004/surf/rh.pial_lgi --sum h.aparc.pial_lgi-csri004.stats */ /* On Thu, Sep 10, 2020 at 7:22 PM Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: Can you send the actual command you ran and all the terminal output? On 9/10/2020 12:58 AM, vittal korann wrote:External Email - Use Caution Yes, I did replace question marks with left and right. Thank you so much, Douglas. With regards Vittal */ /* On Thu, Sep 10, 2020 at 1:11 AM Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: Are you using actual question marks or are you replacing them with l or r? (you have to replace) On 9/9/2020 2:26 PM, vittal korann wrote: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 <mailto: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 <mailto: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 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 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.
External Email - Use Caution
Thank you so much, Douglas.
On Thu, Sep 10, 2020 at 10:20 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Can't you just average the lh and rh values? You can weight by the surface area or number of vertices
On 9/10/2020 12:53 PM, vittal korann wrote:
External Email - Use CautionSorry, Douglas, I might have confused you.
Freesurfer will provide mean thickness for the whole-brain. similarly, can I have mean gyrification for the whole brain (not individual values for left and right hemisphere)?
*Finally, it worked. Thank you, Douglas.* So far I was able to get mean gyrification values for each hemisphere separately.
*What?* I want to club the left and right hemisphere values into a single value.
On Thu, Sep 10, 2020 at 9:50 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
On 9/10/2020 12:08 PM, vittal korann wrote:
External Email - Use CautionFinally, it worked. Thank you, Douglas.
My question is regarding the mean gyrification similar to what we get for thickness as a whole-brain mean thickness.
I'm not sure what you are asking here. gyrification and thickness are different
If there is a way to calculate, please let me know.
What?
Here is a command that I executed and got the mean gyrification value for the left/right hemisphere.
mri_segstats --slabel CSRI004 rh $SUBJECTS_DIR/CSRI004/label/rh.cortex
--i $SUBJECTS_DIR/CSRI004/surf/rh.pial_lgi --sum h.aparc.pial_lgi-csri004.stats
On Thu, Sep 10, 2020 at 7:22 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Can you send the actual command you ran and all the terminal output?
On 9/10/2020 12:58 AM, vittal korann wrote:
External Email - Use CautionYes, I did replace question marks with left and right.
Thank you so much, Douglas.
With regards Vittal
On Thu, Sep 10, 2020 at 1:11 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Are you using actual question marks or are you replacing them with l or r? (you have to replace)
On 9/9/2020 2:26 PM, vittal korann wrote:
External Email - Use CautionI 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 CautionDear 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 CautionThank 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 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 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.
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.edumailto: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.edumailto: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.
freesurfer@nmr.mgh.harvard.edu
-
Alexopoulos, Dimitrios -
Douglas N. Greve -
vittal korann