Re: [Freesurfer] Calculation of MRI intensity

[Douglas N. Greve]

you will have to binarize it first, eg, mri_binarize --i inputimage.mgz 
--min threshold --o binary.mgz, then run mri_segstats --seg binary.mgz 
--id 1 --i inputimage.mgz --sum sum.dat


On 2/7/2024 8:55 AM, Huang, Yujing wrote:


I think mri_segstats –i option will do that - 
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats


Best,

Yujing

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *ERNEST KISSI

*Sent:* Wednesday, February 7, 2024 8:12 AM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] Calculation of MRI intensity

*External Email - Use Caution *

Hi Freesurfer Team,

Please I want to calculate the mean intensity of a skullstripped MRI 
image. I do not want to use recon-all because I do not want to 
parcellate or segment it. Is there such utility or function in freesurfer?


Thank you.

Sincerely,

Ernest Kissi Kontor.


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Re: [Freesurfer] Calculation of MRI intensity

[Huang, Yujing]

I think mri_segstats –i option will do that - 
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of ERNEST KISSI
Sent: Wednesday, February 7, 2024 8:12 AM
To: Freesurfer support list 
Subject: [Freesurfer] Calculation of MRI intensity


External Email - Use Caution
Hi Freesurfer Team,
Please I want to calculate the mean intensity of a skullstripped MRI image. I 
do not want to use recon-all because I do not want to parcellate or segment it. 
Is there such utility or function in freesurfer?
Thank you.
Sincerely,
Ernest Kissi Kontor.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Calculation of MRI intensity

[ERNEST KISSI]

External Email - Use Caution

Hi Freesurfer Team,

Please I want to calculate the mean intensity of a skullstripped MRI image.
I do not want to use recon-all because I do not want to parcellate or
segment it. Is there such utility or function in freesurfer?

Thank you.

Sincerely,
Ernest Kissi Kontor.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.