Can you try ‘mri_segstats’? It will compute statistics on segmented volumes  -  https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats

Yujing

From: Ahsan Ali <ahsan889960@gmail.com>
Sent: Friday, December 15, 2023 10:57 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Huang, Yujing <YHUANG43@mgh.harvard.edu>; Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edu>
Subject: Re: [Freesurfer] Statistical Characteristics of Segmented Fornix from T1-w MR Images

        External Email - Use Caution        

Hi,

Sure.

I have used this command for segmentation: "recon-all -s name -i name.nii -all"

Then I used "mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto_CCseg.mgz -f" command to estimate only fornix. 

Now I have fornix.mgz file in which only one structure, fornix, is there. Now I'm interested to know the statistical values, such as fractal dimension and all. 

I hope I have now conveyed my problem to you. 

With Regards
Ahsan
---------------------------------------------
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics and Biomedical Engineering (AMBE)
Indian Institute of Technology Madras 
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552

On Fri, Dec 15, 2023 at 7:31 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

Hi Ahsan,

Can you specify the commands that you have tried?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ahsan Ali
Sent: Thursday, December 14, 2023 11:02 PM
To: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edu>; freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Statistical Characteristics of Segmented Fornix from T1-w MR Images

        External Email - Use Caution        

Dear Sir/Madam,

I have segmented T1-W MR images from the ADNI database using Freesurfer. From aseg.nii, I have estimated the fornix structure (label number 250). I tried many times to get the characteristics of these structures but couldn't. It would be helpful for me; kindly let me know. 

File name "fornix.nii" at label 250. Its statistical parameters, such as fractal dimension, volume, mean, etc  

With Regards
Ahsan
---------------------------------------------
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics and Biomedical Engineering (AMBE)
Indian Institute of Technology Madras 
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552

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