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 <ahsan889...@gmail.com>
Sent: Friday, December 15, 2023 10:57 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Huang, Yujing
<yhuan...@mgh.harvard.edu>; Fischl, Bruce R.,PHD <bfis...@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
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> wrote:
Hi Ahsan,
Can you specify the commands that you have tried?
Best,
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Ahsan Ali
Sent: Thursday, December 14, 2023 11:02 PM
To: Fischl, Bruce R.,PHD
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>;
freesurfer@nmr.mgh.harvard.edu<mailto: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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