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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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1XMRWtcNlF2TL5x-0oM4ghUUGibHAPIm9piFIZVaHmSUpR0... 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://secure-web.cisco.com/16HDIOgvUoadsdBbURMcYWYGXqLqp0NQzTCYuiDhB_dvc5V... < https://secure-web.cisco.com/16HDIOgvUoadsdBbURMcYWYGXqLqp0NQzTCYuiDhB_dvc5V... .

btw, you can get fornix segmentation from mri_sclimbic_seg

On 12/15/2023 11:34 AM, Huang, Yujing wrote:

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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