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
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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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1csL3BhRuiwuH-Y7OlroCMmv1izTJ0Zy4r2TvlnVA9uz4-HERzQ4SnRNw2LLvP9JC9b6gG-tC2jsrbHqPRsQto80Mq1PtwHsU28oaNwosxS4geP1Omyj0e68DGWLPu0PdPybZAtGHD1PeqS10pg2Cv9yuU0IwmoJi5huFUlVJ9rtlwVwuNMVfv6qfyIUvJuyBA2Dz4Y2hi4z-GYyJ3bobDVpLKMIxHNoDslqiJs2VJlq6Kz1eCH0R7i6g4M5F5YDHgm9eE8uZLPzwv-2vICXhEmlk_UIvaCdPBIU4SFWte9DxTQpY--J1ZyDj0hPJWv4O/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1n6RhvGHwefS5YCMOMCao9q1etx9e4i0WnU7diXn4jRdgYhdXRupQv-xqS8YG0xIV-3yPiY2MKiu9FqJmgP4g7dJj3PD-gChydCjzunt1LnHhkVAN0IQj17iyFaFR9Ezdzxn25YQGb4AlhFb1WmpOoGzIeta9cWinoYM52s4-01uF3KkIP0_QtUwN1nRd96vVJZD7Iq6a27L5VpBHj6UNAMiK8IBZPkpeORmVWhHtVhMAn76-umMQquWctk7Plo1L149j3NYGlLBKLLgAtMulcNUpsqVYp75aOWH3mM9mSifOYyAAuh-KLbyOztGpaka2/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1n6RhvGHwefS5YCMOMCao9q1etx9e4i0WnU7diXn4jRdgYhdXRupQv-xqS8YG0xIV-3yPiY2MKiu9FqJmgP4g7dJj3PD-gChydCjzunt1LnHhkVAN0IQj17iyFaFR9Ezdzxn25YQGb4AlhFb1WmpOoGzIeta9cWinoYM52s4-01uF3KkIP0_QtUwN1nRd96vVJZD7Iq6a27L5VpBHj6UNAMiK8IBZPkpeORmVWhHtVhMAn76-umMQquWctk7Plo1L149j3NYGlLBKLLgAtMulcNUpsqVYp75aOWH3mM9mSifOYyAAuh-KLbyOztGpaka2/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
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