Hello FreeSurfur developers,

When I did:

mergeseg --src brainmask.bin.mgz --merge both.hippo.mgz --o bm+hippo.mgz

The color of the hippo segment (both.hippo) in the bm+hippo.mgz file has become black. Is there any way I can do to change the color of both.hippo segment from back to another color?

Thanks,

Ammar

On Thursday, August 5, 2021, 11:45:12 AM GMT+9, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

To merge the two hippocampi together in one file you can
fscalc left-hippo.mgz sum right-hippo.mgz -o both.hippo.mgz
If you want a binary mask of the brainmask, you can run
mri_binarize --i brainmask.mgz --min 0.5 --o brainmask.bin.mgz
Then run
mergeseg --src brainmask.bin.mgz --merge both.hippo.mgz --o bm+hippo.mgz

On 8/4/2021 12:21 PM, Ammar Shujaa wrote:

External Email - Use Caution
Hello Freesufer developers,

I just want to know how to merge the right and left-hypocampus in one file (hypocampus.gmz), and then merge hypocampus.gmz with brainmask.gmz so that I can get one mgz file having the segmentations with the brainmask. I want to use this file (hypocampus+brainmask.gmz) in another software.

Best regards

Ammar
On Wednesday, August 4, 2021, 11:54:48 PM GMT+9, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
I don't understand what you mean by "join". Can you elaborate?

On 8/4/2021 1:16 AM, Ammar Shujaa wrote:
External Email - Use Caution

Hello FreeSurfur Developers,

I have used binary mask and got the segmentations: right and left-hypocampus.mgz.

I just want to know how to join these segmentations with T1.mgz so that I can get one file containing T1 image with the two segmentations. I also want to save the T1 image with the the segmentions in nifti format.

Thanks in advance.

Ammar
_______________________________________________
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
_______________________________________________
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
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 http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 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

_______________________________________________
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
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 http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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.