How to join certain segmentation with T1.mgz and save them in one file with nifti format
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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
I don't understand what you mean by "join". Can you elaborate?
On 8/4/2021 1:16 AM, Ammar Shujaa wrote:
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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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 regardsAmmar
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 https://secure-web.cisco.com/1kw0m_W7Sg4Mb-g0SUyDzqcgphEU2g9V9YahmmHa-04uVdO...
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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
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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://secure-web.cisco.com/1-3ndcvWjkjeTI9QKGnD85Gyh8wS1fHmP5stU-quLD4XSQ9...
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what are the actual values ("black" does not mean much)
On 8/5/2021 1:21 AM, Ammar Shujaa wrote:
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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 mailto: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
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Douglas N. Greve