External Email - Use Caution 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 <dgr...@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 <dgr...@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. 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