External Email - Use Caution
Dear Support Team,
I'm reaching out for assistance with merging two .mgh files.
As I try to generate a surface mapping for all subjects, I merged all volume files (.nii.gz) by mrcalc. So I get a volume file whose voxel value represents the number of valid subjects. And then I convert it to .mgh using mri_vol2surf. But the value of each voxel seems to be thrown out. Because I found the max value of .mgh is not the same as .nii file.
I guess I should merge files of all subject in mgh format to maintain the number of valid subjects, but it seems to be a volume encoded surface file format. So I don't know how to merge them.
I'm working on Ubuntu18.
I would be very grateful for your assistance.
Best, Rosie
Hi Rosie,
Are you trying to combine all volume files (.nii.gz) into one single volume by stacking all frames? Maybe you should use Freesurfer mri_concat instead of mrcalc?
Here are the help pages for mri_concat and mri_vol2surf:
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_concat https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Rosie Sent: Thursday, February 29, 2024 10:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Assistance Request: Issue with Merging .mgh Files in Ubuntu18
External Email - Use Caution Dear Support Team,
I'm reaching out for assistance with merging two .mgh files.
As I try to generate a surface mapping for all subjects, I merged all volume files (.nii.gz) by mrcalc. So I get a volume file whose voxel value represents the number of valid subjects. And then I convert it to .mgh using mri_vol2surf. But the value of each voxel seems to be thrown out. Because I found the max value of .mgh is not the same as .nii file.
I guess I should merge files of all subject in mgh format to maintain the number of valid subjects, but it seems to be a volume encoded surface file format. So I don't know how to merge them.
I'm working on Ubuntu18.
I would be very grateful for your assistance.
Best, Rosie
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Hi Yujing, Thank you so much for your help. It works well! Cheers, Rosie
At 2024-03-01 21:39:02, "Huang, Yujing" YHUANG43@mgh.harvard.edu wrote:
Hi Rosie,
Are you trying to combine all volume files (.nii.gz) into one single volume by stacking all frames? Maybe you should use Freesurfer mri_concat instead of mrcalc?
Here are the help pages for mri_concat and mri_vol2surf:
https://secure-web.cisco.com/1tLcusmOJJpls_HMuxOKJJmKCYKR_Ppkbo1C4mLApp-4lMH...
https://secure-web.cisco.com/1dNBwTwslJ7ddeVw34J9pR8X5ecwtAz43umMNRC7GAnKcRa...
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Rosie Sent: Thursday, February 29, 2024 10:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Assistance Request: Issue with Merging .mgh Files in Ubuntu18
External Email - Use Caution
Dear Support Team,
I'm reaching out for assistance with merging two .mgh files.
As I try to generate a surface mapping for all subjects, I merged all volume files (.nii.gz) by mrcalc. So I get a volume file whose voxel value represents the number of valid subjects. And then I convert it to .mgh using mri_vol2surf. But the value of each voxel seems to be thrown out. Because I found the max value of .mgh is not the same as .nii file.
I guess I should merge files of all subject in mgh format to maintain the number of valid subjects, but it seems to be a volume encoded surface file format. So I don't know how to merge them.
I'm working on Ubuntu18.
I would be very grateful for your assistance.
Best,
Rosie
freesurfer@nmr.mgh.harvard.edu
-
Huang, Yujing -
Rosie