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