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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@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 [Image removed by sender.]
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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.
