Hi Doug,

First of all sorry to bother you again with that.

We still have an issue with the mri_convert command line and almost all the people in the lab tried without any success.

We have the following nifti file attached and we tried to convert it to surface file. We used a MNI152 2mm brain template and when we look at the image with tksurfer, the image is flipped. (we have this issue with half of the data).

I have attached the screenshot of the NIFTI file displayed with freeview. (file1)

I have attached how we are supposed to see the MGH file (not flipped) in tksurfer

I have attached how we see tne MGH file (flipped)

The command line we have used :

*bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg MNI152_T1_brain.dat --t1 --init-coreg*

*mri_vol2surf --file1.nii --reg MNI152_T1_brain.dat --hemi rh --o file1.mgh*

I have attached one of the nifti file to see if you can replicate the issue.

Thank you very much,

I would really appreciate any help,

Redwan