Hi Doug,

First of all sorry to bother you again with that.

We still have an issue with the vol2surf 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 the 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

Can you try to replicate the issue or give some tips ?

We have this issue with half of the data

Thank you very much,

I would really appreciate any help,

Redwan