Hi,
I had a similar problem and tried two things:
1) Use AFNI to 3dcopy the file.
3dcopy [image1].nii [newname].nii
Somehow (and I don't know how it worked), when I opened the newname.nii it was not shifted.
2) Use fslmaths from a file of the same size but that was not shifted (call it noshift.nii) as the base
image and add your shifted image (image1.nii) to it
fslmaths [noshift].nii -mul 0 -add [image1].nii [newname].nii
Hope it is useful to you,
Jason
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