Hi,
I really do not understand how this is happening.
There is a line that uses immv to rename the existing T1 image to T1_fullfov, which may result in a file with an ending of .nii. However, after this it is only used as an input to robustfov, and so I cannot see how another version is created. Unless you start with one of the images having the name T1_fullfov then I cannot see what goes wrong. I also can't see how averaging images affects this. Are you sure you have not run this twice in the same place?
In order to investigate further can you do the following for me:
- cd into the anat directory
- run fslerrorreport and send us the output
- also send us the *exact* command line you ran, the directory you were in when you ran this command, and the result of "ls -la" in the directory where the input file is
All the best,
Mark
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