Hi, Mark,
Yes, indeed this was the problem. Setting the qform and sform codes prior to forceneurological
appears to have done the trick. In the near future I hope to use fslswap in order
to avoid this problem.
Many thanks,
JED
--- You wrote:
I suspect that this is your problem, although it is increasingly
uncommon (and bad) if files are written with no legal orientation
info, so I would check your original reconstructions and processing
pipeline to see if this information is just never created or is lost
somewhere along the line.
--- end of quote ---
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