I have been trying to use fnirt for spatial normalization in an AFNI
analysis, and seem to have run up against an inconsistency in the header.
The sform_code and qform_code are both set to 4 in the header, which I
understand to mean that they both represent the images position in MNI
space. Unfortunately, the qform indicates that the image orientation is RPI
while the sform indicates that it is LAI. The sform is correct. This
confuses AFNI to no end.
My understanding of the nifti standard is that if the sform_code and
qform_code are the same, then the sform and qform should represent the same
coordinate transformation. Am I missing something here?
Thanks,
John
p.s. This occurs with version 4.1.5.
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