Dear FSL group,
I have a question regarding the FAQ discussion of modifying right-left
orientation of the data. The memo says that for data that is ordered as
neurological and also has header information listed as neurological, both
fslswapdim and fslorient -swaporient should be performed to correctly
transform NIFTI data to radiological. My questions are as follows:
1) When the sform and qform x direction in the header both say right-left,
does that indicate radiological or neurological?
2) When I performed fslswapdim -x y z alone on a Nifti image, the image
flipped in FSL view without a change in orientation listed in the header (as
expected), but when I performed fslorient -swaporient, the header
information changed AND the image flipped in FSL view, such that when both
commands were performed, the resulting "flipped" image was oriented
identically in FSL view to the original image. The image orientation
therefore no longer matched the header information. Why might this happen?
3) I saw in the memo that if the command fslorient is used on Analyze format
files, it will not change anything and the default orientation of
"radiological" will be used. Does this correspond to the header listing
orient as "0"? Does it matter if I convert the files from Nifti files (i.e.
will the orientation information in the Nifti file be preserved in the
Analyze file, or will all Analyze files be listed as radiological regardless
of the orientation information in the Nifti file from which they were
converted)?
Thank you in advance for your help!
Best,
Meredith
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