Matthew,
Thank you for your help. Just to clarify my second question: I did
perform both fslswapdim and fslorient -swaporient on my Nifti image,
which resulted in a flip of the image from neurological to
radiological and then back into neurological orientation in fslview
(although the header information was altered as expected to reflect
radiological orientation). Therefore, when I performed both commands
as the instructions suggested, the resulting image appeared identical
to the original image in fslview rather than appearing flipped
relative to the original image. Does fslview not reflect the true
orientation of the image? Are there defaults I need to change
somewhere? I was just trying to figure out why this might have
happened so that I could remedy it.
Thank you,
Meredith
Quoting Matthew Webster <[log in to unmask]>:
> Hello,
> 1) The best way of determining which orientation an image header is in
> is to run fslorient <image>
> 2) To fully change the orientation of an image you must run both
> fslswapdim _and_ fslorient or the image will end up in inconsistent
> state ( e.g. for both your "partially-processed" images you will see a
> mismatch between voxel co-ords and mm-coords in FSLVIEW ).
> 3) The Analyze format does not contain the full orientation information
> and so NIFTI-orientation information will be lost in the conversion,
> FSL assumes radiological-orientation ( which is what we also assume for
> NIFTI-files with no orientation information in the header ) for all
> Analyze files.
>
> Many Regards
> Matthew
>>
>> 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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