Hi,
Fslview always displays images in radiological orientation - it
will "flip" neurological images accordingly. If you want to visually
verify that the fslswapdim/fslorient has worked correctly, load up
both images into fslview, pick a mm-coordinate in the brain ( check
it's the same intensity in both images) , and see how the voxel co-
ordinates differ...
Many Regards
Matthew
> 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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