Hi,
I agree with David - you need to make sure that ALL of your images are
correct before proceeding with any analysis.
There are two other possible problems that you might be getting
confused with:
(1) It is possible to have nifti images with no orientation
information stored
in them, in which case FSL uses a default orientation, but that won't
be preserved through any image transformations (rotations). You can
check if this is the case by running "fslhd" and looking at the
sform_code
and qform_code. If _both_ codes are zero, then you have no orientation
information stored. If either is non-zero then you do have orientation
information stored.
(2) The registration is failing, in which case the labels will be
taken from
the reference image and will be wrong. Check the registration by
loading both the reference image and the output from the registration
(the transformed input image) and see if they visually are aligned
in an anatomical way (forget the labels).
So if these images are aligned well *and* there is orientation
information in
your nifti images *and* you have set the labels correctly in ALL the
original
images *and* you still have a problem with the labels of the
registration
output, then this is a puzzling matter that we will need to look into
further.
I suspect that this isn't the case though, and that you simply need to
fix one of the above problems first.
All the best,
Mark
On 2 Dec 2009, at 06:53, David V. Smith wrote:
> What exactly was your command in fslswapdim? If you haven't already,
> I would try the following on ALL of your images:
> fslswapdim invol RL PA IS outvol
>
> But, as Mark mentioned earlier, you can't be completely sure about L/
> R orientation without a vitamin E capsule or other orientation-
> related information from the raw images....
>
> Some other useful documentation:
> http://www.fmrib.ox.ac.uk/fsl/avwutils/index.html
> http://www.fmrib.ox.ac.uk/fslfaq/#general_lr (see Q5-7)
>
>
> On Dec 1, 2009, at 11:52 PM, *Shal Hat* wrote:
>
>> Hi,
>>
>> my original images are wrongly labeled in FSL. I used fslswapdim to
>> correct this. However,
>> the image rotates but the labels are still mismatched (i.e. R is
>> always where A should be).
>> How can I correct the mismatch of labels and the anatomy. Do I need
>> to use fslorient, if so
>> I would appreciate details on the command and how I can correct
>> this issue.
>>
>> I also tried using another software to get the nifti file, but FSL
>> seems not to like that nifti
>> file.
>>
>> Thanks ,
>
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