Dear Shal Hat,

I don't quite understand some of your statements here.

You say that registration is fine with Full Search but that
the frontal lobe is facing down - is this in the example_func2standard
or the example_func2highres.  Does your anatomical
scan have the frontal lobe facing down?  It isn't enough
to know this without knowing more information about which
image you are referring to and what the other images involved
are like.

Also, why are you using fslmerge with anatomicals?
I do not understand the reason for this.  All you
need is a single 3D image for your anatomical,
not a 4D one.

You also say that in your functional data, AP should be PA.
This sounds like you have *not* got the original orientation
of these images correct.  This is what David and I have been
saying before.  Nothing is worth doing unless these have
the correct orientation to start with.  If you have a capsule
labelling the anatomical and it was taken in the same session
as the functional, then you can normally determine left and
right by looking careful at the images as normally there is
some left-right asymmetry in how people lie in the scanner,
and you can match this up.

Also, did you check the sform_code and qform_code on
your original *functional* images, as well as the anatomicals?
All images need orientation information to be stored for
things to work well.  If the information is stored but the
labelling is wrong, then you will need to fix this labelling
*before* doing any registrations or any other processing at all.

All the best,
	Mark







On 2 Dec 2009, at 15:24, Shal Hat wrote:

> Thanks Mark, Thanks David,
>
> So here is what I have:
>
> 1) I currently now have a vit. E capsule, so I know the right from  
> the left for the 3D anatomical. However, no Vit. E capsule is  
> present for the functional data.
>
> 2) All the registration is fine when I use Full Search. In fact it  
> is really good.
>
> 3) For the 3D anatomical nifti file derived from fslmerge -t  both  
> sform_code and qform_code are 2. This is also true for the  
> functional data. What does this mean?
>
> 4) David: Yes I have tried your protocol for fslswapdim for nifti  
> and I also used fslswapdim for the original hdr file. However the  
> issue I mentioned earlier still remains; where for example the image  
> will rotate but R is stuck to the anterior position of the brain.
>
> 5) On the functional data AP should be PA.
>
> Also, I'd like to mention again the the registration and post-stats  
> look good. However the frontal lobe is facing down, and an R is  
> placed to one side. I just
> want to make sure that R is is actually Right and is not wrong due  
> to the above concerns.
>
> Best
>
> On Wed, Dec 2, 2009 at 5:52 AM, Mark Jenkinson <[log in to unmask]>  
> wrote:
> 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 ,
>
>