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 ,
