The absolutely crucial question is *are the labels correct*?
That is, are the A P labels in FSLView shown on the correct portions of the brain.
If so, then everything is fine, although it might be simpler if you run fslreorient2std
on all of your images first. However, you can only run this *if your labels are correct*.
If you labels are not correct then you need to take more complicated steps to fix
this (it may be worth trying to reconstruct from the dicom again). See the section
on "Orientation-Related Utilities" on the page:
for more information on what to do if the labels are incorrect.
All the best,
On 1 Jun 2012, at 06:29, Rodrigo Perea wrote:
> So, I am pre-processing the data using the guidelines in http://www.fmrib.ox.ac.uk/fsl/tbss/index.html
> However, when I open all the FA images, I can see that two are classified as NEUROLOGICAL instead of RADIOLOGICAL (using fslorient -getorient).
> So, if I open all of them with fslview, I see them flipped but the L R and A P are also flipped (R L and P A). So essentially they are oriented equally but I can't see them in the same orientation. One has the frontal region to the left of my computer and the other to the right.... :/
> Will this affect the image? How can I flip them so the flipped images look like the others? I tried fslorient -swaporient but fslview still shows me them flipped.
> Thanks in advance,