Hi Colm,
--- "Colm G. Connolly" <[log in to unmask]> a écrit
:
> On 18 Sep 2007, at 15:09, Gwenaëlle DOUAUD wrote:
>
> > I've just had a look at your 4D template.
>
> Thanks of raking the time to do this.
No worries.
> > I'm afraid you will have to play a bit with
> fslswapdim
> > till you reach the normal orientation your images
> > should have (see snapshot attached). As I guess
> BET
> > brain extraction has worked normally on your
> images
>
> yep it worked quite well, except on 3 subjects were
> it left a little
> frontal or dorsal posterior brain out. but i can
> rerun that again to
> tune it.
Maybe fslvbm_1_bet -N -f 0.5 would do the trick...
> > (but please do check this assumption), you could
> > directly reorient the *FAi_brain images. You will
> then
> > only need to re-run the fslvbm_2_template and
> > fslvbm_3_proc commands from your VBM working
> > directory.
>
> Can I do stupid thinks like swap right and left with
> this command?
Yes, that would be:
fslswapdim myimage -x y z myflippedimage.
BUT I do believe that there is nothing wrong for the
L/R orientation of your FAi images when preprocessing
them with tbss_1. The whole orientation of your images
is wrong but I think that if they were in radiological
convention, they still are.
You should definitely have at the end of your
fslswapdim command an image that have the SAME
orientation in fslview that the one I gave to you.
Looking briefly at it, my guess would be:
fslswapdim myFAi_image -y -z x mynewFAi_image
but please do "play" a bit with those x, y, z
parameters dto get familiar with what they are doing
and make sure that doing so, you do not flip L/R your
images (if it is the case, then you will get a message
saying: "WARNING:: Flipping Left/Right orientation (as
det < 0)").
> How do I determine what the current orientation of
> the files is from
> FSL's pov? Out of curiosity what aspect of the NIfTI
> header does FSL
> use to determine the correct orientation of images?
Hmmm... I'm not competent to answer this question,
sorry.
Hope this helps!
Gwenaelle
> Bye,
> --
> Dr Colm G. Connolly
> School of Psychology and Institute of Neuroscience
> The Lloyd Building
> University of Dublin
> Trinity College, Dublin 2, Éire
> Tel: +353-1-896-8475
> Fax: +353-1-671-3183
>
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