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.
> 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.
> (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?
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?
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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