Hi Gwenaëlle,
On 19 Sep 2007, at 14:28, Gwenaëlle DOUAUD wrote:
>
> 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)").
Based on a previous post to this list I think I've found an easier
way to do this I can reorient the nii files using afni's 3dresample
command:
3dresample -orient RPI -prefix RPI.nii -inset 66101_2.anat.nii
fslorient -getorient RPI.nii then says that the they are radiological
orientation.
I also tried 3dresample -orient LPI -prefix LPI.nii -inset
66101_2.anat.nii
but then fslorient -getorient LPI.nii then says that the they are
neurological orientation.
In either case the data looks like the screen shot you attached to
your earlier email. Both the LPI and RPI look identical when overlaid
in fslview.
I had originally thought that LPI would make fsl happier but since
RPI makes fslorient say "radiological" I'm going to try the RPI files
and see how things go. It'll be about 3 days before the job completes.
Thanks for your help,
--
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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