Hi Colm,
I have no idea what might explain the error message. Maybe Steve of Mark J. would have a take on this, but there are not available right now!
I would just say: just inspect visually that no flipping has occurred after the segmentation and if everything looks fine between the T1_brain and the GM images, then forget about the error message.
Usually, the trickiest step to check for a L/R flip is the registration one as this is not easy to see what went on with a naked-eye but you don't seem to have any problem at that stage...
Cheers,
Gwenaelle
--- En date de : Jeu 10.7.08, Colm G. Connolly <[log in to unmask]> a écrit :
> De: Colm G. Connolly <[log in to unmask]>
> Objet: Re: [FSL] vbm, fast and flipping
> À: [log in to unmask]
> Date: Jeudi 10 Juillet 2008, 12h43
> Any takers on this?
>
> On 7 Jul 2008, at 16:21, Colm G. Connolly wrote:
>
> > Hi everybody,
> >
> > I've been running fslvbm on some datasets and I
> have an issue which
> > has me stumped, hopefully someone here can shed light
> on it for me.
> >
> > I convert my original T1 images to RPI and place them
> in a
> > directory, then rescale them (using tbss_1_preproc). I
> then proceed
> > to run fslvbs_1_bet and fslvbm_2_template.
> >
> > When I look in the results of the of fslvbm2a.[oe]* to
> see how the
> > segmentation went I see that fast is complaining about
> image
> > flipping, even though the original images were in RPI.
> >
> > When I try to skull strip and segment the same data
> file by hand,
> > there is no complaint from fast about flipping.
> Likewise, when I
> > copy the ${subject}.anat_brain.{hdr,img} files into a
> separate
> > directory and run fast on it using the same arguments
> as in the
> > fslvbm2a script, I do not receive complaints from
> fast. This has me
> > stumped.
> >
> > Should I be concerned about the complaint about
> flipping during the
> > fslvbm_* pipeline Or can I safely ignore it?
> >
> > If it would help I can make all the data available for
> download.
>
>
> Bye,
> --
> Dr Colm G. Connolly
> School of Psychology and Institute of Neuroscience
> The Lloyd Building
> University of Dublin
> Trinity College, Dublin 2, Éire
> Fax: +353-1-671-3183
>
> Please note that electronic mail to, from or within the
> Trinity
> College Dublin, may be the
> subject of a request under the Freedom of Information Act.
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