Hi again Sushravya,
I think I know what's going on: in the most recent version of TBSS, Steve has changed the way to create the mask for the analyis. Basically, it now takes the *intersection* of all your FA maps.
This is a good way to be aware of some data truncated and lack of overlap across subjects etc...
So it might be the case that your mean_FA_mask is actually correct and points out as one image (possibly several?) being truncated... What happens if you load your all_FA in FSLview and turns on the movie loop? You should be able to spot the images contributing to the reduced mean_FA_mask and either remove them or try to fix what is wrong with them if possible.
Cheers,
Gwenaelle
--- En date de : Jeu 21.5.09, Sushravya Raghunath <[log in to unmask]> a écrit :
> De: Sushravya Raghunath <[log in to unmask]>
> Objet: Re: [FSL] Re : [FSL] tbss_3_postreg mean_FA_mask incorrect
> À: [log in to unmask]
> Date: Jeudi 21 Mai 2009, 17h40
> Hi Gwenaelle,
>
> Sorry about the vague details.
>
> Its human subjects. Control (14) versus MCI (8)
> groups. Similiar is the problem with Control (14) versus
> Remitted(13) groups.
> Yes, the *_to_target.nii.gz images look fine. The
> target was the standard space image image
> (FMRIB58_FA).
>
> Thanks for the quick response,
> Sushravya
>
> p.s : I had run this whole analysis on the previous
> version of fsl and this wasn't an issue then. The mask
> was created right.
>
>
>
>
> On Thu, May 21, 2009 at 11:27 AM,
> Gwenaëlle DOUAUD <[log in to unmask]>
> wrote:
>
> Hi Sushravya,
>
> we would need a bit more context... What species is your
> study on? If human, what kind of population are you looking
> at?
>
> Are your *_to_target.nii.gz images fine and which target
> have you chosen?
>
> Thanks,
> Gwenaelle
>
> --- En date de : Jeu 21.5.09, Sushravya Raghunath <[log in to unmask]> a écrit :
>
>
> > De: Sushravya Raghunath <[log in to unmask]>
> > Objet: [FSL] tbss_3_postreg mean_FA_mask incorrect
>
> > À: [log in to unmask]
> > Date: Jeudi 21 Mai 2009, 16h58
>
>
>
> > Experts,
> >
> > I am using fsl 4.1. tbss_3_postreg -S command creates
> an
> > inappropriate mask
> > with very small area as can be seen in the attachment.
> I
> > checked the results
> > of tbss_2_reg and the images are fine.
>
> >
> > How can I go about debugging the problem? Any help
> would be
> > appreciated.
> >
> > Thanks,
> > Sushravya
> >
>
>
>
>
>
>
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