Hi Sushravya,
sorry I was not clear enough: could you please put *all* the files and images corresponding to this "C_20090417_35938" subject (_FA.nii.gz, *_warp.nii.gz etc.) in a tgz file and upload it?
Thanks,
Gwenaelle
--- En date de : Mar 26.5.09, Sushravya Raghunath <[log in to unmask]> a écrit :
> De: Sushravya Raghunath <[log in to unmask]>
> Objet: Re: [FSL] Re : [FSL] registered images distorted - tbss_3_postreg step
> À: [log in to unmask]
> Date: Mardi 26 Mai 2009, 21h24
> Hi Gwenaelle,
>
> The commands used were tbss_2_reg -T and
> tbss_3_postreg -S for tbss steps 2 and 3 respectively.
>
>
> Have uploaded an example. The reference number is
> 129604.
> Thanks for the reply. Awaiting suggestions.
> Thanks,
> Sushravya
>
>
>
>
>
> On Tue, May 26, 2009 at 2:54 PM,
> Gwenaëlle DOUAUD <[log in to unmask]>
> wrote:
>
> Hi Sushravya,
>
> by no mean a flirt (or any affine) registration would be
> enough to match the WM across the subjects, especially if
> you're dealing with healthy elderly and MCI patients!
>
>
> What you might have found in the archives is that flirt is
> working better than areg (present in an old version of TBSS)
> for placing the best target into the MNI space... This is
> obsolete now (we only use flirt and fnirt) and is not valid
> if you have used the tbss2 -T recommended option anyway.
>
>
> What are the commands/option you're run exactly for
> tbss2 and 3? Could you please maybe upload (http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi)
> an example of one FA_to_target that has failed?
>
>
> Cheers,
> Gwenaelle
>
> --- En date de : Mar 26.5.09, Sushravya Raghunath <[log in to unmask]> a écrit :
>
>
> > De: Sushravya Raghunath <[log in to unmask]>
> > Objet: [FSL] registered images distorted -
> tbss_3_postreg step
>
> > À: [log in to unmask]
> > Date: Mardi 26 Mai 2009, 19h34
>
>
>
> > Experts,
> >
> > I am running TBSS Analysis of Control versus MCI
> human
> > subjects.
> >
> > The _FA_to_target.nii.gz images (resulting after
> > tbss_3_postreg step) are
>
> > distorted. In some cases the regsitered images have
> > truncated edges whereas
> > FA image is complete.
> >
> > I read in older posts that FLIRT registration might
> be
> > better and registered the
>
> > FA image to MNI152_T1_1mm_brain usifn FLIRT. The
> FLIRT
> > registered images
> > look better. The truncated edges are still seen with
> FLIRT
> > registration but they
> > are better than tbss registered images.
>
> >
> > Is this the right way of going about in such
> situation?
> >
> > If yes, how can I have FLIRT registration done in
> > tbss_3_postreg step?
> >
> > Any suggestion would be helpful.
> >
>
> > Thanks,
> > Sushravya
> >
>
>
>
>
>
>
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