Hi Sushravya,

fnirt is the non-linear registration that is (already) used in TBSS. 
You can always include the problematic subject and disregard any result that you would get around the subcortical grey matter, but you might miss something interesting in these regions (unless you're sure there should not be) and you also need to be sure *all* your problematic subjects have exactly the same misregistration problem...

If your sample size can be increased, I suggest leaving out the problematic subjects and trying to focus on the "good" ones.

Cheers,
Gwenaelle

--- En date de : Ven 29.5.09, 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: Vendredi 29 Mai 2009, 18h06
> Hi Gwenaelle,
>  
> Thanks for all the suggestions.
>  
> I did run the analysis for the good ones and it shows
> promising results. Since we are not looking at
> putamen/insula region we thought we could try fNirt first as
> you suggested earlier. How can I include fNirt along the
> tbss steps?
> 
>  
> Thanks again,
> Sushravya
> 
> 
>  
> On Thu, May 28, 2009 at 11:45 AM,
> Gwenaëlle DOUAUD <[log in to unmask]>
> wrote:
> 
> Hi again,
> 
> it might be worth checking first whether you have
> significant results with this 7/6/7 groups.
> 
> The alternative is quite labour-intensive and
> time-consuming and we're not sure it would work
> properly... so it has to be seen as a last resort.
> 
> Cheers,
> Gwenaelle
> 
> --- En date de : Jeu 28.5.09, 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: Jeudi 28 Mai 2009, 15h53
> 
> > Hi Gwenaelle,
> >
> > Thanks a lot for the help that you offered.
> >
> > We, infact, do have a lot of FA images like that!
> > About 6/14 Controls, 2/8 MCIs and about 6/13 Remitted
> group.
> 
> > How do you suggest for us to do?
> >
> > Thanks,
> > Sushravya
> >
> >
> >
> >
> > On Thu, May 28, 2009 at 7:06 AM,
> 
> 
> 
> > Gwenaëlle DOUAUD <[log in to unmask]>
> > wrote:
> >
> > Hi Sushravya,
> >
> > I've looked at your example. First, there is no
> such
> 
> > "truncation", at least on this image.
> It's
> > true that the original FA was not betted properly (in
> the
> > dtifit process), so there is quite a thick
> "rind"
> > around it that the erosion introduced in tbss 1st step
> only
> 
> > partly removes. This is enhanced after the NL
> registration.
> >
> >
> > The problem here is that, quite possibly because of
> PVE
> > together with the quality of the data, the
> external/extreme
> > capsules don't appear clearly on the FA image.
> FNirt (NL
> 
> > algorithm) then struggles to match the
> external/extreme
> > capsules of the FMRIB58 template with something that
> is
> > absent from your image. If you look  at the alignment
> of
> > the white matter except in the putamen/insula region,
> fNirt
> 
> > is actually doing a good job (cf snapshot attached).
> >
> >
> > I'm afraid there is no simple way to solve this
> problem
> > (if any). Using fLirt is certainly not an option.
> Hopefully
> > this does not happen in too many subjects and you
> simply
> 
> > (though painfully) have to reject those subjects from
> the
> > TBSS analysis.
> >
> >
> > If it does occur in too many FA images though, then
> get
> > back to me and we (with Jesper) will try to come up
> with
> 
> > something to try to help the registration.
> >
> > Cheers,
> > Gwenaelle
> >
> >
> > --- En date de : Mer 27.5.09, 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: Mercredi 27 Mai 2009, 17h31
> >
> >
> >
> > > Hi Gwenaelle,
> > >
> 
> > > Sorry about that. Please find all the files at
> > > 466544.
> > >
> > > Thanks,
> > > Sushravya
> > >
> > >
> > >
> > > On Wed, May 27, 2009 at 10:28 AM,
> 
> >
> > > Gwenaëlle DOUAUD <[log in to unmask]>
> > > wrote:
> > >
> > > Hi Sushravya,
> > >
> > > I would actually need **all** the files
> concerning
> 
> > this
> >
> > > subject (to be sure that you put all of them, do
> an
> > ls
> > > *C_20090417_35938* in your FA/ directory).
> > >
> > >
> > > Thanks,
> > > Gwenaelle
> 
> > >
> > > --- En date de : Mer 27.5.09, 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: Mercredi 27 Mai 2009, 15h36
> > >
> > >
> 
> > >
> > > > Hi Gwenaelle,
> >
> > > >
> > > > I have uploaded files as you had asked.
> Please
> > find
> > > it
> > > > at 986721.
> > > >
> > > > Thanks,
> 
> > > > Sushravya
> > > >
> > > >
> > > >
> > > > On Wed, May 27, 2009 at 5:41 AM,
> >
> > >
> > > > Gwenaëlle DOUAUD <[log in to unmask]>
> 
> > > > wrote:
> > > >
> > > > 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
> > > > > >
> > > > >
> > > > >
> > > > >
> 
> > > > >
> > >
> >
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> 
> > >
> > >
> > >
> > >
> >
> >
> >
> >
> >
> 
> 
> 
> 
> 
>