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
> > > > >
> > > >
> > > >
> > > >
> > > >
> >
>
> > > >
> > > >
> > >
> > >
> > >
> > >
> > >
> > >
> >
> >
> >
> >
> >
> >
>
>
>
>
>
