Hi,
my bad.
After a little chat with Steve, it seems that B0 might be better to use with flirt (i.e. affine registration) as it has a better brain/non-brain contrast, whereas you should definitely use the FA image if you want to go for non-linear registration.
Cheers,
Gwenaelle
--- En date de : Lun 7.4.08, Steve Smith <[log in to unmask]> a écrit :
> De: Steve Smith <[log in to unmask]>
> Objet: Re: [FSL] T1 and DTI Registration problems
> À: [log in to unmask]
> Date: Lundi 7 Avril 2008, 16h43
> Yeah - sorry, I'm not sure I do agree with Gwen on that
> one - though
> for affine registration either brain-extracted nodif or the
> FA should
> work fine. I think you're right - that in the past
> I've recommended
> using the nodif image, and that's what FDT registration
> uses by default.
>
> Cheers.
>
>
> On 7 Apr 2008, at 15:29, Lindgren, Kristen, Ann wrote:
> > Is that true? I thought one time when I sent an
> e-mail outlining my
> > steps Steve told me not to use the dti_FA but rather
> the nodif_brain
> > within the FDT gui. I'd be curious to hear what
> others think about
> > this since I'm doing something similar to what
> Ravi is doing. Thanks!
> >
> > Kristen
> >
> >
> > -----Original Message-----
> > From: FSL - FMRIB's Software Library on behalf of
> Gwenaëlle DOUAUD
> > Sent: Mon 4/7/2008 8:45 AM
> > To: [log in to unmask]
> > Subject: Re: [FSL] T1 and DTI Registration problems
> >
> > Hi Ravi,
> >
> > here is my take.
> >
> > First, Kristen is not right: you should definitely go
> for the image
> > that shows a better contrast, so the FA rather than
> the B0 (it's all
> > the more true if you use non-linear registration).
> >
> > Second, if I understand you correctly, you want to
> register T1 and
> > FA to possibly draw some ROIs on the T1 and transfer
> them on the DW
> > space...
> >
> > So what you should do is:
> > flirt -in T1 -ref FA -omat T1_to_FA.mat
> >
> > then:
> > flirt -in T1 -ref FA -o T1_to_FA -init T1_to_FA.mat
> -applyxfm (to
> > check first for the flirt registration)
> > then for your ROIs:
> > flirt -in my_ROI_on_T1 -ref FA -o my_ROI_on_FA -init
> T1_to_FA.mat -
> > applyxfm
> >
> > Hope this helps,
> > Gwenaelle
> >
> >
> >
> > --- En date de : Lun 7.4.08, Lindgren, Kristen, Ann
> <[log in to unmask]> a
> > écrit :
> >
> >> De: Lindgren, Kristen, Ann <[log in to unmask]>
> >> Objet: Re: [FSL] T1 and DTI Registration problems
> >> À: [log in to unmask]
> >> Date: Lundi 7 Avril 2008, 14h31
> >> I'm not sure if there's more you should be
> doing,
> >> but you shouldn't be using the dti_FA image in
> FLIRT to
> >> get the str2diff.mat. Instead you should be using
> the
> >> nodif_brain image. Not sure if that will solve
> your
> >> problem but it might help. Good luck!
> >>
> >> Kristen
> >>
> >>
> >> -----Original Message-----
> >> From: FSL - FMRIB's Software Library on behalf
> of Ravi
> >> Shetty
> >> Sent: Mon 4/7/2008 4:40 AM
> >> To: [log in to unmask]
> >> Subject: Re: [FSL] T1 and DTI Registration
> problems
> >>
> >> Sorry I am not sure if I quite follow. I have been
> >> registering my diffusion
> >> data(dti_FA) to the reference image(T1 weighted)
> and I
> >> believe that would
> >> give me the equivalent of the str2diff.mat. From
> there I
> >> use that matrix to
> >> convert the ROI mask I created on my T1 weighted
> image into
> >> diffusion space.
> >> I then overlay that new diffusion space ROI mask
> onto my
> >> original diffusion
> >> image and see if the images are being registered
> correctly.
> >> I use this
> >> method to check because the images outputed after
> >> registration always seem
> >> to line up pretty well but once I run probtrackx
> my results
> >> were very off.
> >> This just seemed a faster way to check the
> registrations
> >> accuracy. Please
> >> let me know if I seem to be missing a step.
> Thanks.
> >>
> >> On Mon, 7 Apr 2008 08:33:21 +0100, Steve Smith
> >> <[log in to unmask]> wrote:
> >>
> >>> Just a quick sanity check - you _are_
> inverting the
> >> DTI->structural
> >>> transform before using it to transform
> structural-space
> >> ROIs back to
> >>> DTI space?
> >>> Cheers.
> >>>
> >>>
> >>> On 7 Apr 2008, at 03:03, Ravi Shetty wrote:
> >>>> Hi I have been using FLIRT to register my
> T1 and
> >> DTI images to each
> >>>> other but keep running into
> >>>> problems. The registered images produced
> are
> >> always very close to
> >>>> what they should be when I
> >>>> overlay them onto the T1 image. The
> problem I have
> >> is the matrixes
> >>>> don't always reflect the
> >>>> registration image. I create a CC ROI mask
> on the
> >> T1 image/
> >>>> registered image and use the matrix I
> >>>> produced to convert it back into difusion
> space.
> >> Now when I do this
> >>>> with some subjects the ROI will
> >>>> be spot on the CC and for others it will
> be off
> >> somewhere in the
> >>>> cortex or even just into the black
> >>>> void. I can't seem to find any rhyme
> or reason
> >> for this and the
> >>>> variation of how off the matrix is does
> >>>> not seem to be consistent, any help
> figuring this
> >> out would be
> >>>> appreciated. Thanks.
> >>>>
> >>>
> >>>
> >>>
> ---------------------------------------------------------------------------
> >>> Stephen M. Smith, Professor of Biomedical
> Engineering
> >>> Associate Director, Oxford University FMRIB
> Centre
> >>>
> >>> FMRIB, JR Hospital, Headington, Oxford OX3
> 9DU, UK
> >>> +44 (0) 1865 222726 (fax 222717)
> >>> [log in to unmask]
> >> http://www.fmrib.ox.ac.uk/~steve
> >>>
> ---------------------------------------------------------------------------
> >>> =
> >>> =
> >>> =
> >>> =
> >>> =
> >>>
> ====================================================================
> >
> >
> >
> >
> _____________________________________________________________________________
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> >
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
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