Dear Cherif,
the FA is indeed giving much better results to
register the images. That's why we're using an FA
template in TBSS for instance. Most of the time, using
Bo images does not give satisfactory results...
The difference between the two is that there is much
more "information" in the FA scans as they are showing
a very good contrast between WM and GM or WM and CSF,
on the contrary to Bo images.
Hope this helps,
Gwenaelle
--- Cherif Sahyoun <[log in to unmask]> a écrit :
> Hi All,
>
> Matt, that is actually very interesting about the FA
> giving better
> registration! Would you recommend doing that by
> default? Anyone else has
> thoughts on this?
> Actually, since the FA is calculated after all
> volumes have been registered
> to the b0 in preprocessing, shouldn't the difference
> be minimal?
>
> thanks,
> Cherif
>
> On 10/1/07, Yoshiko Yamada <[log in to unmask]>
> wrote:
> >
> > Great! Thank you very much for your info, Tim and
> Matt!
> >
> > -Yoshiko
> >
> >
> >
> > On Mon, 1 Oct 2007 13:12:48 -0400, Matt Glasser
> <[log in to unmask]> wrote:
> > > Yes that would also work. We have actually
> found that the FA often
> > gives a
> > > better registration than the b0 to T1 images,
> but that would require
> > running
> > > DTIFIT.
> > >
> > > Peace,
> > >
> > > Matt.
> > >
> > > -----Original Message-----
> > > From: FSL - FMRIB's Software Library
> [mailto:[log in to unmask]] On
> > Behalf
> > > Of Yoshiko Yamada
> > > Sent: Monday, October 01, 2007 12:39 PM
> > > To: [log in to unmask]
> > > Subject: Re: [FSL] overlaying DTI b0 images onto
> structural images
> > >
> > > Thank you for your information, Steve.
> > >
> > > My understanding is that the registration option
> in FDT requires BEDPOST
> > > directory, so this means that we need to run
> BEDPOST to run the
> > > registration option. Am I right?
> > >
> > > I'm wondering if, in FLIRT GUI, we could choose
> the "Low res image -->
> > High
> > > res image --> Reference image" opetion, enter a
> b0 image as the Low res
> > > image and structural as the High res image, and
> have the b0 and
> > structural
> > > registered (without running BEDPOST, which
> requires a long processing
> > time).
> > >
> > > Thank you again for your advice!
> > >
> > > -Yoshiko
> > >
> > >
> > >
> > >
> > > On Sat, 29 Sep 2007 08:03:06 +0100, Steve Smith
> <[log in to unmask]>
> > > wrote:
> > > > Hi - if you use the registration option in the
> FDT GUI, you will end
> > > > up with transformations between diffusion
> space and structural space
> > > > (and standard space).
> > > > You can use ApplyXFM GUI to apply the relevant
> transform to get the
> > > > B0 image into the right space for overlaying
> on top of the structural
> > > > for validation.
> > > > Cheers.
> > > >
> > > >
> > > > On 28 Sep 2007, at 20:50, Yoshiko Yamada
> wrote:
> > > >
> > > > > Dear List,
> > > > >
> > > > > I'm wondering if there is a way to overlay
> DTI b0images onto the
> > > > > structural image of the same
> > > > > subject. I'd like to check data quality
> (especially subtle EPI
> > > > > distortion) before starting full analysis. I
> > > > > understand that, in FSL View, b0 images have
> to have the same
> > > > > resolution and FOV as the
> > > > > structural image to be overlaid. Is there
> any other way we can
> > > > > overlay these two types of images?
> > > > >
> > > > > Thank you for your input!
> > > > >
> > > > > -Yoshiko
> > > > >
> > > > >
> > > > > --
> > > > > Yoshiko Yamada, Ph. D
> > > > > Research Associate
> > > > > Brain Development Lab
> > > > > Psychology Department
> > > > > 1227 University of Oregon
> > > > > Eugene, OR 97403-1227
> > > > > Phone: 541-346-4841
> > > > > Fax: 541-346-4271
> > > >
> > > >
> > > >
> >
>
------------------------------------------------------------------------
> > > > ---
> > > > 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
> > > >
> >
>
------------------------------------------------------------------------
> > > > ---
> > > >
> > >
> >
>
>
>
> --
>
------------------------------------------------------------------------------------------
> Cherif P. Sahyoun
> HST-MEMP
>
> Developmental Neuroimaging of Cognitive Functions
>
> C: 617 688 8048
> H: 617 424 6956
> [log in to unmask]
>
> "Live as if this were your last day. Learn as if
> you'll live forever"
> Ghandi
>
-------------------------------------------------------------------------------------------
>
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