If there is a lot of distortion in the phase-encode direction of your images,
then this could be a bit problematic.  These distortions are caused by
changes in the magnetic field that arise because of different magnetic
susceptibilities between tissue and air. This subject seems to have quite
large frontal sinuses, so there may be a bit more spatial distortion than
usual.

Coregistration in SPM only uses a rigid-body transformation, and does not
attempt to correct for these spatial distortions.  This means that it is not
always possible to achieve good alignment between distorted EPI data, and
relatively undistorted T1w.

If you collect field maps when you scan, then it may be possible to correct
the artifact.  If not, then it's a bit tricky as there's nothing yet included
in SPM that could model this distortion. Others have published papers on
correcting it using nonlinear image registration, but I'm not aware of any
freely available software that would do the job.

Best regards,
-John

On Tuesday 24 February 2009 16:49, ramtilak gattu wrote:
> Thanks a lot,
>
>  that clearly works . I just segmented the T1 image and used the WM as the
> target image .
>
> But I have a small minor problem, if you look at the attached image where
> the cross hairs are pinpointed on the sagittal view.
>
> The top end of the genu of the corpus collosum on the FA image is matched
> to the center of the genu of the corpus collosum on T1 image. it literally
> looks like the genu in FA is pulled down. Is there a way to correct it (
> for a better view look at the axial slice).
>
> Thanks again for the valuable suggestion.
>
> Regards
> Tilak
>
> On Tue, Feb 24, 2009 at 5:56 AM, John Ashburner
<[log in to unmask]>wrote:
> > Maybe try coregistering with a skull-stripped version of the T1w.  You
> > can do
> > this by segmenting, and masking the T1w (or a bias corrected version)
> > with the sum of the GM, WM and CSF.  The masking can be done using
> > ImCalc.
> >
> > Best regards,
> > -John
> >
> > On Tuesday 24 February 2009 02:48, ramtilak gattu wrote:
> > > Hello SPM users,
> > >
> > > I apologize if it is a re-posting of my message
> > >
> > > I am trying to co-register Fractional Anisotropy (DTI_FA -
> > > resolution-1.8*1.8*4-33 slices) of a subject to his T1 image (
> > > resolution-0.98*0.98*3-60 slices) using spm 8b. I even tried spm5. Both
> >
> > the
> >
> > > images are in Analyze format
> > >
> > > I played with different objective functions but of no use.
> > >
> > > Please see the attached image before registration (top row) and after
> > > registration (bottom row).
> > >
> > > Could anyone guide me whats going wrong with coregistration .
> > >
> > >
> > >
> > > Thanks for the help in advance
> > >
> > > Regards
> > > Tilak