There is a second matrix hidden in the headers of the imported images.
If you do the following in MATLAB, it should show the native and
imported images in alignment with each other:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Select images (native first, imported second)
P = spm_select(2,'.*c1.*\.nii','Select native, then imported');
% Show the two images together
spm_check_registration(P)
% Get the secret information used by spm_check_registration
global st
% Make the hidden matrix the one that spm_check_registration uses.
st.vols{2}.mat = st.vols{2}.private.mat0;
% Something to update the view
spm_orthviews('maxbb')
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
If it does not, then it would suggest that one of the images has had its
header changed.
Best regards,
-John
On Thu, 2010-02-11 at 07:12 -0800, Alireza Salamy wrote:
>
> Thank you John for the reply!
>
> But neither of those cases are hold here. I used new Seg algorithm
> which writes both native and imported c1 images at the same time.
> Looking at c1 and rc1, reflects that they are a bit rotated (see
> attach c1 and rc1). In the first figure, the top row reflect c1t1
> while the lower row reflects imported image(rc1t1). There is about 20
> mm differences (in the transformation matrix) between two image.
> In the second figure, the top row reflects applied normalization and
> warp to the native images while the bottom row reflects applied the
> same normalization and warp to imported images.You can obviously see
> that they are not align properely. Further more the one the one in the
> bottom (swrt1) is perfectly align with MNI.
> Is it wrong to apply the warp to imported data(rc1) not to?
> Any suggestion would be highly appreciated!
>
> Alireza
>
> --- On Thu, 2/11/10, John Ashburner <[log in to unmask]> wrote:
>
>
> From: John Ashburner <[log in to unmask]>
> Subject: Re: [SPM] Dartel Normalization
> To: "Alireza Salamy" <[log in to unmask]>
> Cc: [log in to unmask]
> Date: Thursday, February 11, 2010, 6:06 PM
>
> The manual is correct in stating that the original images can
> be aligned
> using deformations estimated from the imported scans. There
> are however
> some exceptions. In particular, if the original scans are
> repositioned
> after their segmentation. For example, if their origin is
> changed then
> they would no longer align with the imported scans. Another
> cause may
> be if the scans are coregistered so that they match some other
> data. If
> coregistering after segmenting, then the other images should
> be moved
> into alignment with the anatomicals - rather than move the
> anatomicals.
>
> Best regards,
> -John
>
> On Thu, 2010-02-11 at 06:14 -0800, Alireza Salamy wrote:
> > Dear John and others,
> >
> > I read in the mailing list that John has suggested to apply
> warping to
> > the native space of c1 images (using SPM8 Normalize to MNI
> button)
> > rather than imported rc1 images, but he said that he didn't
> know how
> > much differnce it makes in practice:
> >
> (https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0904&L=SPM&P=R7426)
> >
> > In my exprience, when I used normalize to MNI using dartel
> in SPM8 and
> > apply the warps to native c1 images, the result is biased
> from tpm
> > gray matter (MNI template) but when I apply the warps(using
> normalize
> > to MNI in SPM8) to imported rc1, it is nicely inline with
> MNI (see
> > attach).I have even checked c1 before applying warp and it
> seems not
> > to be far from MNI and even if I normalize it using new seg,
> normalize
> > Gray matter option, it will be nicely inline with MNI.
> >
> > Could it be something that needs to be further investigated
> or the
> > manual is mistakenly written?
> > If this is true than I guess the con* images need to be
> imported to
> > Dartel and then one can use normalize to MNI option using
> dartel in
> > SPM8 for warping and normalization?
> >
> > Thanks
> > /Alireza
> >
>
>
> --
> John Ashburner <[log in to unmask]>
>
>
>
--
John Ashburner <[log in to unmask]>
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