Could there have been a mis-match between the order in which the flow
field file names were selected, and the order that the c1 images were
selected? If you are using the latest version of SPM8, then the
normalise to MNI space option should be working properly (as described
in the manual).
Best regards,
-John
On Thu, 2010-02-11 at 09:21 -0800, Alireza Salamy wrote:
> Thanks a lot John!
>
> It seems that they are perfectly align. My last question which is
> still unknown is why then the results is different when we apply
> wrapping to rc1 compare to c1. The results when I applied warping to
> rc1 (imported ) is perfectly align with MNI while the results is a bit
> biased (from MNI) when I applied wrapping to c1?
> In the attach figure,the top left figure is the result of wrapping and
> normalizing to MNI (using Dartel in SPM8) applied to c1 while the top
> right figure is the results of wrapping and normalizing to MNI applied
> to rc1. As you can clearly see, the result of the top right is
> perfectly align with MNI (the bottom) but not the top left? This is
> the main confusion that I got from the beginning!
> Many thanks
> /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: [log in to unmask]
> Date: Thursday, February 11, 2010, 7:57 PM
>
> 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]>
>
>
--
John Ashburner <[log in to unmask]>
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