Is there any possibility that the image you segmented in order to
obtain the spatial normalisation parameters was moved in some way
after running the segmentation? For example, was it coregistered so
that it matches some other image? As an analogy, if you put a coin A
on top of a coin B, then coin A should match coin B (ie they are
aligned). If you then put coin A on top of coin C, then coin A is no
longer aligned with coin B. However, if you had instead put C on top
of B, then all three would have been aligned. In other words, if a
structural image (A) is segmented in order to align to match it to MNI
space (B), it would not be a good idea to then move the structural
image (A) to match the functional data (C) as the spatial
normalisation parameters will no longer work.
Another possibility is that the spatial normalisation of that subject
didn't actually work well. Maybe check the spatially normalised
images.
I've run out of other possible causes. Maybe someone else has an idea.
Bye for now,
-John
On 18 September 2012 19:59, Firstname Lastname
<[log in to unmask]> wrote:
> Hi John,
>
> Thanks for your answer!
>
> I used "check Reg" to examine the alignment between warped L_precentral.img and raw image. It is similar to that displayed in MRIcron. The warped L_precentral is still in the skull of the raw image.
>
>
> I also tried "Coreg: reslice" and got the resliced "rL_precentral.img". I checked this rL_precentral.ing with raw image. It is also in the skull of the raw image.
>
> It looks like deformations Utility, spm_write_sn and Coreg_slice, all of them can apply "subject_seg_inv_sn.mat" to L_precentral.img and make similar changes. However, none of them exactly transform L_precentral.img from MNI space to native space.
>
> Are there any problems with my steps???
>
> (P.S. in my first mail, I made a mistake. I wrote using "spm_write_sn ('subject.img', 'subject_seg_inv_sn.mat')", in fact, I used right command "spm_write_sn ('L_precentral.img', 'subject_seg_inv_sn.mat')")
>
> Anyone has already tested transforming smpT.img from MNI space to native space??
>
> Any idea will be appreciated!
>
> Li
>
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