The output from running the script would suggest that the imported GM and
GM images are correct relative to each other. Perhaps you could try a
Check Reg between the segmented grey matter and the original image. The
script assessed whether the imported GM and GM are in alignment, but
perhaps the GM and original image are not aligned. When you normalised the
original image, which did you use? The reoriented one, or the
un-reoriented one? Which one matches the GM image? My guess is that this
one would be spatially normalised OK via Dartel.
Best regards,
-John
On 20 May 2015 at 13:57, Bakker Jindra (SP) <
[log in to unmask]> wrote:
> Dear John,
>
> I had another good look at the manual and I think I followed it quite
> correctly. (First I manually reoriented the images.) I segmented and
> imported the images, I created a DARTEL template, and as you say I think it
> looks all right now. After that I used the Normalize to MNI space function
> to put the template into MNI space and warp the anatomical scans. The
> output of this last step is in the bottom right corner of the image I
> attached earlier; it is not aligned with the template, it is moved backward
> and rotated forward. Since I thought it might have something to do with me
> reorienting the images before starting the Dartel procedure, I did the
> following (which you suggested in
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1002&L=spm&D=0&1=spm&9=A&I=-3&J=on&K=3&d=No+Match%3BMatch%3BMatches&z=4&P=434300
> ):
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> % 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')
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> At the last step the images were in aligment with each other, so not sure
> whether this really is the problem…
>
> The other two images (top right and bottom left) are indeed original MRI
> images, top right after manual reorientation, bottom right before manual
> reorientation. To me it seems as if the output of the Normalize function
> did double the manual reorientation (the bottom right picture is moved
> twice as far to the back and oriented twice as far forwards compared to top
> right picture). Do you see what I mean?
>
> I really hope you could help me with this.
>
> Kind regards! Jindra
>
> *PhD student SMARTSCAN project | School for Mental Health and Neuroscience
> | Division II: Psychiatry & Neuropsychology | Maastricht University*
>
>
>
> From: John Ashburner <[log in to unmask]>
> Date: dinsdag 19 mei 2015 20:36
> To: Jindra Bakker <[log in to unmask]>
> Cc: "[log in to unmask]" <[log in to unmask]>
> Subject: Re: [SPM] Dartel normalization problem
>
> I'm not sure what we're looking at here. The average GM in the Dartel
> template seems to be OK. The other images seem to be the original MRI
> images. Try applying the warps estimated by Dartel to these, to see if
> they come out aligned together. Chapter 45 of the SPM manual says more on
> the subject.
>
> Best regards,
> -John
>
>
> On 19 May 2015 at 13:40, Jindra Bakker <
> [log in to unmask]> wrote:
>
>>
>
