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