Dear All,
I sent an email last week regarding the application of updated
positional information to the sn_seg-file (see
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0704&L=SPM&P=R21714&I=-3
I mentioned that my problem was that if I segment an image, then move it
by coregistering it to another image, I may not be able to still use the
information gathered during the initial segmentation (as I have moved
the image in the meantime).
I had asked for help in applying the coreg parameters to the sn_seg.mat
file. I thought that I solved this with
epi = spm_select;
ana = spm_select;
[p nm e v] = fileparts(ana);
g = fullfile(p,['c1' nm '.img']);
w = fullfile(p,['c2' nm '.img']);
% coregister gm to EPI
x = spm_coreg(epi,g);
% apply parameters; take along T1, wm and
M = inv(spm_matrix(x));
all_images = char(ana, g, w);
MM = zeros(4,4,size(all_images,1));
for iii = 1:size(all_images,1)
MM(:,:,iii) = spm_get_space(deblank(all_images(iii,:)));
spm_get_space(deblank(all_images(iii,:)), M*MM(:,:,iii));
end;
% update positional information of original image, coded
% as VF.mat in seg_sn-file
[p nm e v] = fileparts(ana);
sn_file = fullfile(p, [nm '_seg_sn.mat']);
load(sn_file);
VF.mat = VF.mat * M;
% store updated position
if spm_matlab_version_chk('7') >= 0,
save(sn_file,'-V6','VG','VF','Tr','Affine','flags');
else
save(sn_file,'VG','VF','Tr','Affine','flags');
end;
This changes the positional information in the original files and the
seg_sn-file as requested.
However, when I then write out the segmentations again (using Christian
Gaser's toolbox) the segmented images are similar but, using i1-i2, not
exactly identical: for testing purposes, I tilted the image a little and
now get a rim of negative values on one side and a rim of positive
values on the opposite side. This hints towards there being more to it
then adjusting the positional information as contained in VF.mat when
wanting to apply the parameters again. I also fiddled with combining M
and Affine but to no avail (it either over- or undercorrects the problem).
So bottomline, I am somewhat further but not quite there yet, so if
anyone has an idea on how to modify the seg_sn.mat using the
coregistration parameters, I would be truly grateful :)
Any hints will be appreciated. Thanks in advance,
Marko
PS: I know, the obvious solution is to not move the GM but the EPI, but
for the heck of it...
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Marko Wilke (Dr.med./M.D.)
[log in to unmask]
Universitäts-Kinderklinik University Children's Hospital
Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology)
Hoppe-Seyler-Str. 1, D - 72076 Tübingen
Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473
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