Try changing from: VF.mat = VF.mat * M; To: VF.mat = M * VF.mat; I think that should work. Best regards, -John -----Original Message----- From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Marko Wilke Sent: Tuesday, April 24, 2007 3:27 PM To: [log in to unmask] Subject: [SPM] Apply coregistration parameters to seg_sn.mat, 2nd attempt 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... -- ===================================================================== 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 =====================================================================