spm_check_orientation gives me this error when trying to run a GLM on my postprocessed data: "The orientations etc must be identical for this procedure."
It seems they were not reslice, but isn't that what I specified in the batch script (see below) with normalise.estwrite... ?
First the EPI images were realigned and then normalized to a template (using estimate and write). However if I open two arbitrary processed (wr*.img) files from the same scan with spm_get_space, I get slightly different numbers...
please spot the mistake, it must be something here:
jobs{2}.spatial{1}.realign{1}.estwrite.data{1} = f;
jobs{2}.spatial{1}.realign{1}.estwrite.eoptions.quality = 0.9;
jobs{2}.spatial{1}.realign{1}.estwrite.eoptions.sep = 4;
jobs{2}.spatial{1}.realign{1}.estwrite.eoptions.fwhm = 5;
jobs{2}.spatial{1}.realign{1}.estwrite.eoptions.rtm = 0;
jobs{2}.spatial{1}.realign{1}.estwrite.eoptions.interp = 4;
jobs{2}.spatial{1}.realign{1}.estwrite.eoptions.wrap = [0 0 0];
jobs{2}.spatial{1}.realign{1}.estwrite.eoptions.weight = {''};
jobs{2}.spatial{1}.realign{1}.estwrite.roptions.which = [2 0];
jobs{2}.spatial{1}.realign{1}.estwrite.roptions.interp = 4;
jobs{2}.spatial{1}.realign{1}.estwrite.roptions.wrap = [0 0 0];
jobs{2}.spatial{1}.realign{1}.estwrite.roptions.mask = 0;
jobs2{1}.spm.spatial.normalise.estwrite.subj.source{1} =f(1,:);
jobs2{1}.spm.spatial.normalise.estwrite.subj.wtsrc = '';
jobs2{1}.spm.spatial.normalise.estwrite.subj.resample =editfilenames(f,'prefix','r');
jobs2{1}.spm.spatial.normalise.estwrite.eoptions.template{1} = 'D:\TEMPLATE\sm05mA2400.img';
jobs2{1}.spm.spatial.normalise.estwrite.eoptions.weight = '';
jobs2{1}.spm.spatial.normalise.estwrite.eoptions.smosrc = 3.75;
jobs2{1}.spm.spatial.normalise.estwrite.eoptions.smoref = 0;
jobs2{1}.spm.spatial.normalise.estwrite.eoptions.regtype = 'subj';
jobs2{1}.spm.spatial.normalise.estwrite.eoptions.cutoff = 25;
jobs2{1}.spm.spatial.normalise.estwrite.eoptions.nits = 16;
jobs2{1}.spm.spatial.normalise.estwrite.eoptions.reg = 10;
jobs2{1}.spm.spatial.normalise.estwrite.roptions.preserve = 0;
jobs2{1}.spm.spatial.normalise.estwrite.roptions.bb = [NaN NaN NaN;NaN NaN NaN];
jobs2{1}.spm.spatial.normalise.estwrite.roptions.vox = [2.63, 2.33, 5];
jobs2{1}.spm.spatial.normalise.estwrite.roptions.interp = 4;
jobs2{1}.spm.spatial.normalise.estwrite.roptions.wrap = [0, 0, 0];
jobs2{1}.spm.spatial.normalise.estwrite.eoptions.cost_fun = 'mi';
jobs2{1}.spm.spatial.normalise.estwrite.roptions.prefix = 'w';
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