I encountered the same problem and I'm wondering whether anyone has come up with an SPM solution.
When I try to normalize the EPI images after injection of the contrast agent (Endorem) to the baseline scans before injection, the result looks completely distorted.
These are the parameters I used, maybe something could be changed here? The contrast agent EPIs are much darker, but not more distorted. Also the brain is almost exactly in the same position anyway, so is there a way to further penalize large stretching/warping?
jobs2{1}.spm.spatial.normalise.estwrite.eoptions.smosrc = 3.75; (corresponds to 1.5x the voxel size)
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];
|