What is the default mask for SPM2 batch?
Take the example batch script available from, e.g.,
http://en.wikibooks.org/wiki/SPM-Example_batch_script. As far as I can
determine there is no explicit setup of the mask, but a default setup
occures in the spm_fmri_spm_ui function and is applied in the spm_spm.m
function? This default mask includes the voxels above 80% of the estimated
global (gray matter) mean. This mean is computed as "g = mean(V(V >
(mean(V)/8)))" in spm_global. In the code below the THs are approximately
80 and Y, setup from spm_get_data, is normalized so the gray matter global
mean is 100. Is all this correct?
spm_fmri_spm_ui.m:
378 GM = 100;
384 g(i) = spm_global(VY(i));
393 gSF(SPM.Sess(i).row) = GM./mean(g(SPM.Sess(i).row));
412 try
413 TH = g.*gSF*defaults.mask.thresh;
414 catch
415 TH = g.*gSF*0.8;
416 end
417 SPM.xM = struct( 'T', ones(q,1),...
418 'TH', TH,...
spm_spm.m:
613 Y(i,Cm) = spm_get_data(VY(i),xyz(:,Cm));
614
615 Cm(Cm) = Y(i,Cm) > xM.TH(i);
http://www-psych.stanford.edu/~kalina/SPM99/Tools/glm_specmask.html
http://www2.imm.dtu.dk/~fn/ps/Nielsen2005Statistical_slide.pdf
Sincerely
Finn
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Finn Aarup Nielsen, NRU Rigshospitalet & IMM DTU, Denmark
http://www.imm.dtu.dk/~fn/
http://nru.dk/people/fnielsen/
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