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Dear Guillaume

Thanks a lot. This is really an effecient way to generate masks compared to generating masks in either FSL and SPM Anatomy toolbox.  I did your approach in extracting mask-related RAW data from residual volumes and SPM.mat, but I've few more questions. Here is what I did:

          xA = spm_atlas('load','Neuromorphometrics');

for residual volumes I did:
          V = cellstr(spm_select('FPList',glmDir,'^Res\_[0-9]+\.nii$'));

for SPM.mat I did - but I'm not sure if V here is correct????

            V = spm_vol(SPM.xY.P); ???
            V = SPM.xY.VY; ????
then:            
            roiMat = zeros(numel(V),numel(xA.labels));
            for m = 1:length(xA.labels)
                roiName = xA.labels(m).name;                
                for i=1:numel(xA.labels)
                  mask = spm_atlas('mask',xA,xA.labels(m).name);
                  roiMat(:,m) = spm_summarise(V,struct('def','mask','spec',mask),@mean);
                end                
            end 

I'm just wondering if there is a way to use spm_atlas masks in VOI batch (given that its Y is already adjusted for confounds)
    
    matlabbatch{1}.spm.util.voi.roi{2}.mask.image =????????? -> how can I use "mask = spm_atlas('mask',xA,xA.labels(m).name)" here
    matlabbatch{1}.spm.util.voi.roi{2}.mask.threshold = 0.5;
   
Also, is there a way to generate max probability masks???. I checked V = spm_atlas('maxprob',xA,thresh), but I'm not sure how to integrate it within the above script.

Many Thanks,

Maaly