Dear FS experts I do GRF correction using mri_glmfit-sim --grf in volume. I find --grf pos and --grf neg, but not --grf abs. My first question is, is the --grf just used for ONE-side correction? For instance, we can test, are the FCs of patients larger than that of healthy controls or smaller than the healthy controls? If I want to test the difference of FCs between patients and healthy controls, how do i do that? Please help me to check the following commands i used to do the TWO-sides correction (for example. voxel-wise p: 0.05, cluster-wise p: 0.05): mri_glmfit-sim --glmdir g2v0 --grf 1.3 pos --cwp .05 mri_glmfit-sim --glmdir g2v0 --grf 1.3 neg --cwp .05 Then i use the following commands to combine the 'pos' and 'neg' results together mri_convert grf.th1.3.neg.sig.cluster.mgh grf.th1.3.neg.sig.cluster.nii.gz mri_convert grf.th1.3.pos.sig.cluster.mgh grf.th1.3.pos.sig.cluster.nii.gz fslmaths grf.th1.3.pos.sig.cluster.nii.gz -add grf.th1.3.neg.sig.cluster.nii.gz grf.th1.3.sig.cluster.nii.gz Finally, i think the result grf.th1.3.sig.cluster.nii.gz is what i want, which is the difference between patients and healthy controls with GRF corrected, with vertex-wise p< 0.05 and cluster-wise p<0.05. Is it right?
2. The other question is, If i do the two-sides GRF correction(vertex-wise p<0.05 and cluster-wise p<0.05) with 'pos' or 'neg', should the vertex-wise or cluster-wise be 0.05/2 and 0.05/2? or 0.05 and 0.05? for example, we should write like this mri_glmfit-sim --glmdir g2v0 --grf -log10(0.05/2) pos --cwp 0.05/2 mri_glmfit-sim --glmdir g2v0 --grf -log10(0.05/2) neg --cwp 0.05/2 3. If i want to do cluster-based FDR correction, is there any FS command to do it? is it right if i load the statistic p map into MATLAB and do the FDR correction, then i use 'mri_volcluster --minsizevox' to threshold it to remove voxels smaller than the cluster size i set. Thank you very much for any help! All the best, Meiling
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