Dear Doug,
When I run the: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 10000 3 permcsd \ --sim-sign pos \ --cwpvalthresh .05
I am not getting my clusters file permcsd.sig.cluster.mgh with the clusters summary so as you recommended I am running the
mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 norm.mgz --csdpdf Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh
My question is: it is OK if I am not mentioning any registration or what should I input under --reg while I running the mri_volcluster if my for DTI preprocessing I used the dt_recon which computes for each subject an fa.nii and register.dat using the Talairach registration and later I registered all my subjects on the CVS space?
Thank you. AK