Hi list,I'd like to perform functional connectivity analysis between thalamus and whole cortex. I have two groups (control and disease) and I' d like also to assess between groups differences.I'm performing these steps. Please, could you check if these are corrected and could you respond to some questions? Thanks, Stefano 1. Analyze anatomicals in FreeSurfer (recon-all)2. Create subjectname file.3. Preprocessingpreproc-sess -s sessionid -fwhm 5 -surface fsaverage lhrh -mni305-2mm 4. Parameters configuration to creates a text file describing the FC seed for an individual. fcseed-config -segid 1010 -fcname L_Thalamus.dat -fsd bold -mean -cfg mean.L_Thalamus.config Create nuisance variables:fcseed-config -wm -fcname wm.dat -fsd bold -pca -cfg wm.configfcseed-sess -s sessionid -cfg wm.configfcseed-config -vcsf -fcname vcsf.dat -fsd bold -pca -cfg vcsf.configfcseed-sess -s sessionid -cfg vcsf.config 5. Configure analysesmkanalysis-sess -analysis fc.lthalseed.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg L_Thalamus.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -fsd bold -TR 1.1 -mcreg was not found! Why? 6. First Level Analysisselxavg3-sess -s sessionid -a fc.lpccseed.surf.lh ces.mgz - contrast effect size (contrast matrix * regression coef)cesvar.mgz - variance of contrast effect sizesig.mgz - significance map (-log10(p))pcc.mgz - partial correlation coefficient map 7. Group-level analysiss - Higher Level Analysis (isxconcat-sess, mri_glmfit)isxconcat-sess -sf sessidlist -analysis workmem.sm05.lh -contrast encode-v-base -o my-group 8. Correction for Multiple Comparisons (mri_glmfit-sim)mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage lh --glmdir my-glm.wls --nii.gz --fsgd group1.fsgd --C group.diff.mtx --C group1.mtx --C g1g2.intercept.mtx Is it corrected? 9. Multiple correction
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