Hello I am just doing a simple functional connectivity analysis using an atlas ROI as a seed (middle frontal gyrus). My output looks a little strange; for some subjects I have a significant ring effect around the head but I removed motion from my ROI time series and included motion as regressors of no interest in the final 3dDeconvolve. Also when I do the group analysis and look at the grps vs 0, I have to turn the threshold so far up to get legible results and again there are rings around the head although the 2 sample ttests look reasonable. I am pasting my process below. Did I do something wrong? Thanks!
Creating ROI seed
3dSynthesize -cbucket ${subj}${day}_${run}_cbucket+tlrc -matrix ${subj}${day}_${run}_buc.xmat.1D -select baseline -prefix ${subj}${day}_${run}_EofNI
3dcalc -a ${subj}${day}_${run}_scale+tlrc -b ${subj}${day}_${run}_EofNI+tlrc -expr 'a-b' -prefix ${subj}${day}_${run}_clean
3dmaskave -quiet -mask R_PFC_atlasmask_masked_resampled+tlrc ${subj}${day}_${run}_clean+tlrc > ${subj}${day}_${run}_rPFCseed.1D
Connectivity analysis
3dDeconvolve -input ${subj}${day}_${run}_scale+tlrc.HEAD \
-polort 3 \
-num_stimts 4 \
-stim_file 1 ${subj}${day}_${run}_rPFCseed.1D -stim_label 1 Seed_corr\
-stim_file 2 ${subj}${day}_motion_demean_${run}.1D'[3]' -stim_base 2 -stim_label 2 Roll \
-stim_file 3 ${subj}${day}_motion_demean_${run}.1D'[4]' -stim_base 3 -stim_label 3 Pitch \
-stim_file 4 ${subj}${day}_motion_demean_${run}.1D'[5]' -stim_base 4 -stim_label 4 Yaw \
-xjpeg ${subj}${day}_${run}_buc_conn \
-x1D ${subj}${day}_${run}_buc_con \
-fitts fit_bl4 -errts ${subj}${day}_${run}_resid_file_con\
-fout -rout -tout \
-bout -nofull_first \
-cbucket ${subj}${day}_${run}_cbucket_con \
-bucket ${subj}${day}_${run}_buc_con \
Converting results to Correlation then to Z
3dcalc -a ${subj}${day}_${run}_buc_con+tlrc'[10]' -b ${subj}${day}_${run}_buc_con+tlrc'[8]' -expr 'ispositive(b)*sqrt(a)-isnegative(b)*sqrt(a)' -prefix ${subj}${day}_${run}_CorrR
3dcalc -a ${subj}${day}_${run}_CorrR+tlrc -expr 'log((1+a)/(1-a))/2' -prefix ${subj}${day}_${run}_CorrR_Z
