Hello,

I am doing a seed based analysis on resting state data and instead or looking at correlations within the entire brain, we wanted to restrict the analysis to neocortex. I figured I would adjust my mask in 3dDeconvolve to analyze just neocortex (as indicated below ***) but in order to create that mask, I would have to add 100 or so ROIs. Is there a way that I could say, rather, (this atlas - regions (x+y+z)) rather than regions 1+2+3...100. Or even an easier way with 3dautomask or something?

this is the way I normally generate ROIs
3dcalc -a $atlas -expr "equals(a,34)+equals(a,33)" -prefix ${ROI}.nii

3dDeconvolve -input $dset \
-mask anat_mask_rs+tlrc'[0]'\ ***** Change anat_mask to neoctx_mask*******
-polort -1 \
-jobs 8 -float \
-num_stimts 1 \
-stim_file 1 ${s}_${ROI}.1D \
-stim_label 1 ${ROI} \
-tout -rout -bucket ${s}_buc_${ROI} -overwrite


Thanks as always!!