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Hi. I have created an atlas-based mask on my group-level contrast image in standard space (rendered_thresh_zstat1.nii.gz). I would like to apply this mask to each of my subjects to query average activation over the timecourse in this mask for the purpose of doing a PPI. Below are the steps I have pieced together from the FAQs, support forum, etc., using more of my own guessing/inference than makes me comfortable. Please let me know if this will work, or how I've gone wrong and what I should do instead(explicit examples appreciated). Thanks very much for your help. -Terry To get the transformation matrix: flirt -in individual_subject_mean_func -ref group_bg_image -omat func2standard.mat To invert the transformation matrix: convert_xfm -omat func2standard.mat -inverse standard2func.mat To apply the transformation matrix to the standard space mask: flirt -in standard_space_mask -ref individual_subject_mean_func -applyxfm -init func2standard.mat -datatype float -out functional_space_mask To threshold and binarize the mask: fslmaths functional_space_mask -thr 0.5 -bin individual_subject_functional_space_mask To query average activation in the mask for a single subject: fslmeants -i filtered_func –m functional_space_mask –o Subject#_timecourse_in_mask.txt