Thank you Rick for your response!

1. Of course after one asks their question they find their answer (http://afni.nimh.nih.gov/afni/community/board/read.php?f=1&i=22175&t=22174&v=t). I have altered my 3dcalc program to reflect your previous post. I appologize for making you address the same issue twice.

I wanted to make sure I was in using 3dcalc correctly. I was thinking that voxels that were present in half or more of the subjects should also be included in the mask, thus here was my process: Each individual mask has a value=1 so when averaged the resulting file would have values from 0.00.. to 1.0. These values may also represent percent prevelant, such that a voxel value of .5 would indicate a voxel in 50% of the subjects. In using using astep, I was telling 3dcalc to write a value of 1 to each voxel that had an abs(value) > 0.5. Was this correct usage of 3dcalc?

2. I went back to look at our afni_proc scripts, and we did use -regress_est_blur_errts. The in the proc script it looked as such:
foreach run ($runs)
3dFWHMx -detrend -mask full_mask.$subj+orig errts.$subj+orig"[$b0..$b1]" >> blur.errts.1D
@ b0 += 105
@ b1 += 105
end
Now in the Instructions/tutorial I got the impression to only use 3dFWHMx once while in the proc script processes per run. I going to make this assumption, when I ran it independently and with no sub-brick selector, it calculated the entire errts file. When the above runs the process, it processes the errts file in entirety but breaks it up into "per run" chucks. The alternative, it processes the complete errts 4x's over. I am unfamiliar with the use of "@ bo += 105." Is my assumption correct (only need to run it once with no subbrick selectors), or if running 3dFWHMx independently does it need to be reprocessed and added to a subject file the same # of time as # of runs? This may be for future knowledge.

Since, I did run this step with afni_proc, I can collect all the 1D files. Now I am unsure what my intended outcome should be (i.e. the format AlphaSim takes this information). Do I simplely want 3 numbers so I can manually fill in -fwhmx .. -fwhmy .. -fwhmz ..? or Do I want a time series 1D file with the Average Blur across Subjects for each TR? I assume the former is what you, meant by 3dTstat each subject, then 3dMean the resulting files.

Again, thank you so much for your help. Your knowledge indubitably valuable!