Good afternoon,

I am pretty new to AFNI, and I am working with an unusual data type in which I only have anatomical data sets (no time component). Using my images, I get overall signal drop-off as I go from the top to the bottom slice, but the % signal change by region relative to the overall slice intensity appears to remain constant. So, I hope to correct for this problem before brain registration so that I can later run statistics. I think I can do this by normalizing signal intensity voxel-by-voxel per slice.

Here is the general plan of what I wanted to do: 1) mask the brain, 2) take an average intensity for a given slice within the masked brain, 3) divide the signal intensity for a given voxel by the brain slice average intensity and multiply by 100 to get a signal intesity change, 4) output the final, normalized data set.

The largest problem I am having is that I cannot find a way to get an average value of either the entire 3D space or of a single slice. I think I have the rest worked out. Can anyone help me?

Thanks very much.
Matt