Hi Jim,

I do not believe there is an command-line version of the reorder
plugin. Therefore you might have to do some scripting to reorder
and average the sub-bricks, based on the contents of the map file.

So I was picturing something like this:

set trs_per_cond = 12
foreach cond ( A B C ... )
foreach index ( `count -digits 1 1 $trs_per_cond` )
set pattern = $cond$index
3dMean -prefix mean.$cond.$index EPI_dset+orig\[`awk ... SEE OTHER DISCUSSION
end
3dTcat -prefix ave_$cond mean.$cond.*+orig.HEAD
end

That's a little more work than the plugin, but it could be made
generic for a subject list very easily. The 'SEE OTHER DISCUSSION'
section would be just extracting the sub-bricks matching your
$pattern (the condition and index).

Note that if $trs_per_cond is more than 9, the 3dMean output
might have to be changed because the datasets will no longer
be alphabetical (according to the index, since mean.A.10+orig
comes before mean.A.2+orig, for example).

Anyway, it's just an option that you can ponder.

- rick