>If you use
>avwstats thresh_zstat -l 0.001 -R
>you'll get the correct 'positive' image range. Similarly,
>avwstats thresh_zstat -u -0.001 -R
>gives you the right 'negative' intensity range. Use these for the
>overlay call and things should work fine

wonderful, thanks.  i did this and it works:

% avwstats ica/stats/thresh_zstat20 -l 0.001 -R
2.760078 12.001950
% avwstats ica/stats/thresh_zstat20 -u 0.001 -R
-9.468304 0.000000
% overlay 1 0 ffd_49 -a \
 ica/stats/thresh_zstat20   2.760078 12.001950   \
 ica/stats/thresh_zstat20  -0.01        -9.468304               over20e
% slicer  over20e  -s 0.6  -A 500  oversli20e_060_500.png

(nb: i needed to change <s2min> from 0.00 to something smaller in
order to get out of the greyscale range.  i saw this logic in

>Alternatively, you can directly change the code in and

i considered this but since most programs in FSL are called with an
absolute pathname, ie, $FSLDIR/melodic, i would have to redefine
$FSLDIR to point to my test directory which snowballs into lots of
extra work.  if calls to programs were not prefaced with an absolute
path, i could define my own $PATH environment variable such that
the directory containing my test binaries were defined in $PATH
prior to the inclusion of $FSLDIR in $PATH.

also, i want to crop the overlaid volume to remove "gutter" space
within each slice.  my final goal is to have the .png images contain
as much image information in as small an area as possible.  this cuts
down on scrolling and allows the us to get a quick "overview" of the
spatial map.

another question that i cannot resolve:  how do i include the
colorbar in the .png?

when i run avwstat -w on the overlaid image, i get coordinates that
indicate no cropping can be done.  do you put some artificial pixel
in the corner of the volume in order to do this overlay?

thank you for all your help.  greatly appreciated,
- bettyann
BettyAnn Chodkowski                       F.M. Kirby Center
e: [log in to unmask]          Kennedy Krieger Institute
v: 443.923.9524                           707 N. Broadway
f: 443.923.9279                           Baltimore, MD, USA  21205