Hi Emily,

It isn't clear to me how to put the 3 cardinal images together,
unless you do something like a screen capture. But collecting
them is easy because it's scriptable.

For example, if you have a list of many coordinates and thresholds,
you could do something like the following.

- rick

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#!/bin/tcsh

set coord_list = ( "-42.6 32 5.9" "21 -3 17.4" ) # FIX
set thresh_list = ( 3.5 5.5 7.5 9.5 11.5 ) # FIX


# ------------------------------------------------------------
# TODO: start afni as shown, and setup colors sub-bricks, etc.
#
# cd SOME_DATA_DIRECTORY
# afni -niml -yesplugouts &
#
# set your underlay and overlay datasets, or script that, too
# also, set your color bar
# ------------------------------------------------------------

# save all of the images
foreach cindex ( `count -digits 2 1 $#coord_list` )
foreach tindex ( `count -digits 2 1 $#thresh_list` )

set coord = "$coord_list[$cindex]"
set thresh = $thresh_list[$tindex]

plugout_drive -com "SET_DICOM_XYZ A $coord" \
-com "SET_THRESHNEW A $thresh" \
-com "SAVE_JPEG axialimage axial.$cindex.$thresh.jpg" \
-com "SAVE_JPEG coronalimage cor.$cindex.$thresh.jpg" \
-com "SAVE_JPEG sagittalimage sag.$cindex.$thresh.jpg" \
-quit

echo saving images at coordinates $coord, threshold $thresh

# give afni a chance to think, may not be needed
sleep 2

end
end
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