Editing Scanco User Instructions (section)

===Combine two volumes to create transparent image===

First create your two start "seg.aim" images
Start by running either the normal eval, or $ voi to get one _seg.aim file of one region

Rename it to a better name in the session manager, e.g. c0001234_all.aim

Then either by choosing different contours, or a different threshold, start the $ voi or the normal evaluation again, which will create another _seg.aim file.

Load them in the 3D viewer ('all files') to check that they look like expected.

Now we will go into IPL and concatenate those two volumes.

<pre>
$ ipl
/read all xx_all.aim
/read trab xx_seg.aim
/transparent
  -input_solid               trab
  -input_transp              all
  -output                    out
</pre>

Note: the solid volume is OVERWRITING the transparent input volume, so usually, it
is the smaller (inner) of the two.

<pre>
/write out xxx_transp.aim
/quit
</pre>

Then load the _transp.aim file in 3D, go to 3D program FAQ to see how to change transparency levels in the Display options there.

See IPL FAQ or 3D program FAQ if you need help with these parts.

<b>Step by Step Example:</b> Showing your chosen trab VOI within whole bone
:* $ voi, enter threshold in ipl_voi.com, start 3d eval WITHOUT contours
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_all.aim
:* Start up normal eval program, draw trabecular contours, check threshold in ipl_fixed_batch_v4.com, start 3D eval.
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished 

<b>Step by Step Example:</b> Showing high-dense volume surronded by lower density volume

:* Start normal 3D eval with HIGH threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_high.aim
:* If wished: read out 3d result database with $ uct_list
:* Start normal 3D eval with LOW threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished


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