Editing Scanco Administration (section)

===UCT_EVALUATION SOP===
====Start 3D evaluation from terminal for XtremeCT II====

Logged into the terminal as "xtremect2" you can see the evaluation scripts in <code>IDISK1:[XTREMECT2.EVAL]</code>

The morphological evaluation: Control file #25. It basically runs auto contouring (#23) and then the morphological analysis.
* <code>UCT_EVALUATION_V6_XT2_DT61.COM</code>
* <code>IPLV6_EVAL_CORT.COM</code>
* <code>IPLV6_EVAL_TRAB.COM</code>
* <code>IPLV6_EVAL_TOTAL.COM</code>


* <code>UCT_3D_LIST_CORT_XT2.TXT</code>
* <code>UCT_3D_LIST_TRAB_XT2.TXT</code>
* <code>UCT_3D_LIST_TOTAL_XT2.TXT</code>

Contouring scripts:
* <code>IPLV6_AUTOK.COM</code>: Creates automatically the standard GOBJ. Control file #22.
* <code>IPL_AUTOK_CTTB.COM</code>: Creates automatically the CORT, TRAB and PORE.GOBJ (previously CRTXPO). Control file #23.
* <code>IPLV6_AUTOK_CTTB_CORR.COM</code>: Creates automatically the CORT and PORE.GOBJ, after manual correction on the TRAB.GOBJ. Control file #24.

Laplace- Hamming scripts:
* <code>IPLV6_UPAT_EVAL_LH61_XT1DB.COM</code>
* <code>IPLV6_UPAT_EVAL_LH82_XT1DB.COM</code>

Results will be generated in the <code>IDISK2:[XTREMECT2.RESULTS]</code> directory, in the same way as they are generated for the cortical analysis on XtremeCT I, i.e. using the uct database and appended text files.

Laplace Hamming evaluations will generate results in the upat_list database. The direct measurements will be stored in the uct_list database.


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====Symbols for XtremeCT II vs XtremeCT I====
<code>microct</code> account you get

  "MICROCT_BIN" = "DISK1:[MICROCT.]" (LNM$PROCESS_TABLE)
       = "DISK0:[MICROCT_COMMON.3309.]"
       = "DISK0:[MICROCT_COMMON.]"

for <code>xtremect2</code>

  "MICROCT_BIN" = "DISK1:[XTREMECT2.]" (LNM$PROCESS_TABLE)
       = "DISK0:[MICROCT_COMMON.]"

So 3309 has its own directory where the software versions for the two scanners are different, e.g.

  xtremect: DISK0:[MICROCT_COMMON.][MAIN]IPL_SCANCO_M.EXE
  microct: DISK0:[MICROCT_COMMON.3309.][MAIN]IPL_SCANCO_M.EXE

We have defined some symbols for the different ipl versions:

  IPL
  IPLREG
  IPLFE
  IPL_BATCH
  IPLREG_BATCH
  IPLFE_BATCH

In the scripts you can directly use these symbols instead of ipl_scanco_prog (old style).

IPL and IPL_BATCH are different for the two scanners because the newest version is not officially released for XT1.
IPL of the microct account (XT1) cannot read data of the xtremect2 account (XT2). The other way around it works.

IPLREG and IPLREG_BATCH point to <code>$DISK1:[XTREMECT2.MAIN]IPL_SCANCO_REGIS_V107.EXE</code> for both accounts.


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====Stop the annoying beep====

Typically a job ends and a beep is sounded in the user window. This can be annoying if somebody is running many jobs.

You cannot add a <code>/nonotify</code> via the advanced parameters in uct_evaluation script editing. However, you
could:

a) Create a copy of <code>uct_evaluation_v6.com</code>, e.g. <code>uct_evaluation_v6_nonotify.com</code> and change the line from

  $ SUBMIT/NOPRINT/NOTIFY/QUE='EVAL_EQUEUE'/LOG='EVAL_LOGFILE2'/NAME='JOBNAME' -

to

  $  SUBMIT/NOPRINT/QUE='EVAL_EQUEUE'/LOG='EVAL_LOGFILE2'/NAME='JOBNAME' -

or

b) Turn of the beep on the workstation you are sitting at:
Go to the session manager, <code>Session -> Keyboard ... -> Bell Volume disable</code>

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====Start 3D evaluation from terminal for microCTs====

[[Image:Bones2.jpg|20px]] <b>Warning:</b>Do not change <code>uct_evaulation_v4.com</code> and <code>ipl_fixed_batch_v4.com</code> in .eval, but only work on your own file (i.e., eval_steve).

First, an explanation of how the normal evaluation runs by hitting the 'Start 3d' button.
<pre>$ scanco_submit_command ue:uct_evaluation_v4.com/para=(xxx,yyy,zzz,…)</pre>
There are 8 parameters:
*P1: number of print outs of our results sheet
*P2: the ISQ filename
*P3-5: start x (pos x), y, z
*P6-8: dim x, y, z
The parameters p3-p8 come from the white bounding box. The problem is that when you start from the terminal you do not have these. This problem can be overcome by using the <code>isq_to_aim_gobjbox.exe</code> and then give the relevant parameters. You can 
<code>$ run um: isq_to_aim_gobjbox.exe </code>
to see what it's asking for.
By using gobjbox you do not need p3-p8. Therefore you can start the evaluation by giving:
<pre>$ scanco_submit_command ue:uct_evaluation_special_josh.com –
/para=(1,dk0:[microct.data.0000275.0000245]c0000332.ISQ)</pre>
*You can make <code>uct_evaluation_special_josh.com</code> such that there is no need for P1 (change p2 to p1 in the script, etc).
*Alternatively to using the gobjbox you could use the normal isq_to_aim, but hard code the dim and pos.
*Then call whatever IPL files you want to call. Look into <code>fixed_batch_v4</code> to see how we turn on the database always on the first line of every IPL part, and how we calculate parameters.


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====Temporarily change evaluation for UCT_EVALUATION====

In a terminal window, we need to redefine the logical that determines which
3D evaluation is associated with the <code>UCT_EVALUATION</code> tool.

For example, typing <code>VOI</code> runs the <code>UCT_EVALUATION</code> tool
by executing <code>UE:UCT_EVALUATION_VOI.COM</code>

Type
<pre>$ show logical UCT_EVALUATION</pre>
and then you can redefine this to point to another evaluation script.
<pre>$ define UCT_EVALUATION UE:UCT_EVALUATION_CUTOUT.COM</pre>

This is only redefined in the particular terminal you are using, and it
will reset to its default in a new terminal.  It will also not work if you
try to submit the job to a queue.  It only works interactively.


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====Assign special evaluation to UCT_EVALUATION====

'''Warning''': This is for advanced users ONLY.  Do not attempt this without contacting Steve!

This will show how to set up <code>$ eval_kyle</code>:
It is easy to set up multiple .COM files for the 3D evalulation tool, one such set-up is already prepared on your computer:
<pre>
$ eval_special
</pre>
will do something similar to <code>$ voi</code> where the normal contour program opens, but if you start the 3D eval, the special script <code>um:uct_evaluation_special.com</code> is called (associated with eval_special), which then in turn calls <code>ipl_fixed_batch_special.com</code>, where you can specify your own set of thresholds, etc.

So it is a daisy chain of files which we will need to follow to set up a special <code>xxx_kyle.com</code> script, and where ever we encounter <code>_special.com</code>, we copy and change it to <code>_kyle.com</code>.

So to set up <code>$ eval_kyle</code> you will need to do the following:

*1. Edit <code>disk1:[microct]microct_setup_user.com</code> (double-click on file), please be careful here, it's very important! (and I hope you have done your 'weekly full backup' regularly, so you could always retrieve a good version of login.com...)

*2. Then, towards to bottom and duplicate the line
<code>$ eval_special :== @com:eval_var.com um:uct_evaluation_special.com</code>
and change duplicate to
<code>$ eval_kyle    :== @com:eval_var.com um:uct_evaluation_kyle.com</code>

This will make this command <code>eval_kyle</code> available after you login freshly. Save and Exit.

*3. Then go to <code>disk1:[microct.eval]</code> and copy the file <code>uct_evaluation_special.com</code> to the name <code>uct_evaluation_kyle.com</code> ('Commands', 'Copy ...', BUT CLICK ON THE THREE DOTS and give new output name. 
If you do not see the <code>eval_special:</code> go to terminal, <code>$ dir ue:*special*.com</code> and take it from the <code>microct_common</code> directory)

*4. Edit the <code>_kyle.com</code> file: at the top, change <code>ipl_......_special.com</code> to <code>_kyle.com</code>

*5. Copy <code>ipl_fixed_batch_special.com</code> to <code>ipl_fixed_batch_kyle.com</code>

*6. Edit <code>ipl_fixed_batch_kyle.com</code> to your liking. If you want <code>$ eval_kyle</code> to not perform the full evaluation, but only something akin to <code>voi</code>, then, in the steps above, copy <code>uct_eval_voi.com</code> to <code>uct_evaluation_kyle.com</code>, and <code>ipl_voi.com</code> to <code>ipl_fixed_batch_kyle.com</code> (thus you take the <code>voi</code> script as template for the <code>_kyle</code> script).

*7. Then open a new terminal ('applications', 'decterm'), <code>$ eval_kyle</code> should work now!

'''Notes''': When you start the 3D eval, then
<code>$ que</code>
will show you your batch job with your name on it now!

And now a few more explanations how the whole thing works: in all eval programs, hitting 'Start 3d' just submits the logical <code>uct_evaluation</code>, <code>$ show log uct_evaluation</code> shows you that by default, this points to <code>ue:uct_evaluation_v4.com</code>.

Those little <code>voi</code> and <code>eval_steve</code> scripts then just temporarily redefine this logical so that a different script is submitted when you <code>'start 3d eval'</code>.

About the '''corelut eval''': Then we start a whole different eval program: the <code>.exe_corelut</code>. So, if you set up a <code>eval_steve_c</code> (or whatever you want to call it): Produce a <code>eval_var_c.com</code> in the directory commands (maybe copy from microct_common to [microct.commands]), and there, on the last line, instead of starting
<code>$ uct_evaluation</code>
(the normal program), replace by
<code>$ evalc</code>
which starts the <code>.exe_corelut</code> - and because the <code>eval_var.com</code> has over-ridden the <code>uct_evaluation</code> logical just before, then you are starting different script upon starting 3d eval.
NB: we have a logical AND a symbol called <code>uct_evalution</code>. Sorry for confusion. Symbol <code>uct_evaluation</code> starts normal <code>eval</code> program, so this is what you replace by symbol <code>evalc</code> now).


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