Editing Scanco User Instructions (section)

==Import Foreign Data to Scanco System==
Only RSQ and ISQ files can be imported into the database, however it is possible to convert other types of data into ISQ files (i.e., stacks of BMPs into ISQ).

<b>PART 1:</b>

After transfering your data to the VMS system (use the data disk <code>disk2</code>, NOT the user disk <code>disk1</code>), use the IPL commands <code>/import_freeformat</code> or <code>/read_aim function</code> to import your data for conversion to an ISQ.

For AIM files, navigate to the location of the AIM file.  Then open IPL by:

<pre>$ IPL</pre>

In IPL, read in the .AIM file:

<pre>ipl> read in [.AIM file]</pre>

IPL will do the following:

<pre>ipl> read in STUDYID_001_RL.AIM

/read
  -name                      in
  -filename                  STUDYID_001_RL.AIM
!> Reading AimVersion020 

!%  /read completed:  CPU: 00:01.03  ELAP: 00:01.55  </pre>

For DICOM files, start IPL and run the <code>/dicom</code> function to import. For DICOM, if your object is a single 3D file (-multifile false) or many many individual slice files (-multifile true, and give beginning of filenames, and –extension).

There may be requests by IPL to convert your data to <code>signed short</code> or <code>signed char</code> from other data types. Obey these requests and do it by running the <code>/convert_unsigned</code> function.

Then, write the ISQ file using either the "toisq" or "from_aim" commands:
<pre>ipl> toisq
-aim_name                  [in] >[leave blank as you defined “in” as .AIM file.]              
  -isq_filename              [default_file_name] > C0001234.ISQ [Create a 1 letter and 7 digit file name]
  -square_flag               [true] > false
  -original_position         [true] > false

ipl>toisq_from_aim
  -aim_name                  in
  -isq_filename              C0001234.ISQ
  -square_flag               false
  -original_position         false

!%  Dimensions of ISQ file: dim.x dim.y dim.z 558 638 168
Write_ctdata_headerext_new: no mhext found. Init mhext.
Extended header successfully added of type            8

!%  Writing ISQ slice   167  (Done:   168/168)

!%  /toisq_from_aim completed:  CPU: 00:05.12  ELAP: 00:10.47  </pre>
 
Type ipl>help toisq [or ipl>help from_aim] to see details of the command.

This writes the ISQ file. Make note of the ISQ file name.

<b>Remember</b>, the ISQ name must be 8 characters long (1 character followed by seven digits)!!! The letters and numbers can be chosen freely.

Exit IPL:

<pre>ipl>quit</pre>

<b>PART 2:</b>

To VIEW the ISQ, refer to [[Scanco_User_Instructions#Open_default_ISQ|'''Open default ISQ''']].

The measurement can be verified by looking at the Header Information. (File, Header)

If you only needed to view the ISQ, delete the file when finished by:

<pre>$ dir/sincet
$del [.ISQ file]</pre>

<b>PART 3:</b>

To use the ISQ further (e.g. for evaluations, contouring, etc.) create a sample in the database and write down the sample and measurement number. Then, run:

<pre>$ run um:uct_import   ! will import both RSQ and ISQ (modify patient index, etc)</pre>

and give the new ISQ file, the new sample-number and check that the feedback is correct (i.e., that the name from the database is matching the name from the ISQ file header).  If the Patient Name in the ISQ header doesn't match the measurement database Patient Name (very likely), then upon importing the RSQ/ISQ the headers will be updated to the new Patient Name.

Operator and controlfile can be left 0 if you want.  However, controlfile should be set appropriately if the data being imported is for the XtremeCT patient database.

If you are also importing the RSQ, put it in the same directory as the ISQ.

Then it changes the sample and measurement number in the ISQ file, makes the correct directory on <code>DK0</code>, and gives you the line on the screen of how to rename the file to the correct, new directory. Take this line and use it on the command line.  Done!  

You can now use the normal <code>uct_evaluation</code> program with this file.  If the control file was set properly, then the evaluation will be done correctly (i.e., for XtremeCT patient measurements).

<b>Note:</b> Any AIMs created from the original ISQ should be recreated.  So, it is important that you re-evaluate your newly imported ISQ.  It is OK to move the GOBJ from the old directory to the same directly as the newly imported ISQ (it does not have a 'registry' in the database).


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