Editing Scanco Administration (section)

==Other FAQ==

===View Sample info===
<pre>
$ mcr um:uct_info 1234
</pre>
will show you sample-name and date-of-birth of sample-number 1234
<pre>
$ mcr um:uct_info -m 1234
</pre>
will give you some (stupid) info about meas 1234

'''Note:''' If you use this function all the time, put the following into <code>microct_setup_user.com</code>
<pre>
$ uct_info  :== $um:uct_info
</pre>
and then the usage info will even be correct.


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===List measurements for data and backup location===

*To generate a list of measurements that are registered in the database, to determine where backups are stored, or if the data is still on disk:

::<code>$ write_info</code>

*Ask you for a range of measurement numbers or sample names.
*Create a <code> sys$scratch:info.txt</code> file.

<pre>
$ write_info
UCT_WRITE_INFO.EXE V1.2
-----------------------
Sample Index from [0]: 
Sample Index to   [0]: 1000000
Sample Name  from [ ]: DRF
Sample Name  to   [ ]: DRF
Extended Info ?   [T]: F
       1383  DRF_001                                 
       1383  DRF_001                                 
       1385  DRF_002                                 
       1385  DRF_002                                 
       1383  DRF_001                                 
       1383  DRF_001                                 
       1383  DRF_001                                 
</pre>
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===Anonymize patient name and DOB===

Here is the link to [[Media:SOP_Anonymize_patient_name_dob.pdf | Scanco's SOP]] to change a long list of patient's name and/or DOB to de-identify the data. As of 2025 it seems that the executable proposed to be used in the SOP is no longer available.

Instead, the DOB and Patient Name can be updated manually by running <code>uct_sample</code> to update patient information.

This does not affect the headers of past RSQ, ISQ or AIM files.



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===Fix a wrong scan site code===

This is done if accidentally scanned using the wrong control file. 
For example scan site RR is scanned mistakenly under RL, or TL scanned by mistake using the control file for TR ect.


To see our site codes, e.g. 20 = RL, 21 = RR etc using 

<pre>$ show log *eval*</pre>

;Scenario 1: 

If the correction commands (<code>uct_correct_meas_site</code> and <code>updh_site</code>) are already in your account (which is the case for the xtremect2 and xt2recalib accounts on the XtremeCT cluster)

 $ cd util
 $ dir *site* 

and you see two programs (<code>uct_correct_meas_site</code> and <code>updh_site</code>). Set priviledge to bypass first

 $ run ut:uct_correct_meas_site

and enter the meas. number to be corrected and then enter in the correct site code (20 = RL, 21 = RR, 38 = TL, 39 = TR). 
*This modifies the database, so the correct site is displayed in the eval program. 
*Enter meas. number 0 to exit program.

Then we must also correct the ISQ and RSQ files (has to be restored from tape if not on disk):

 $ run ut:updh_site      !'updh' = update header</pre>

*Enter the <b>full (i.e. pathname included)</b> ISQ or RSQ filename. For DISK6 data should use DISK6:[xtremect2.data....]. 
*Then enter the correct site number.


;Scenario 2: 
 
Normally the correction commands (uct_correct_meas_site and updh_site ect.) are only provided in a calibration account to prevent from misusage. We have to login as user calibration to make the change.  

 $ set host 0
 $ username: [enter calibration account, e.g. calib3401]
   
Then we use the same steps in <b>Scenario 1</b> to change the site code in both database and ISQ and RSQ files. 
*Make sure to <code>logout</code> from user calibration afterwards.


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===Fix a wrong sample, measurement or patient name===

Sometimes the ISQ or RSQ might have incorrect information:

 Patient Name : DRF_053
 Patient Index : 2751
 Measurement Index : 13990

You can modify the measurement index, etc, in the ISQ/RSQ header. As a regular user, use the utility:

 $ run IDISK1:[CALIBRATION.UTIL]UPDH_SAMPLE_MEAS_NAME.EXE

<b>NOTE:</b> Running this program will not affect the database, only the file. If you want to move a measurement to another sample number, use the <code>import</code> function.

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===Fix for results fail to print/list/show after evaluation===

There are a number of reasons the results may not print:

====Incorrect first measurement number====
When sample information (such as patient name, DOB, remark) is changed DURING scanning, this can over write the 1st Scan measurement number, resulting in the evaluation sheet not being printed, and data not shown when running upat_list. For example, this happens when:

1) open sample program, enter name, hit save, leave program open

2) start scan (which would write correct record with 1st meas. in sample database)

3) in sample program: then only enter DOB, and hit 'save' again in the sample program --> it 'overwrites' the 1st meas. with an empty string again.

If you want to enter DOB after the scan has started, you HAVE to 'Find...' and re-load that patient first (so it correctly loads the 1st meas. entry also). It is best to just not use the sample management program whilst scanning is taking place. 

However, if you do encounter this problem, use the following to fix (shown using patient 668 as an example. 1st scan measurement number was 2672):
<pre>
 $ set host 0
 calibration
 xxxxx

 $ spb
 $ @[microct]microct_setup
 $ run [calibration.util]uct_correct_first
 $ r UCT_CORRECT_FIRST

 Patient Nr.: 668
 SampleNr.:          668
 First:            0

 2672

 Patient Nr.:
</pre>
and continue with next non-working patient, give patient number 0 to exit.

 $ logout


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====Evaluation completed with results not written to database====
If the first measurement number and DOB are correct... check the .log file of the evaluation... However, if there is no upat*.log file available for that scan, use:

upat_list -v=2 and you will see (for eg sample 594):

<pre>
Found sample 594, CAMOS_0018
Found measurement 2536 made 19-MAR-2007 12:52:58.48
Measurement site RL found in list at index 0
Measurement 2536 within measurement period
ERROR finding evaluation for measurement 2536

No valid evaluation found for measurement 2536
</pre>

So it seems the 3D upat eval never wrote anything to the database for that scan. In this case, you can run:

<pre>
$ @ue:ipl_upat_eval_again_quick.com
</pre>
and let it run for the missing data. 
'''NOTE''' it will only need the aim files and gobj files that you still have in your 'models' directory.


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====Incorrect sequence of measurement numbers====
Finally, if none of these options work... check the order of measurement numbers: especially if an import has occured, first check the first measurement number is correct (as above). Then run sys$Scratch:uct_correct_prev_next.exe and correct the order of the measurements: The database keeps a 'daisy' chain of meas. numbers, each meas. knows which one was the previous meas and the next meas.

0 means: no prev. meas (or no next meas) So corrected the order for you like this:

<pre>
$ r UCT_CORRECT_prev_next

Measurement No. (0 to stop) [0]: 2821
MeasNo.:         2821 PatientNo:          723

Previous [0]:   <-- leave 0
Next     [0]: 2828  <-- give next meas number
Measurement No. (0 to stop) [2828]:
MeasNo.:         2828 PatientNo:          723

Previous [0]: 2821  <-- give prev. meas number
Next     [0]:  <-- leave 0 for very last meas.

</pre>
Please note: the series of meas. numbers per patient is NOT separate per meas. site, thus radius and tibia meas. are linking to each other. '''Do not mess up!'''


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====Strategies for finding correct measurement numbers====
If <code>upat_list</code> does not output anything I normally check if the database entry for the corresponding measurement is ok. In this case

 $ uct_list 13918

This showed a wrong sample name and number.

Then you could do <code>uct_list</code> (and enter all default) of the complete database and search for the patient string CSI_0051.

Then you would figure out the possible measurement numbers:

13986,13987,13988,13989.

In this example, the only one missing was 13986.

This case example was difficult because the ISQ file was not in the standard directory. I figured out that the corresponding AIM file was
not generated by the current evaluation. So I check the procedure log of the aim file with <code>aix -l</code>. There you can see the original ISQ file

 Original file dk0:[xtremect2.data.00002750.00013986]d0012143.isq;

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