Editing Scanco Administration (section)

=Calibration and QC=

==System Updates==
{| class="wikitable"
|-
! scope="row"| XtremeCT II
|
*22-OCT-2020:  Calibration Update
*01-OCT-2020:  Calibration Update
*31-JUL-2020:  Pixel Correction
*21-FEB-2019:  New X-ray source, Recalibration
*25-JAN-2018:  Calibration Update
*28-APR-2016:  Calibration Update
*07-APR-2015:  Calibration Update
*04-NOV-2014:  Calibration Update
*21-MAY-2014:  New Daily QC Phantom (Scanco concluded minimal differences from previous)
|-
! scope="row"| XtremeCT I
|
|-
! scope="row"| vivaCT80
|
*20-OCT-2020:  Filter changer replaced, Recalibration
|-
! scope="row"| vivaCT40
|
*20-OCT-2020:  New x-ray source, Recalibration
*09-NOV-2010:  Recalibration (70KV energy only)
*01-NOV-2010:  New x-ray source, Pixel Correction, Recalibration
|-
! scope="row"| µCT35
|
*20-OCT-2020:  New x-ray source, Recalibration
*15-JUN-2011:  Recalibration
*21-MAR-2011:  Recalibration
*10-FEB-2011:  Recalibration
*26-NOV-2010:  Pixel Correction
*29-OCT-2010:  Recalibration 
|}


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

==Calibration and Conversion==
===Attenuation measured by µCT===
A micro-CT 3D image of an object is basically a 3D map of local x-ray absorption in the object. The reconstruction from multiple angular views provides information on how much x-ray absorption is happening within each cubic voxel element of the scanned volume.

It is important to understand what is meant by “density” in a µCT image. The reconstructed grey-scale intensity of each image voxel does not relate directly to mass density alone, thus do not expect it to correspond with measurements of weight per volume, e.g. g.cm-3. The primary entity that is measured is x-ray absorption, defined as the x-ray linear attenuation coefficient in units of
1/distance, specifically, 1/cm. This is determined both by mass density and x-ray mass attenuation coefficient which is determined by the elemental composition of the material. The x-ray linear attenuation coefficients of typical material is shown blow.

[[File:Mu_comparison.JPG|thumb|center|600px|X-ray linear attenuation coefficient µ of typical material (image curtesy of Dr. Ying Zhu)]]

The images we obtain from the scanner are in a special scanner manufacturer format called AIM files. Each voxel in these images contains a scaled linear attenuation value (mu-value) to save disk space. 

{| class="wikitable"
|-
! scope="col"| Symbol
! scope="col"| Name
! scope="col"| Unit
! scope="col"| Value Range
! scope='col'| Meaning or Comments
|-
! scope="row"| µ
| x-ray linear attenuation coefficient
| 1/cm
| µ > 0 
| A constant that describes the fraction of attenuated incident photons in a monoenergetic beam per unit thickness of a material
|-
! scope="row"| mu_value
| linear attenuation in Scanco images
| 1/cm
| -8～8 typically
| mu value represented in Scanco images
|-
! scope="row"| pixel_Scanco
| pixel intensity value in Scanco images
| -
| −32768～32767
| Original format of Scanco images in 16-bit signed
|-
! scope="row"| pixel_uint
| pixel intensity value in converted Scanco images
| -
| 0～65535
| Converted format of Scanco images in 16-bit unsigned, using the same slope (unscaled) but an updated intercept
|}

<pre>
pixel_Scanco = mu-value * scaling_factor
</pre>


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===Calibration by BMD===
When we know that the x-ray absorption of a material is dominated by one specific material, then we can relate the measured x-ray linear attenuation coefficient (mu_value) to the mass density of that material. The calibration of [[Scanco_User_Instructions#Descriptive_Statistics_.28Mean.2C_Median.2C_SD.29_of_Calibrated_Voxel_Values| '''Bone Mineral Density (BMD)''']] is an example of this. We assume that the x-ray attenuation within mineralized tissues such as bone, dentine and enamel is dominated by, and can be approximated as, the x-ray attenuation of the mineral compound calcium hydroxyapatite (CaHA) which has the formula Ca5(PO4)3(OH). 

Then we obtain “phantoms” with two or more known mass concentrations of CaHA. By linking these mass concentrations of CaHA with measured mu_value in the micro-CT images, we can establish calibration linking the two quantities, allowing us to infer from the micro-CT measured linear attenuation coefficient (mu_value) in a mineralized tissue, to the density of CaHA in mg.cm-3. 

*The assumption of linear correlation between the two quantities is based on a well-applied beam hardening correction and the phantoms' diameter matching with the size of bone within the sample.

*This calibration system could be used to calibrate measurement of other substances apart from CaHA and bone, where x-ray absorption is known to be dominated by a certain substance and phantoms can be prepared with known concentrations of that substance.

{| class="wikitable"
|-
! scope="col"| Symbol
! scope="col"| Name
! scope="col"| Unit
! scope="col"| Value Range
! scope='col'| Meaning or Comments
|-
! scope="row"| BMD 
| Bone Mineral Density 
| mg HA/ccm
| 0～3000 
| Volumetric density of calcium hydroxyapatite (CaHA) in a biological tissue in terms of mg/cm^3
|-
! scope="row"| BMD_value
| Bone Mineral Density in Scanco images
| mg HA/ccm
| -1500～3000 typically
| BMD value in Scanco images
|}
 

[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===Conversion between Attenuation and Bone Density===
<pre>
BMD_value = mu-value * slope + intercept

mu-value = (BMD_value – intercept) / slope

pixel_Scanco = scaling_factor * (BMD_value – intercept) / slope

</pre>

For example, to convert mu_value of 1.7923 (1/cm) to BMD (mg HA/ccm):
<pre>
BMD_value = 1.7923 * 3.67162994e+02 + -2.06399002e+02 = 451.667 (mg HA/ccm)
</pre>

For example, to convert the lower threshold of 125 mg HA/ccm that is in the IPL script to pixel intensity in Scanco images:
<pre>
pixel_Scanco = 4096 * (125 - -2.06399002e+02) / 3.67162994e+02 = 3697 
</pre>

*You could get the scaling_factor, intercept and slope values from the AIM header of your scan by using aix -l command:
[[File:Aix.JPG|400px]]


*Reference: [[Media:Jbmr.141.pdf|Bouxsein ML, Boyd SK, Christiansen BA, Guldberg RE, Jepsen KJ, Müller R, Guidelines for assessment of bone microstructure in rodents using micro-computed tomography. J Bone Miner Res. 25(7): 1468-86. 2010.]]


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===Convert CT numbers to mg HA/ccm / Houndsfield units (HU)===

The two byte numbers (short) can be converted to mu values by first dividing by mu_scaling which is probably 4096 (uCT35, vivaCT40) or 8192 (XtremeCT). 

<b>Houndsfield units (HU)</b>

Here is the conversion formula from mu (lin.att. in 1/cm, our original, 'physical' image numbers) to HU:

<pre>HU(pixel) = -1000 + mu(pixel) * 1000/mu(water)</pre>

so the mu(water) is the 'constant' that is needed for this conversion of any pixel value mu(pixel) to HU of that pixel.

divide the 2-byte numbers in our dicom/aim/isq files by 4096 to get mu. (4096 -->  'mu_scaling' in our headers). E.g. you see
gray-scale number 8192 in our files -->  mu = 2 [1/cm].

A reasonable result for the uCT35 is:

<pre>HU = (CT / 4096) * 1718.19 - 1000</pre>

and that means 1000/mu(water) = 1718.19 --> mu(water) = 0.58299 which is a reasonable number.

<b>mg HA/ccm</b>

<pre>
mg HA/ccm = (AIM/mu_scaling) * slope + intercept
mg HA/ccm = (AIM/4096) * 295.494 - 189.695    ! vivaCT40
mg HA/ccm = (AIM/4096) * 256.51 - 172.99         ! uCT35
mg HA/ccm = (AIM/8192) * 1402.549 - 340.953  ! XtremeCT
</pre>

These numbers are available in the AIM header, or the ISQ header (<code>$ run ut:ctheader</code>).

To look up slope, intercept and mu_scaling, check either the AIM header
<pre>$ aix C1234567.AIM</pre>
or
<pre>$ run ut:uct_update_calibration</pre>
and look at a record, and you'll find slope and intercept and mu-water.

<pre>
vivaCT40
!---------------------------------------------------------------------- 
Mu_Scaling                    4096 
Calibration Data              55 kVp, 200mg HA wedge, 4096 scaling 
Calib. default unit type      2 (Density) 
Density: unit                 mg HA/ccm 
Density: slope                2.95493988e+02 
Density: intercept            -1.89695007e+02 
HU: mu water                  0.58200 
!----------------------------------------------------------------------
</pre>
<pre>
XtremeCT
!-------------------------------------------------------------------------------
Mu_Scaling                                       8192
Calibration Data              60kVp, BH: 200 mg HA/ccm, Scaling 8192            
Calib. default unit type      2 (Density)                                       
Density: unit                 mg HA/ccm                                         
Density: slope                         1.40254895e+03
Density: intercept                    -3.40953003e+02
HU: mu water                                  0.23900
!-------------------------------------------------------------------------------
</pre>


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===Fix the calibration data stored in the RSQ header===

You can see what calibration file is stored with your scan a few ways. One is to use <code>aix -l</code> to view the log file. You should see this part:

 !-------------------------------------------------------------------------------
 Mu_Scaling                                       8192
 Calibration Data              60kVp, BH: 200 mg HA/ccm, Scaling 8192            
 Calib. default unit type      2 (Density)                                       
 Density: unit                 mg HA/ccm                                         
 Density: slope                         1.40254895e+03
 Density: intercept                    -3.40953003e+02
 HU: mu water                                  0.23900
 !-------------------------------------------------------------------------------

Another is to use the extended header command for RSQ and ISQ files:

 $ run ut:UCT_EXT_HEADER_DISPLAY.EXE
 UCT_EXT_HEADER_DISPLAY V 1.3
 Raw-Data-File []: DK0:[MICROT.DATA.00000006.00000011]C0002519.RSQ
 Reading Raw Data ...
 Found valid hext of type CALIBRATION:            8
 Found valid hext of type UCT_BH-Corr:            7
 Hext type [8]:8
 hext            8  read.
 Calibration No.             1
 Valid Flag              1
 Description     60 kVp, BH: 200 mg HA/ccm, Scaling 8192
 Scanner-ID              3307
 Energy [V]             59400
 Intensity [▒A]              0
 Antiring Enable             0
 Beamhardening Enable            1
 Beamhardening Coeff file UCTD:UCT_BH_COEFF_60KV_0200HA_3418.TXT
 Beamhardening Checksum           0
 Default unit type (1=▒, 2=mg, 3=HU, 4=Custom)           2
 ▒ Enable              1
 ▒-scaling               8192
 Density Enable             1
 Density units  mg HA/ccm
 Density Slope       1489.406
 Density Intercept    -370.3510
 HU Enable             1
 ▒ of water   0.2447000
 CUSTOM Enable              0

If you need to fix it, use the <code>UCT_EXT_HEADER_ADD_CALIB.EXE</code> command:
 run ut:UCT_EXT_HEADER_ADD_CALIB.EXE
 
 UCT_EXT_HEADER_ADD_CALIB V 1.1
 Raw-Data-File []: DK0:[MICROT.DATA.00000006.00000011]C0002519.RSQ
 Reading Raw Data ...
  IDX Calib Description
   1      1 68 kVp, BH: 0200 mg HA/ccm, Scaling 8192
 Calibration Record No [0]:1

[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===Calibration FAQ===
====Change brightness scaling====
*Refer to [[Media:Mu-scaling.pdf|'''Change the brightness scaling''']].


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

====Update a scan after pixel correction====
Contact Lab personnel with system-level priviledges to perform
<pre>
$ set host 0
                 !  Username: calib2339       (µCT35)          
                 !  Username: calib5019       (vivaCT40)           
$ spb            ! set priviledge bypass to write in other user accounts
$ run ut:pixel_corr_apply

        PIXEL_CORR_APPLY Version 1.5
        Scanner ID from UCTD:UCT_SCANNER_2339.DAT : 2339       !2339 for µCT 35,  5019 for vivaCT 40
        Is this Scanner ID correct ? [?]:  y
        Give RSQ-Filename (leave empty to exit)  []: DISK4:[BONELAB.DATA.00005283.00011668]C0005128.RSQ
        ...
        ...
        Copy .RSQ to _CORRECTED.RSQ befor correction ? [?]:   y

$ logout
</pre>


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

====Update calibration in ISQ====
If DICOM files are converted to ISQ with IPL and then used for patient evaluation, the calibration data in the ISQ header needs to be present and correct. If this information is missing, utilizing upat_list to extract the values will say 'Error: Density calibration not valid'. In order to add calibration data to an ISQ file, do the following as user calibration:
<pre>
$set proc/priv=bypass ! gain read/write access to the files
$mcr ut:uct_ext_header_add_calib ! provide ISQ file name and header type (I chose [2])
</pre>

If you need to adjust the calibration of a file, without changing the system calibration data, copy the calibration database into a different directory, e.g. sys$scratch. Then, add a new calibration record to this temporary calibration database. This way your new, temporary values will not show up in the scan program.

  $ copy uctd:uct_calibration_3401.dat sys$scratch:

Define the following logical in a terminal MAKE SURE TO DO THIS!!!!

  $ def UCT_CALIBRATION_DATABASE sys$scratch:uct_calibration_3401.dat

Run uct_update_calibration and click trough the current calibration record (always enter).

  $ r ut:UCT_UPDATE_CALIBRATION.EXE
  select current calibration record
  enter...

  $ r ut:UCT_UPDATE_CALIBRATION.EXE

Then select the last number (New Record), copy all values from above, change slope and intercept.

Then use

  $ mcr ut:uct_ext_header_add_calib

for ISQ and RSQ.

At the end, close the terminal!


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

==Quality Control (QC)==
===Scope===
*Only Authorized XCT and µCT Operators are permitted to perform QC scans, including both scan acquisition and analysis.    
*Authorization is a formal process. If you are not sure whether you have or should have authorization, speak to Dr. Boyd or Dr. Hallgrimsson or the MoJo Operations Manager. 
*Authorized XCT and µCT Operators are responsible for ensuring a QC schedule is maintained.
*Only the manufacturer can calibrate the scanner!  QC only checks the calibration.


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===Overview===
*Micro-CT systems cannot directly measure the density of a material, however, the density is linearly correlated to the x-ray absorption (assuming a proper beam-hardening correction is applied), which can be measured by micro-CT.  Density is therefore determined by measuring a reference material of known density (i.e., a phantom) to define a conversion function to relate x-ray absorption to density. Quality control of density and structural measurements for the micro-CT systems is achieved through weekly checks of phantom values to their reference values and recalibrating the system (i.e., defining a new conversion function) as necessary. 

*Performing QC is essential to the:
# Safety of our study participants and lab members
# Validity of our research data

[[File:QC_phantom.jpg|thumb|center|600px|Scanco Medical quality control phantom (a) and its CT scans of the density QC1 (b) and the structural QC2 (c)]]

*Reference:  Koller B, Laib A (2007) Calibration of micro-CT data for quantifying bone mineral and biomaterial density and microarchitecture. In: Advanced bioimaging technologies in assessment of the quality of bone and scaffold materials: techniques and applications. Springer, pp 79-84.


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===Density QC1===  
QC1 measures the density of 5 different rods of known hydroxyapatite (HA) densities within the QC phantom: approximately 0, 100, 200, 400, and 800 mg HA/cm3.  This tests 3 things:

# That the scanner’s last calibration is still valid.  This is done by comparing daily QC values to an acceptable range.
# The presence of drifts and shifts in the calibration.  This is done by plotting daily QC results over time and using Shewart’s Controls to mathematically look for drifts and shifts.  (Shewart’s Controls replaces visual assessment.)
# The correct functioning of scanner hardware and electrical components.  This is done by visual inspection for image artifacts. 

*QC1 is checked daily or 3 times a week on XtremeCT scanners whenever used and weekly on microCT scanners.


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===Structural QC2===  
QC2 measures the volume of 3 fine aluminum rods within the QC phantom (Al rod volume measurement).  This tests for:

# Alignment of the gantry (or stability of architectural parameters)
# The correct functioning of scanner hardware and electrical components.  This is done by visual inspection for image artifacts. 

*QC2 is checked weekly on both XtremeCT and microCT scanners.


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===QC Scan Instructions===
*XtremeCT QC Scan Instructions: Boyd Drive:\02 - Operations\01 - Scanner QC, Specifications, & Maintenance\QC Workflows\QC 001.2 - XCT Quality Control.docx
*[[Media:Calibration-instructions-for-uct35.pdf |µCT35 QC Instructions]] or  [[Media:uCT35_Calibration.pdf|µCT35 QC another Instructions]]
*[[Media:Calibration-instructions-for-vivact40.pdf |VivaCT40 QC Instructions]] or [[Media:VivaCT40_Calibration.pdf| VivaCT40 QC another Instructions]]


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===Print out QC reports===
After running a QC1 or QC2 analysis, the results are output to: 
*DISK4:[BONELAB.PROJECTS.QC] for XtremeCT QC results
*DISK3:[MICROCT.PROJECTS.CALIBRATION] for microCT QC results performed by BH lab
:*login with microct account 
*DISK5:[BONELAB.PROJECTS.CALIBRATION] for microCT QC results performed by Bone Imaging lab
:*RESULTS_QC1_UCT35.TXT;2 
:*RESULTS_QC1_VIVACT.TXT;4 
:*RESULTS_QC2_UCT35.TXT;2 
:*RESULTS_QC2_VIVACT.TXT;2 


As usual as [[Scanco_User_Instructions#Print_out_report_sheets|'''print out report sheets''']], you have two options.
On new systems you can simply run:
  @ut:qc_list_qc1 sys$scratch:qc1.txt
  @ut:qc_list_qc2 sys$scratch:qc2.txt
Or the more traditional approach is:
  $ upat_list
When it asks for a template, you can select for a graphical report
  UU:UCT_EVAL_PHANTOM_SCANCO.PS
or for a text output
  UU:UCT_3D_LIST.TXT
  UU:UCT_3D_MEANS.TXT

[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===System Stability and Precision===
System Stability and Precision here is based on the QC measurement, QC1 for density variations and QC2 for structure variations.
{| class="wikitable"
|-
! scope="col"| System Stability and Precision
! scope="col"| XtremeCT
! scope="col"| vivaCT40
! scope="col"| µCT35
|-
! scope="row"| Long Term Precision
| 
*QC1:  ± 8mg HA/cm3
*QC2:  ± 2.0%
| 
*QC1:  ± 0.4%
*QC2:  ± 0.7%
(Ref term: 26-NOV-2010 to 8-APR-2011)
| 
*QC1:  ± 1.0%
*QC2:  ± 1.6%
(Ref term: 26-NOV-2010 to 8-APR-2011)
|-
! scope="row"| Short Term Precision
| 
*QC1:  ± 8mg HA/cm3
*QC2:  ± 2.0%
| 
*QC1:  ± 0.4%
*QC2:  ± 0.9%
(Ref term: 4-MAR-2011 to 8-APR-2011)
| 
*QC1:  ± 1.0%
*QC2:  ± 0.7%
(Ref term: 6-MAR-2011 to 8-APR-2011)
|}


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===QC FAQ===
====Determine calibration drift for microCT QC1====
The microCT QC1 analyses provide an estimate of the calibration drift by considering 'mean5' values.  Use <code>$ uct_list</code> and make sure to use UU:UCT_3D_MEANS.TXT as the template.  Then give the measurement numbers of the QC1 measurements (or all of them and remove what's not needed later).


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

====Update QC1 contours====
If the QC contours don't line up on the phantom, then the contours need to be updated on the system.  Normally this should not happen unless the phantom has become loose - if this is the case, re-fix it.

1. Login as user system.  Do not use the <code>$ set host 0 </code> command since you will not be able to open windows for program.<br>
2. Run the login script for the user that does the QC scans so that Scanco logicals point to that scan database.
          $ @adisk1:[microct]login.com     on the XtremeCT cluster
          $ @adisk1:[microct]login.com     on the vivaCT cluster
          $ @disk1:[microct]login.com       on the µCT100 cluster

3. Run the evaluation program.
          $ uct_evaluation
4. Load the most recent QC scan and locate the contours. File-->Load Gobj... Filter:  <code>uctd:*.GOBJ</code>. Locate the contours for the phantom: <code> UCT_PHANTOM_KP_HA_XXXX_Y.GOBJ  </code> where XXXX corresponds with the scanner ID (XtremeCT 3309, vivaCT 5019, µCT35 2339, µCT100 6002) and Y corresponds with the rod number (1-5 and results mean1 - mean5. <br>

5. Adjust the contours to centre on the rods.
    Load a contour.
    Move the contour on the first slice to be centred on the rod.
    Copy the contour.
    Delete the contours on slices 2 to the end.
    Paste the contour on the last slice.
    Morph between the two contours.
    Save the contours.  They should be saved to (A)DISK0:[000000.MICROCT_COMMON.DATABASE].
6. Perform a new QC scan as the standard (i.e., microct) user.  Check that the contours line up for the evaluation.  Evaluate and check the results.


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

====Update Gobj for QC1 Analysis====
Refer to  [[Media:Fix_QC1_gobj.pdf| '''Fix QC1 Gobj''' ]] for instructions.


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

====Update XtremeCT QC1 calibration====
This procedure needs to be done for each beam hardening correction (e.g., QC1 with 200 mg HA/cm3, QC1 with 1200 mg HA/cm3) and for each scan energy.


1. Perform 3 back-to-back QC1 scans, which ensures the x-ray tube is very warm.<br>
2. Evaluate the last QC1 scan.<br>
3. After the evaluation is done, determine parameters for the new calibration
<pre>
$ uct_calib_phantom
UCT_CALIB_PHANTOM Version V1.0
 
Reading UCTD:UCT_CALIB_PHANTOM_KP_HA_3309.TXT
Phantom Type in file:              6
Phantom Number in file:          304
Voltage in file:                   0
No of Materials in file:           1
With each, no of  steps:           5
and mus:                    1.000000
No. of Cylinders:                  5
Measurement No. (0 to Stop)     [0]: 11404
 
Mus: 0.2382 0.3163 0.3823 0.5358 0.8112
*****************************************************
Calibration: Slope Intercept:      1398.628  -339.819
Enter in Calibration Records if wished.
*****************************************************
Measurement No. (0 to Stop)     [0]:
End of program
$
</pre>

4. Save the above screen output in a file called CALIB_3309_YYYY-MM-DD.TXT.

5. Now update the calibration.  For most settings, you will use the default value by pressing return.  You need to choose the correct calibration record, the one that corresponds with the energy and beam hardening correction used in the QC1 scans you did.  Next, you need to update the slope, intercept, and mu water values to those determined in step 3 (copy and paste values to avoid typos).  The new values should be similar to the old ones.  Finally, if you have not made any mistakes, then save the record.
<pre>
$ run ut:uct_update_calibration
UCT_UPDATE_CALIBRATION V2.5
 
 IDX Calib/Rec. Description
  1      1/42   60kVp, BH: 200 mg HA/ccm, Scaling 8192
  2      2/43   60kVp, BH: 1200 mg HA/ccm, Scaling 4096
  3      3/0    New Record
Choose Calibration Record (IDX): [2]: 1
Valid Flag [1]:
Scanner-ID [3309]:
Energy [V] [59400]:
Intensity [µA] [0]:
Description [60kVp, BH: 200 mg HA/ccm, Scaling 8192]:
 
Antiring Enable [0]:
 
Beamhardening Enable [1]:
Beamhardening Coeff file [MICROCT_COMMON:[DATABASE]UCT_BH_COEFF_60KV_0200HA_3309.TXT;5]:
Beamhardening Checksum [0]:
CCD_CORR: Read to mem: 500 bytes to correct 1 pixels (588 bytes allocated)
 
Default unit type (1=µ, 2=mg, 3=HU, 4=Custom) [2]:
µ Enable [1]:
µ-scaling [8192]:
 
Density Enable [1]:
Density units [mg HA/ccm]:
Density Slope [1402.549]: 1398.628
Density Intercept [-340.953]: -339.819
 
HU Enable [1]:
µ of water [0.239]: 0.2382
 
CUSTOM Enable [0]:
 
HW Filter Code [0]:
HW Filter Description []:
 
Save Record ? [Y]: Y
End of program
$
</pre>

6. Save the above screen output in a file called CALIB_3309_YYYY-MM-DD_ENTERED.TXT.  Send both text files to support@scanco.ch for them to archive.


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

====Update microCT QC1 calibration====
Refer to [[Media:QC1_Calibration_Update.pdf|'''QC1 Calibration Update''']] for instructions for the VivaCT40 and uCT35.  


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

====Update a scan with new calibration or BHC====
If the QC1 range was out of range but it was not possible to update the system calibration before scanning, you can update the scan with the new density calibration (i.e., slope and intercept).  It is also possible to change the beam hardening correction that is applied (e.g., from 200 mg HA/cm3 to 1200 mg HA/cm3).

{| class="wikitable"
|-
! scope="col"| Type of Update ||RSQ||ISQ||AIM
|-
|QC1 was out of range, need new slope and intercept 
(e.g., after updating the system calibration)
|Yes||Yes||No, Create New
|-
|Change beam hardening correction type 
(e.g., 200 mg HA/cm3 to 1200 mg HA/cm3)
|Yes||No, Reconstruct||No, Create New
|}

Use the UCT_EXT_HEADER_ADD_CALIB program to update an RSQ and, if appropriate, repeat for the ISQ.  
*Use default values for all prompts except those commented after !.
<pre>
$ mcr ut:uct_ext_header_add_calib
 
UCT_EXT_HEADER_ADD_CALIB V 1.1
Raw-Data-File []:    !give the name of the RSQ/ISQ with full path if not in that directory
 
Reading Raw Data ...
 IDX Calib Description
  1      1 45 kVp, 200mg HA wedge, 4096 scaling
  2      2 55 kVp, 200mg HA wedge, 4096 scaling
  3      3 70 kVp, 200mg HA wedge, 4096 scaling
  4      4 General, non-bone-density-calibrated scan, scale 4096
  5      5 45 kVp, BH: 1200 mg HA/ccm, Scaling 4096
  6      6 55 kVp, BH: 1200 mg HA/ccm, Scaling 4096
  7      7 70 kVp, BH: 1200 mg HA/ccm, Scaling 4096
 
Calibration Record No [0]: !specify the new calibration, e.g. 6
 
Calibration No.           6
Description 55 kVp, BH: 1200 mg HA/ccm, Scaling 4096
Scanner-ID        5019
Energy [V]       55000
Antiring Enable             0
Beamhardening Enable            1
Beamhardening Coeff file UCTD:UCT_BH_COEFF_55KV_1200HA_5019.TXT
Default unit type (1=µ, 2=mg, 3=HU, 4=Custom)           2
Same type already found. Setting old to invalid
SUCCESS: calib hext written
updating header...
SUCCESS: Header successfully updated.
 
 
Calib record indicates that BH-Corr is usually applied.
Info: There is a BH-Corr corr already in hext.
Add another BH-Corr from file again? (Y/N) [N]:  Y
</pre>


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

====Update a scan with new QC1 calibration====
Refer to  [[Media:Update_Scan_with_new_QC1.pdf|'''Update Scan with new QC1''']] for instructions.


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

====Fix: un-centered QC1 Gobj====
The contour for the QC1 scan is not centered on the on hydroxyapatite rod, which will result in erroneous low density values.  

This can occur for a couple of reasons:
*The metal spindle has come loose on the phantom, in which case re-glue it and update the contours
*The slot on the phantom's spindle was not correctly aligned
*For the vivaCT 40, the sample bed was not pushed to the right before locking it in place
[[File:Phantom_not_pushed_right.jpg|600px]]


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

====Fix: rods in QC2 images====
The QC2 scan has aluminum rods AND hydroxyapatite rods.  This happens because the slot on the phantom's spindle was not correctly aligned and the phantom positioning is off slightly.  Adjust the phantom and re-scan.

[[File:Phantom_spindle_not_in_right.jpg|600px]]


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]



====Fix: the GOBJ is missing or corrupted ROI====

If you find that the GOBJ for QC1 is missing or corrupted and doesn't apply the ROI correctly it's possible somebody accidentally created or edited one of the files. You can usually fix this by deleting the incorrect file and reverting back to the good copies. 

The GOBJ files are found here (as user <code>system</code>):

 cd DISK0:[MICROCT_COMMON.DATABASE]

To see the GOBJ files:

<pre>
$ dir UCT_PHANTOM_KP_HA_3401*/col=1/date

Directory DISK0:[MICROCT_COMMON.DATABASE]

UCT_PHANTOM_KP_HA_3401_1.GOBJ;3
                     21-FEB-2019 09:16:42.41
UCT_PHANTOM_KP_HA_3401_2.GOBJ;3
                     21-FEB-2019 09:16:06.78
UCT_PHANTOM_KP_HA_3401_3.GOBJ;3
                     21-FEB-2019 09:15:30.00
UCT_PHANTOM_KP_HA_3401_4.GOBJ;3
                     21-FEB-2019 09:14:49.86
UCT_PHANTOM_KP_HA_3401_5.GOBJ;3
                     21-FEB-2019 09:14:00.50
</pre>

There should <b>not</b> be any GOBJ files in the directory below, but as you can see there are (as user <code>xtremect2</code>):

 $ dir IDISK1:[XTREMECT2.DATABASE]*.gobj/date
 
 Directory IDISK1:[XTREMECT2.DATABASE]
 
 UCT_PHANTOM_KP_HA_3401_5.GOBJ;2
                      14-APR-2025 15:10:27.12
 UCT_PHANTOM_KP_HA_3401_5.GOBJ;1
                      14-APR-2025 13:34:51.54

So, we simply delete these GOBJ files and the QC1 should work fine:
 $ del UCT_PHANTOM_KP_HA_3401_5.GOBJ;2
 $ del UCT_PHANTOM_KP_HA_3401_5.GOBJ;1

Some explanation from Stephan Weiss:

The problem is that you have different control files in the two accounts. In the control files, there is a default evaluation set. This is just an index to an evaluation script that is written to the ISQ header. The QC1 index of <code>xtremect2</code> is the same as the standard radius evaluation of <code>microct2</code>.

One option is to change the setup such that the default gobj of QC1 cannot be written anymore. In every account you need to add the following line to
<code>microct_setup_site_specific.com</code>:

 $ DEFINE UCT_PHANTOM_KP_HA_GOBJ_CHECK -
   DISK0:[MICROCT_COMMON.DATABASE]UCT_PHANTOM_KP_HA_'SCANNER_ID'_5.GOBJ

Other options that would be more challenging to implement are:

1. Remove the default evaluation from the control files. If you do this,
then you have to select the correct evaluation script for every
evaluation. Currently this you have to do anyway if you measured with
the <code>microct2</code> account and evaluate with the <code>microct2</code> account.

2. Merge the evaluation scripts from both accounts and use only one
evaluation script database. Here we would need to update the default
evaluation in the control files as well. But then, you could evaluate
with both accounts the same way.

[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]