Oregon Brain Preservation
A Non-profit Organization

Manual - CT Scanning

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Our OmniTom CT Scanner is used during every case prior to verify adequate perfusion of fixative or cryoprotectant. 



The machine should always be plugged in when not in use or the batteries will gradually drain.  To move the machine, go to the Transport tab on the scanner. Press and hold the "UP" button until the machine is fully raised and the arrow turns gray. The machine can then be moved using the transport bar. Once positioned, press and hold the "DOWN" button until the machine is fully lowered onto the translation wheels and the arrow turns gray.



Power on scanner first. Press the power button. Wait for the login screen on the LCD. Use pin to log in. Then, log in to the tablet using the username and password in the wiki. If the tablet is off, use its power button. To power off, first shut down the tablet by selecting shutdown in the lower left. If already logge off, then use the power button on the tablet. Once the tablet is shut down, the scanner can be shut down by pushing the green button for 5 seconds. The tablet has a dedicated wifi connection to the scanner, and the scanner has a wifi connection to the PACS server. If the blue light on the scanner is flashing or steading that means it's charging or fully charged.


Daily Calibration

-Make sure the bore is empty.

-On the scanner LCD touchscreen, press "syst" at lower right.

-Select Daily Calibration.

-Press Begin. 10 seconds to leave room

-There will be 4 short scans.  Remain behind the barrier or out of the room for the entire process.

After about 5 hours, it might get down to about 50% or less, which will require another calibration. The purpose of calibration is to prevent ring artifacts. If calibration is done daily, it takes about 90 seconds. If it's been 3 days or more since calibration, then tube seasoning will be required. If tube seasoning is suggested, don't click past that screen. Skipping tube seasoning is hard on the tubes. It takes about 15 minutes. While scanning, the tube heat starts at 100% (cool). As it is used, it quickly gets hot and the percentage drops. After about 3 scans in a row, it might turn yellow, indicating that it's getting too hot.


Daily Quality Assurance

Frequently skipped when exact HU numbers are not important.

-On the workstation computer, Main Menu, click Tools, Quality Assurance.

-Place the foam and acrylic phantom into the scanner.

-Turn on laser.

-Align the top two lasers on the cross, and align the axial lasers to the groove. The other lasers can be ignored.

-Laser turns off on its own and might need to be turned back on to finish alignment.

-On the tablet, click begin.

-On the scanner, click scan.

-There will be one long scan followed by the display of a report.  All materials should fall within the listed acceptable parameters.

-Remove phantom

-If scan is outside parameters, try again. If still failing, we probably need to call the repair technician.


Software Tabs

The software has five tabs, which you will regularly switch between while working.


Patient Registration

Click the Manual button to start a series for a new patient.  Instead, to start a new series for a recent patient, click the Browser tab, highlight a patient, and click Register.



If this tab is not grayed out, then you are in the middle of a series of CT scans for one patient.  Only after completely done with this patient, click the Finalize button. This will cause the Acquisition tab to be grayed out and will require a new registration to begin another series, even for the same patient.  After each acquisition, you can move to the other tabs without causing the series to be finalized.  It is possible to take multiple series on the same patient before finalizing. But we've decided it's probably best to finalize after each scan and send to the PACS server.



We do not use this tab.



The grid at the left lets you select patients, while the panel at the right lets you select scans for that patient.  This is where you send to Archive (PACS server). Just send the axial scan series, not the dose SR.



This tab has 3 selection areas at the left:

2D: Typically view 1 or 4 slices at a time.  Use the mouse scroll wheel to move between slices.  This is the only place where the Region of Interest (ROI) tool is available.  This is the tool used to quantify HU (see below).

MPR (Multiplanar Reformation): In each of the 3 viewframes, drag the crosshairs around to see different sections.  Possibly zoom and pan to enlarge brain if it's very small.

3D: Not used.



The protocols are already set up ahead of time specifically for our needs.  Each of our custom protocols begins with OBG.

120 kV, 7mA, 4 seconds per rotation, 0.625mm thickness, 16 slice, axial not helical.

No scout (prescan) images are ever taken because we don't need to minimize radiation.


In the Acquisition tab, click Protocol, Begin.  Then click start on the LCD screen.  Before the timer gets to zero, get back 10 feet or get behind the wall.  The background radiation at 10 feet is equivalent to background.  Wait for a few minutes for the slices to load into the workstation.  While images are being reconstructed, other tabs in software will be disabled.  After it's done, click View.


Hounsfield Units (HU)

HU values are quantitative measurements of radiodensity in a material.  In very simplistic terms, it's the grayscale on the images, with higher HU values showing as white.  Below are the HU values relevant to our needs. The Cryoprotective Agent (CPA) is an equal mix of DMSO and ethylene glycol (EG).  The DMSO shows on CT scans as significantly more radiopaque due to the sulfur atoms, but the EG does not affect the attenuation. 


Substance HU
Water 0
Brain 20-45
Brain, 60% CPA  
Brain, 65% CPA (target)  
Brain, 70% CPA 210*
Bone 700+


*The number listed above for cryoprotected brain is only given as a preliminary example.  Better ranges will soon follow for a variety of percentages.



Windowing is a mapping of HU values to grayscale for image creation.

Window Level (WL): The center of the mapped range

Window Width (WW): The total range of the window

For example, WL/WW of 35/80 would show a range of HU values between -5 and 75, displayed as a 256 value grayscale from black to white.  Everything below -5 would show black, and everything above 75 would show white.  This is a typical brain window, as it does a good job of showing the detail in a non-cryoprotected brain.


Here are some examples of how we typically use windowing with standard presets:

Overview: 120/240 (0-240): This captures detail of normal brain as well as cryoprotected brain.  This is the window that will later be colorized for the case report.

Cryoprotection: 180/80 (140-220): This is a narrower window.  Normal brain completely disappears as black, but cryoprotected brain shows in shades of light gray and white.  This makes it very easy to quickly visualize the extent of adequate cryoprotection. 

Target: 205/10 (200-210):  Extremely narrow window not used as much.  Image essentially looks black and white.  Can give a quick indication of which areas are at target concentration of CPA.


In each case, after setting the window, a quantitative measure of HU is needed to determine the level of cryoprotection.  Go to the Viewing tab, MPR, pick a representative slice, and use the region of interest (ROI) tool to draw a small circle to get an actual HU.  Repeat this process to show 4 ROI's on one slice.  Subzero cooling can only proceed if the measured HU for the entire brain indicates adequate cryoprotection.