Oregon Brain Preservation
A Non-profit Organization

Manual - CT Scanning

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Our CereTom CT Scanner will be used during every case prior to subzero cooldown to verify adequate cryoprotection. The photo below is in our old facility.  The CT Scanner is currently offline and unavailable for use




The machine should always be plugged in when not in use or the batteries will gradually drain.  To move the machine, press and hold "UP" toggle until the Lift Status on the LCD panel changes to "Transport".  The machine can then be moved into position freely on all four casters.  Once positioned, press and hold the "DOWN" toggle until the Lift Status on the LCD panel changes to "Scan". 



Log in to the laptop workstation using the username and password in the wiki.  Most functions are carried out on this laptop, but a few functions make use of the built-in LCD touchscreen on the gantry.  The CT software is set to run automatically when Windows starts up, although Windows can still be accessed for such things as file management and updates using Ctl-Alt-Del.  The laptop establishes a WiFi connection directly to the scanner, as can be seen in the Windows notification toolbar.  If the WiFi connection fails, one option is to reboot both the scanner and the laptop.



Dr. Sparks is the only one allowed to initiate a scan of any kind, including calibration.  Other staff undergo regular training, but are not yet trained well enough to satisfy state requirements.  Other staff regularly edit and move files on the workstation without initiating any radiation.


Daily Calibration

(Dr. Sparks only)

-Make sure the bore is empty.

-On the gantry LCD touchscreen, press Select Cal.

-Select Daily Calibration.

-Press Accept Protocol.

-Press Start.

-There will be one long scan, followed by 12 short scans.  Remain behind the barrier or out of the room for the entire process.


Daily Quality Assurance

(Dr. Sparks only) 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 laser top and bottom to the groove on phantom.

-Turn off laser.

-Click Prepare on the workstation.

-Click Scan on the LCD.

-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, 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 Patient 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.  Because this is not a clinical setting, there is no urgency to clicking the Finalize button.  After each CT Scan, just click the Protocol button again to take another scan for the same patient instead of Finalizing.


Post Reconstruction

We do not use this tab.


Patient Browser

The grid at the top lets you select patients, while the grid at the bottom lets you select scans for that patient.  Double click on a scan to launch it in the Viewing tab.  If you don't see an expected scan, click refresh.



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 Reconstruction): 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 OC.

120 kV, 7mA, 4 seconds per rotation, 1.25mm thickness, 8 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 shielded glass.  The background radiation at this distance 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.