NP/CT · database

Normalization scan instructions (pdf)

For both the full calibration or the cal check, a Ge-68 tank should be placed in the center of the bore. Use the back lasers to align in x-y plane. For the z-axis, align the handle of the tank such that the front, rotating laser hits the bars (the tank will be further into the bore than for a normal scan).

If putting the tank directly in the bore, support with half-annulus of foam, and do not place as far into scanner: laser should hit between the edge and the tick mark, as shown in the second photo.
Note: this is no longer recommended due to the weight it places on the bore liner

In the top GUI menubar, select Calibration→PET. A window will appear. Fill in the information using Ge-68 as the isotope and radiopharmaceutical. Preferably, enter the dose on the tank (use the form on the calculations page), but it is also okay to enter 0 for the dose and remaining dose. No need to enter a date/time, it will just use calibration start time. Start Daily QC or Start Full Calibration as desired. The daily QC (“cal check”) takes about 10-15 minutes, full calibration takes about 45 minutes. After the calibration has already started, a second "Start PET protocol" window will pop up. Just ignore it and don't push either button. Daily QC should be done any day there will be scanning, full calibration should be done weekly or biweekly. The status will start at "400" and go until "411". When it is done it will be "1000". To check that the cal check finished successfully: Use putty to ssh to proto02 and enter the following commands:

        cd /data/Calibration/
        ls –ltr
      

You should see CalCheck_SN001_[date]_[time]_Success. If it says “InProgress” wait for the test to finish. If it says “Failed”, or stays at "InProgress" for too long, contact PDSi for service, or try restarting scanner and calibrating again. You can also check in the “Reports” directory for details:

        cd /data/Calibration/Reports
        less Cal_Report_SN001_[date]_[time].txt
      

All tests should show PASS

Short Version

• Position scanner as desired, with -5cm and +22cm of clearance and zero
• Patient Registration tab → Manual → Enter Name (and other relevant info) → Register
• Acquisition tab → Protocol → Click "head" dot → Select desired protocol
• Edit protocol if necessary
• Enter dose, or 0 if dose is unknown, and click Begin
• If CT-first
  • Pop says to move scanner 5mm.  Don't, just start
  • CT scan must be started from scanner touch screen
• If PET-only
  • Click continue to put into PET mode -- scanner will move into position
  • Click start to begin listmode acquisition
• Let scan reconstruct, or click Cancel Scan, Cancel Exam, Finalize
  • Wait until "Recon State" says "3 Prebinner" before canceling
  • Ignore "Last PET scan failed" message, it's not real
• Copy scan to proto08 (recon computer)

  • rsync -varP /data/master/[patientID] proto08:/data/master/

See bottom for troubleshooting steps.

*** For scans longer than 1 hour, follow these instructions after starting the scan ***

IN DEVELOPMENT

Using the reconstruction GUI on proto08

Log into proto08 as usual.

Open a VNCviewer window vncviewer :1 &.
If GUI is not yet running, open terminal window, setup environment using pdsi_setup.
Open GUI using npctOfflineGui.

Each tab of the GUI is explained below:

Patient browser

Search looks for patient name as entered in GUI

Recon

Scan must have normalization associated with it -- date of scan must be within the date range of one of the normalizations in the Normalization tab.

Batch sys

List of running and queue jobs.
Priority of jobs can be increased/decreased
*** deleting a job deletes the entire series ***

Normalization

"Dataset" is actual scan data (list mode and such)
"Fileset" is the final normalization files used during reconstruction of a scan
Normalization dataset can be added and reconstructed to generate normalization fileset, or an existing filest can be loaded (with correct reconstruction software version)
"Update dataset" can be used to modify the time range for that normalization data to be used. To include multiple time ranges, add the same dataset but with a new name.

          ssh [email protected]
          pdsi_setup
        

You can also just use pdsi_setup /PDSI/base/pet/[otherversion] if you want to set up the reconstruction using a different software version.

Check that there is not another reconstruction already in progress:

ps -fu daq

If ImagingChain2 is running, wait until it is done, or if it is okay to stop it, run ImagingChainStop.sh

All scans are stored in /data/master. Go to the desired scan:

cd /data/master/[patient]/[study]/[series]

In the [series].prot file make sure the line global.parameters.id.patient= has the correct patient name (scans on proto08 are generally renamed to something more informative).

Version 38 +: In the [series].prot file make sure the line global.parameters.id.patientdir= has the correct patient name.

Create a new series, so as not to overwrite existing reconstructions:

ManageSeries -new [patient]/[study]/[series]:[newSeriesName]:[newNonAcSeriesName]

Creating a new series in V38+ has different syntax:

ManageSeries -newdir [patientdir]/[studydir]/[seriesdir]:[newSeriesDirName]

The series will appear under the [study] directory.

From within the new series directory, check that the protocol is set up correctly. Some lines that possibly need to be changed are the scale and shift parameters (sometimes they default to (null) and certain versions of the reconstruction don't work unless the numbers are specified).

Optimal scale and shift parameters (the default are probably okay now):

            ac.parameter.mumapScaleXY.float=1
            ac.parameter.mumapScaleZ.float=1.04
            ac.parameter.mumapShiftX.float=1
            ac.parameter.mumapShiftY.float=0
            ac.parameter.mumapShiftZ.float=-2.3
            recon.parameter.ScaleXY.float=1.013
            recon.parameter.ScaleZ.float=0.98
            recon.parameter.ShiftX.float=1 #was 0
            recon.parameter.ShiftY.float=0 #was -1
            recon.parameter.ShiftZ.float=-2

Other places to update the protocol file (newer scans will have most of these already set up):

              ...
              InterFilterKernelSize=1.250000
              InterFilterType=1
              ...
              PixelSize=1 # 0=2 mm (128x128), 1=1 mm (256z256), 2=4 mm (64x64)
              ...
              PostFilterKernelSize=1.850000 #can set to zeros if do not want final smoothing
              PostFilterType=1
              ...
              RecipeName=MLEM_256_1.recipe # Recipes are in /PDSI/base/pet/Current64/build/Recipe
              #Name should match PixelSize (e.g., PixelSize=0 &rarrow; MLEM_128_2.recipe)
              #Name should match ThreeDIterationType (e.g, ThreeDIterationType=2 (FBP) &rarrow; FBP_128_2.recipe)
              ...
              ReconACType=2  # 0=No recon, 1=non-AC only, 2=AC only, 3=AC and non-AC
              ...
              ScanType=STATIC  # can also be DYNAMIC, and the Frames.txt files is used for setting the time frames
              ...
              ThreeDIterationType=1 # 0 for OSEM (in development), 1 for MLEM, 2 for FBP
              ...
              recon.parameter.NIter.int=100
            

Make sure that /data/Calibration/CurrentMaps soft link points to a normalization that matches the scan. Directories are labeled with datetime that normalization was acquired, and date_time it was processed. The mcf*.txt files indicate parameters used in the creation. The energy and timing cuts must be set in the recipe to match one of the normalizations in CurrentMaps, e.g. Norm_256x215.17x116.9_92x51x256x256_400-650_10.mat is the normalization for reconstructions using 256x256 grid, ECutLow = 400, ECutHigh = 650 and TimingCut = 10.
To change the link to a different normalization:

              rm /data/Calibration/CurrentMaps  # Note: no trailing "/" ! ;
              ln -s /data/Calibration/[desired_norm_dir] /data/Calibration/CurrentMaps
            

If the reconstruction should be dynamic, edit the Frames.txt file to use the desired time frames. Note that each frame has a start time and duration (not start and end times). Also, frames cannot overlap, but there can be gap between frames.

Edit the protocol file to indicate that it should de dynamic, ScanType=DYNAMIC, otherwise the Frames.txt file will be ignored!

Once the protocol file is setup as desired, start the reconstruction chain, and check that it is working:

nohup ImagingChain2 [series].prot &> output[date].txt & ;
              less output[date].txt
            

Each frames takes about 30 minutes to complete.

To stop a reconstruction that is running:

ImagingChainStop.sh

Check that all associated Matlab processes have also stopped:

              ps -fu daq
            

If any processes remain, kill them!

Debugging:

If the reconstruction stops prematurely, check the log file (output[date].txt) for error messages. Make sure that the recipe selected in the protocol file, RecipeName=[Name], has parameters

              bin.parameter.TimingCut.float=10
              bin.parameter.ECutLow.float=400
              bin.parameter.ECutHigh.float=650
            

that match those of the calibration that is linked to under /data/Calibration. (Recipes are in /PDSI/base/pet/Current64/build/Recipe/.)

The calibration file that is used will be CurrentMaps for newer recon software or CurrentXMap, CurrentEMap, CurrentNorm for older reconstructions (soft linked to the actual directories).

The recipes in /PDSI/base/pet/Current64/build/Recipe/ can be edited, although it is best to create a copy of the recipe with a descriptive name and edit that. Just make sure to update the .prot file with the correct recipe under RecipeName. For instance, to turn off scatter correction, change

              global.control.scatterVersion.int=11
            

to

              global.control.scatterVersion.int=0
            

If the reconstruction finishes binning and then fails (e.g. tries to do AC, but finds no CT scan), you can restart from after the binning (and save a lot of time) by changing

              global.control.binnerVersion.int=4
            

to

              global.control.binnerVersion.int=0
            

Place Ge-68 tank in scanner, centered as best as possible. The front laser should hit about 1 cm below the start of the Ge tank.

Scan the tank using the Ge tank, 15 minute protocol. This includes both standard CT and 15 minutes of PET.

Let the scan reconstruct with the default recipe (should be MLEM_256_1.recipe)

Run the uniformity script:

                pdsi_setup /PDSI/base/pet/Current64/;
                cd /PDSI/base/pet/Current64/PerformanceMeasurement/uniformity
              

Create a config file for the Ge tank scan, and edit for correct patient, study, series

                cp [olderfile].cfg sn001GeTank[scandate].cfg
                emacs sn001GeTank[scandate].cfg  #edit the patient, study, and series name
                matlab -nodesktop -nodisplay -nosplash -r "pmUnifRun('sn001GeTank[scandate].cfg'); exit"
              

A file named unifReport.pdf will be created, along with the same file date/time stamped

Plot the singles, delayed, and victims rates of a given scan

Move to grogg directory on proto08 or proto02, then run matlab plotting code:

                  cd ~/grogg
                  matlab -nodesktop -nodisplay -nosplash -r "plotSinglesVsTime('','',''); exit"
                

Inside the single quotes, put the subject, study, and series names. The code will generate pdf files of the plots in the same directory where the code was run.
The file names are based on the patient directory name.
An epoch is 6 seconds.

This is no longer required (2016.06.01)

to be done after every NeuroPET/CT reboot ***

Below are instructions on how to disable the gating packets for each module on the scanner after a reboot. 

*** This is to prevent a dead time issue – i.e. it is very important ***

1. From the scanner’s Main Computer (proto02) open a telnet session to one module at a time using port 2024
   1. The modules are named module01 to module07.
   2. It should not ask for a user name or password
   3. Example: telnet module03 2024
2. Issue a “  SET_MONGOOSE FALSE” command.
   1. All caps
   2. The telnet session is not happy with back spaces so type slowly.
   3. If you type incorrectly is it best to close the telnet session with Control-D and open a new one.
   4. For some odd reason you have to enter 2 blank spaces before the command.  So the command you type is actually  “  SET_MONGOOSE FALSE”
   5. e.      When you enter the command it will echo the command you entered (minus the two extra chars).    If the echoed command is all you get then it was successful.
   6. If you spell it wrong or forget to add the two spaces it will tell you the command is unrecognized.
3. After you successfully enter the SET_MONGOOSE command use control-D to exit the telnet session
4. Release for module01 to module07.
5. Make sure you get all 7 modules.

Example session: 

telnet module01 2024
                    Trying 10.10.1.2...
                    Connected to module01.
                    Escape character is '^]'.
                      SET_MONGOOSE FALSE
                    SET_MONGOOSE=FALSE
                    <control-D>
                    Connection closed by foreign host.