KGS Lab Manual

Functional Session: Running Anatomicals

Localizers

There are a few different types of localizers that are used. Most KGS-lab scans start with a 3-plane scan.

3pln (3-plane)

This scan will give you 9 slices from one of each plane:sagittal; coronal; axial. It's useful for verifying that the subject's head is properly placed in the center of the scanner bore, and for proscribing other localizers (or, if needed, inplanes can sometimes be directly proscribed off of these).

Select 3pln/localizer scan.
Save Series.
Prepare to Scan.
Alert subject that localizers are coming.
Select Scan in Scanner Control area.
Scanner will automatically run a prep for about 30seconds followed by the localizer scan. When scanner stops, images should be displayed in miniviewer in upper-right of display¹.
Maximize to enlarge display
Scroll through localizer images. Use scroll bar on the right-hand side of the viewer. Select the coronal slice which is the center of the brain. Write down the image number. You will use this slice to prescribe the sagital localizer scan

Sagittal localizer

In different protocols they have slightly different names. These are 60 sagittal T1 weighted images. We collect them for 2 purposes:

To use them to prescribe the inplanes & functional slice orientation and location.
Align the volume collected in this scan to the 3D hires volume anatomical from which the subject's brain was reconstructed.

Select localizer series: sag localizer / 3D anatomy scan in Rx Manager.
If desired, enter/change slice-thickness (in millimeters) in bottom of Scan Parameters.
Select Graphic Rx in Scan Parameters
Select desired localizer image using the slider on the left-handside of display: should be the widest coronal slice; usually around the center of the brain.
Prescribe slab for the sagittal scan. Should cover the head left to right & up/down. If it doesn.t cover left to right change slice thickness.
Set Fallback to R0.²Accept.
Save Series.
Protocol selection should automatically select and download the localizer scan. If this is the case, the Scanner Status area on the left-hand side of the display should indicate that series 2 had been downloaded.
Prepare to Scan.
Alert subject that localizers are coming.
Select Scan in Scanner Control area. Scanner will automatically run a prep for about 30seconds followed by the localizer scan.
When scanner stops, images should be displayed in miniviewer in upper-right of display. Maximize to enlarge display; scroll through localizer images. Use scroll bar on the right-hand side of the viewer. Adjust brightness and contrast. Press middle mouse button Drag target up/down to increase/decrease brightness. Drag target left/right to increase/decrease contrast. Select slice that extends most posterior (towards the back of the skull) and that has a good view of calcarine sulcus.
Note slice number (slice number appears on upper left corner of image display) for inplane prescription and screen save.

Inplanes

Select Inplanes2D or Inplanes3D series in Rx Manager.
Select slice-orientation indicated by Plane under Imaging Parameters.
If desired, enter/change slice-thickness (in millimeters) in bottom of Scan Parameters.
Select Graphic Rx in Scan Parameters.
Select desired localizer image using the slider on the left-handside of display.Adjust brightness and contrast, if necessary.

Prescribe slices:

For 2-D inplanes: (inplane anatomicals)
- Click mouse left-button to make slice-prescription visible.
- Orient prescription into appropriate position³
For 3-D inplanes: (inplane 3d)
- Drop slab by clicking mouse left-button.
- Orient slab into appropriate position. Note that here there will be 4 more slices than the functional inplanes!
- In the CV panel make sure that gain is set to 10.
For both 2-D inplanes and 3-D inplanes:
- Set Fallback to R0.
- Accept.
- Make sure Freq DIR in Acquisition Timing section below Autoview window is not set to R/L⁴
- Save Series. For 3-D inplanes, you should print screen or write down obtain start-end locations ( L/R; A/P; S/I).
PRINT SCREEN- save picture of Graphic Rx localizer: Print screen by hitting
Print
on the printer.
Prepare to Scan (wait while inplanes download). Scanner control display (small monitor to the right of scanner interface) should show timing for the new series.
Alert subject that he/she will move.
Move to Scan.
Alert subject scan is coming.
Scan. Prep will run for 30 seconds, followed by Inplane scan.
Functionals can be setup while Inplanes are being collected. See Functionals steps 1-5.
When scanner is done running, examine Inplanes in viewer or browser to make sure all is well⁵.
If manual prescan (2D inplanes only):

Alert subject.

Auto Prescan.

Manual Prescan.: Manual prescan window opens.

In window, click on Scan TR (R1/R2) at top right.

Adjust Digital Gain slider sothat R2 values fall within 30-70% range (typically30-40%).

Done.

Screen Save

Must be done prior to Data Management. Can be done as soon as Inplanes are done.
* Click browser icon in upper-left
* Within image-view window, click browser left-hand side
* Select current patient in left-hand window
* Select appropriate series in right-hand window
* Select chosen slice in bottom-window
* Viewer
* With image slider, choose localizer image number that was used to do the inplane graphic Rx.
* In blank area at lower-left of screen, type xr s# * (# = inplane series number,usually 2)
* Save Screen
* Click browser and choose the screen save series when it appears Viewer Adjust brightness and contrast using middle mouse so that brain and slice prescription are easily visible Print screen by hitting Print on the printer. Write and protocol name on the back of the screen save and take notes about each individual scan (Pfile numbers, etc.).

1 If localizer images aren't displayed, select update to load them.

2 If fallback is not on, then the acquired volume will be centered on the slice that you prescribe from. This can screw up the functional volume position if you copy the inplane Rx while a slice other than that which you prescribed from is displayed! The volume will be the same as the inplanes in two dimensions, but in the third dimension it will be centered on the currently displayed slice. If this is all too confusing, just be sure to turn fallback on for both inplanes and functionals. As long as your subject's head is appropriately landmarked, everything should work fine with fallback on.

3 There are three markers on the bottom slice of the slice prescription. Left mouse button down-pressed on markers will change number of slices and prescription rotation. Left mouse button down-pressed with drag motion will change position of the whole prescription.

4 May be set to either A/P or S/I depending on slice orientation.

5 If images not visible:
* Click on browser icon (the upper-right most of the six icons on the leftof the screen)
* Click browser button on left-hand side in middle of screen
* Click on subjects name in left-hand window
* Click on inplane series in right-hand window
* Click on selected inplane in bottom window
The differences between the 2 series are the TR (1 or 2s) and the flip angle which differs for different TR. You could use the same series and change the TR value but then you need to update the flip angle according to your new TR.
If you are going to use Sprl TR 1 and Sprl TR 2 within one session make sure to copy the slice prescription from the inplanes (either from the graphic RX manager or using the location value). When you switch between the series types the 'move to scan button' may light up. Please ask the subject if the bed has moved. IT SHOULD NOT MOVE. If the bed has moved you probably didn't update the slice prescription properly. Please update it and the bed will move to original location!

Last modified 2004-Feb-25 05:28 GMT.