KGS Lab Manual

Most KGS-lab protocols have 2 basic functional series saved:

• Sprl TR 1
• Sprl TR 2

Running the functionals:

1. Select FunctionalSeries in Rx Manager window.
2. Make changes to slice-orientation and slice-thickness consistent with changes made to Inplanes, when the Scan Parameters window updates with the series6
3. Copy Inplane slice-prescription into the Functional series.
4. If 2D Inplanes were acquired:
   • Graphic Rx
   • Select Series
   • Select Localizer series from Graphic Rx dialog box.
   • Copy Rx on left of display
   • Select appropriate Inplane series for slice-prescription7 Set Fallback to R0.
   • Accept.
   If 3D Inplanes were acquired:
   • Copy start-end field locations in Scanner Range section from inplane screen printout. There are 6 start end locations all-together. Make sure number of slices in the Scanner Range corresponds to the number of slices indicated by the protocol (should be 4 less than locs per slab of the inplane 3D).
   • Important: the bed should not move between the inplanes and the functionals; please verify with the subject!
5. UserCVs. Adjust as specified by protocol and researcher preference.
   • o external trigger: 1 for automatic triggering 0 for manual trigger
   • o nframes: as desired
   • o nextra (number of extra shots): usually 3 for TR=2; 6 for TR=1.
     Note that the extra shots are not included in the P-files, so there shouldn't be any stimulus running at this time. (Stimuli tend to have e.g. a blank screen or countdown.)
     (nframes+nextras)*TR[s] should be the total duration of your experiment
   • o number of interleaves: usually 0
   • o xfer data (autorecon): 31 (unless doing realtime fMRI )
6. Save Series.
7. Prepare to Scan, wait for series to download to scanner. While Prep is running, prepare stimulus display.
8. Alert subject that Prep is coming.
9. Prep Scan.
10. Alert subject that Scan is coming.
11. Scan. ⁹
12. start stimulus/trigger (subject or operator) once scan light on keyboard flashes ¹⁰

When scan is over, check for Pfile (type "ls -l P*" in /usr/g/mrraw) and write down the Pfile number. Then check to see if the Pxxxxx.7.mag file has been created and keep track of it as it grows in size. Do not ftp the mag file until the autorecon is done. If the auto recon fails to create a .mag file, type:

>> grecons -O Pxxxxx.7

Additional Functionals: repeat last 4 steps.

Changing User CVs between scans

Some User CVs, like the number of frames in a scan, number of discarded frames, or scan triggering, can be changed between scans without starting a new functional series, or re-running the prep scan. Note when things like TR change, you can not do this, and should start a new functional series.

To change the CVs:

1. Move the mouse cursor to the "UserCVs" menu toward the left of the bottom row in the scan screen.
2. Hold down the right mouse button. A context menu will appear.
3. Select "UserCVs"
4. In the "CV Name" field, enter the name of the variable -- e.g. 'nframes' for # of frames.
5. In the "Value" field, enter the new value.
6. Accept.

Checking Raw Functionals

expandonefile -f 1 Pxxxx.7.mag filename nslc nframes npix mdisp filename.*

6 There is an older function called recon31, which also does this. It's not clear at the time of this update if this is still good to use, but it's worth noting. To use, type recon31 xxxxx (xxxxx = Pfile #, leading zeros not needed, but no '.7')

7 Most protocols use an oblique slice prescription. Other options include: sagittal, coronal, or axial. If you have made a change in slice-prescription orientation, you must make the same change in the Functional series orientation. If you have made a change in slice-thickness value, you must make the same change in the Functional series.

8 Usually there will be one Inplane series from which to choose. However, if for some reason the Inplanes had to be repeated, there will be one series for each set of Inplanes collected.

9 Operator may either select Scan in the Scanner Control area using the mouse or push StartScan on upper-row of keyboard.

10 As long as the external trig is set to 1 in UserCVs, the machine displaying the stimulus will trigger the scanner to start.

Last modified 2004-Oct-28 05:28 GMT.