KGS Lab Manual

The most important parameter that governs the quality of our scans is that the gain/scale factor parameter in the CV window be set to a value of 10.

At the 1.5T, there is a choice of two coils: one large (white coil :"HEAD") and one small ("SMHEAD"). The smaller head coil gets ~50% signal-to-noise. However, not everyone's head fits inside this coil. The large head coil is a GE coil and it is encased in light-colored plastic. The small head coil is encased in dark gray/black plastic. Our protocol is currently set up for "SMHEAD" if you choose the other coil "HEAD", you must make a change to all the series in the protocol to be setup for "HEAD" instead of “SMHEAD. The Wandell lab (and Gary) prefer anatomy collection at the 3T. This uses the "FMRIC" coil. The Wandell lab collects these with the protocol: wandell-helmet-anatomy-mprage-fspgr [old, should be verified/replaced].

The subject's head is stabilized inside the coil with foam pads. There is no display ¹ to set up for these scans. Like the functional scans, it is necessary to know the subject's weight and birthday.

Volume Anatomy Scanner Instructions

Set Up

1. Enter scanner mode: click scanner icon in upper-leftcorner of display.
2. If exam is in progress, select End Exam in Rx Manager and Confirm.
3. Click New Patient.
4. In Patient Position area:
   • Patient ID: kgrillspector xxx (xxx are your initials).
   • Patient Name: subject's full name.
   • Weight: subject's weight.
   • Exam description: brain dob mm/dd/yyyy (date of subject's birth)
5. Put subject in scanner. Landmark subject.
6. Protocol Selection (schematic representation of human body)
   • Protocol set to Site (not GE).
   • Click the head of the body schematic (protocols will appear).
     On the 1.5T: select kgs-vAnat-smhead-082002
     On the 3T select: wandell-helmet-anatomy-mprage-fspgr
   • Accept.

Scout

1. Select scout series. This series scans in 3 plane : 7slices per plane.
2. Save Series
3. Prepare to Scan
4. Alert subject that scout is coming.
5. Select Scan in Scanner Control area. Scanner will automatically run a prep for about 30 seconds followed by the scout scan.
6. When scanner stops, images should be displayed in miniviewer in upper-right of display. images aren’t displayed, select update to load them
7. Maximize to enlarge display. Use scroll bar on the right-hand side of the viewer.
8. Adjust brightness and contrast. Press middle mouse button. Drag target up/down to increase/decrease brightness. Drag target left/right to increase/decrease contrast.
9. Scroll through localizer images. Choose the longest axial slice. You use this slice to prescribe the coronal slices of the localizer scan.
10. Write slice number of longest axial slice.

Localizer

1. Select localizer series. Localizers in this case are coronal slices.
2. Choose Graphic Rx.
3. Prescribe coronals off the longest axial slice. Slices should cover the whole brain front to back. Try to get middle slice co-aligned with the middle of the brain. Calculate brain length:
   

   # slices * (slice thickness + gap)/10.

   
   This will give you brain length in cm.
4. Print screen
5. Save Series
6. Prepare to Scan
7. Alert subject that localizers are coming.
8. Select Scan in Scanner Control area. Scanner will automatically run a prep for about 30 seconds followed by the localizer scan.
9. When scanner stops, images should be displayed in miniviewer in upper-right of display. If localizer images aren’t displayed, select update to load them
10. Maximize to enlarge display. Use scroll bar on the right-hand side of the viewer.
11. Adjust brightness and contrast Press middle mouse button. Drag target up/down to increase/decrease brightness Drag target left/right to increase/decrease contrast.
12. Scroll through localizer images
13. Write down slice number of widest coronal slice.

3D Anatomy

1. Hilight 3D Anatomy series in Rx Manager. This scan is ~24 min.
2. View/Edit
3. Select Graphic Rx in Scan Parameters.
4. Scroll through and select chosen Localizer image using ImageNumber Slider on the left-hand side of display. Adjust brightness and contrast, if necessary
5. Turn-off/deselect Auto W/L.
6. Prescribe slices:
   These are 3D inplanes and are prescribed as such.
   • Drop slab by clicking mouse left-button.
   • Orient slab so it will cover the brain R/L.

     If the skull doesn't fit inside the slab, adjust FOV:

     • Erase all (in Graphic Rx)
     • Accept.
     • Adjust as necesary:

       FOV in Scanning Range	adjusts the FOV along the coronal and axial directions (the y direction in Graphic Rx view).
       Slice Thickness in Scanning Range	adjusts the FOV along the sagittal directions (the x-direction in Graphic Rx view). Increase slice thickness in increments of 1/10 (i.e. 1.2 -> 1.3).

     • Return to Graphic Rx.
     • Select chosen slice.
     • Drop and orient slab again with one left-click of the mouse. slab should appear wider now.

7. Set Fallback to R0.
8. Accept.
9. Make sure Freq DIR in Acquisition Timing section below Autoview window is not set to R/L. May be set to either A/P or S/I dependingonslice orientation.
10. Save Series
11. Prepare to Scan (wait while inplanes download).
12. Scanner control display (small monitor to the right of scannerinterface)should show timing for the new series.
13. Alert subject that he/she will move.
14. Move to Scan
15. Alert subject scan is coming.
16. Scan.Prep will run for 30 seconds, followed by Inplane scan.

Screen Save

Can be done only after 3D anatomy is collected.

1. Click browser icon in upper-left.
2. Within image-view window, click browser left-hand side.
3. Select current patient in left-hand window.
4. Select Localizer series in right-hand window.
5. Select chosen slice in bottom-window.
6. Viewer
7. With image slider, select chosen image.
8. In blank area at lower-left of screen, type xr s#
   (# = inplane series number, '3' in this case)
9. Save Screen

Acquiring hires volumes anatomies on the 3T:

• 128 sagittal slices: 1.2 mm thick
• protocol name: wandell-helmet-anatomy-mprage-fspgr In this protocol you can use of two 3D sequences : mprage or fspgr. Opinions vary as to which type is easier to segment; consult someone in Brian or Kalanit's lab.
• This protocol is used for acquitting hiresolution brain volumes for reconstruction and flattening. The scanning instrux are the same as for the 1.5t instructions except that series name are different:
  1. anatomy localizer (3pln)
  2. anatomy localizer (coronals)
  3. fspgr 128 slices; FOV=24; thickness=1.2mm (approximately 24minutes)
  4. mprage 128 slices; FOV=24; thickness=1.2mm (approximately 24minutes

Data Management: preparing and anatomies and moving them to local drives

1. From Tools window, open shell, login to lucas:

   
   >> ssh [anatomy computer] -l heeger [this will change] Password: [contact kalanit]
   >>
   >> cd /local/heeger b. Run script: If the volume anatomy was collected at the 1.5T, run:
   >> anattrans.sh If the volume anatomy was collected at the 3T, run:
   >> anattrans3.sh You will be promted with the following: Subject:
   >> mmddyyXX (XX initials) Localizer series #:
   >> 2 (coronals) Inplane series #:
   >> 3 (sagittals) Screen save series #:
   >> 99

2. When the script is done running, copy over the anatomies to a local disk:

   
   >> ssh -l username moach
   enter your password
   >> cd /biac1/kgs/mri/

   
   From the destination location type:
   >> scp -r heeger@[anat computer]:/local/heeger/mmddyyXX .
   Enter 'yes' at warning.
   Enter password at prompt:
   >> [see Kalanit]

1 Although there's no stimulus to set up, sometimes the operator will set up the display and play a dvd off of a computer to keep the subject occupied.