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7/7/98...Draft 3
Roger and Nancy ³How to do an fMRI scan² notes

I. Log into the fMRI logger on the Instascan terminal If Netscape isn¹t running, you can pull it up by holding down on any patch of patterned background with the right mouse button depressed and selecte the Netscape logger (alternatively, if you see a Netscape icon on the icon set at the bottom of the screen, it is defaulted to pull up the logger).

A. Enter your password in the logger
B. Enter the study number
(To choose the study number, review the recently acquired exams (on the right half of the Signa screen) and increment by one). C. Enter the Signa ID (your choice, but by convention should identify whose scan (e.g., your initials) and the subject identity e.g., RW-Subject_name)
D. Select items from the other menus appropriately
E. Push ³Submit form² at the bottom
F. If you get an error, use Back-up in Netscape to avoid having to retype everything (may have to hit it twice)

II. Make sure the following windows are available on the instascan console:
Shim
Autoshim
APD II
These can also be pulled up from the colored background as describe for the logger above

III. On the Signa console, you must fill out the sign-in screen before you can place a subject in the scanner.
A. If the New Exam menu is not present on the left, hit ³Cancel²
B. Choose New Exam
C. Required fields:
Signa ID (same as above for logger)
Name (of subject)
Sex
Age
Weight
Description (something other people will understand) D. Press ³Accept²

IV. You can now position the subject in the scanner
Consent the subject if you haven¹t already
Make sure metal screen
Position subject with their shoulders just touching the head cradle
Headphones or ear plugs (hanging on the scanner)
Lateral padding to reduce movement (may be in pt. comfort cabinet)
Emergency escape bulb (black bulb hanging on the scanner)
Goggles (sitting on the counter)
Microswitches (in the tall wooden cabinet beyond the counter¹s end)
Position the subject (before goggles)
Press ³Align On² on the scanner itself
Move using ³Fast in², ³Slow out², et al.
Move in or out to put light beam cross just above brow
Rotate head as needed
Mark position (Press ³Landmark²)
Put goggles on
Slide cage down over subject¹s face
Press ³Advance to scan²

V. Subject environment and communication issues
Microphone to talk to subject has off-on switch
Away turns off, towards turns on
Volume control to subject from Mac is on Signa console
Radiobuttons control input (radio, stereo, VCR, Mac)
Off-on switch for goggles is in the computer room next door
Red button on top of the Signa console turns off the subject emergency out alarm
All discussion in control room is clearly audible to subject
Wouldn¹t a camera to the Mac be nice so they could see as well as hear?

VI. Now it¹s time to shim (can also do VII before VI if you prefer)

Signa:
List/Select protocol
Pick #12: isshim
Should default to an axial protocol (2nd line in 1st protocol)
Press ³Review Screen² to verify R/L is selected
Autoprescan
May have to hit cancel on right side of screen to clear prior displayed image if you get error message about ³looping failed to startŠ²
Manual prescan
Move peak to 4th of 5 vertical lines by typing e.g., ³-20 Enter² on keyboard
DO NOT HIT CANCEL
Push Backup button
Shim window:
Toggle auto<-> manual until Autoshim window appears
Autoshim window:
Check data path (may need to reset to disk of day, taped to top of monitor)
APDII window
Verify that APDII is set to store data on same disk as shim:
MENU File:Open database
Disk will be listed for verification
Scan set up
Wait until cued
Signa:
Scan
Wait for scan to reconstruct (viewable in the APD II window)
Autoshim:
Display/Analyze
Want line width <35 (<15 is even better)
Accept and Done (NOT OPTIONAL)

VII. Now it¹s time to do a quick sagittal scout to choose axial slices
Signa:
Cancel
New series (NOT NEW EXAM!!)
List/Select protocol
Pick ³Quick and Dirty scout² (top of first page)
Scan Ops
Scan
Use big round dials to adjust contrast and brightness
Display the scan you want to use to prescribe your ³high resolution² scan

VIII. Now acquire co-planar ³high resolution² scan
Signa:
Cancel
New Series
List/Sel protocol
27. Marco¹s SRC (2nd page) (or whatever protocol you use)
Axial co-planar resolution (or whatever one you want)
Scanning range:
Position cursor at bottom
Start
Roll cursor to other extreme
End
Use erase slice or adjust as needed
(Adjust moves the whole grid upward)
Make sure vertical line is centered on head to avoid wraparound (track ball)
Save screen
Review screen
Acquisition time (48 seconds should be displayed if you choose 26 slices)
Make sure you¹re using 4 NEX protocol to avoid 1 NEX stripes
Frequency
R/L to avoid shocking subject
Scan Ops
Autoprescan
Manual prescan
Backup
APDII
Scan set up
Wait for cue
Inform subject of impending din
Signa:
Scan

IX. Now acquire functional data
Signa:
Cancel
New series
View protocol (if next scan has been precanned, otherwise List/Select)
Choose appropriate scan (e.g.,7 Axial functional)
User CV¹s
Pick proper values
Scanning range (if functional has fewer slices than prescription)
Fall back
Select slices on sagittal as before
Review Screen
Frequency R/L
Scan ops
Autoprescan
Manual prescan
APD II:
Scan setup
Wait for cue
Signa:
TURN OFF MICROPHONE!!!!!
Scan
Coordinate scan start with stimulus
Note: 4X TR (about 10 seconds) of scan time is not protocol time


X. Log out of the scanner using the fMRI logger

XI. Liberate subject
Fast out (back to landmark let¹s you reinsert them without remarking)
Put everything away where it came from

Trouble shooting

Aborting a functional study:
Press ³Stop scan² a plastic button
APDII: ³Stop acquisition²
Cope with error messages
Scan setup
Wait for cue
Signa:
Scan


If you get message: ³Looping failed to startŠ² Press cancel on the right side of the screen


From original by: Roger Woods and Nancy Sicotte 7/7/98

Edited&posted to how2 page 7/7/98, R. Lee