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1. Log into the fMRI Logger
| A. |
On the Instascan terminal, open
Netscape |
| B. |
Enter your password in the logger
|
| C. |
Enter EXPERIMENTER NAME |
| D. |
RESEARCH PROTOCOL |
| E. |
Enter the exam number On
the right half of the Signa screen, press [list/select exam] Review
the most recently acquired exam number and increment by 1. |
| F. |
Enter the Signa ID (e.g. sch001
for Aftercare) |
| G. |
Select items from the other menus
appropriately |
| H. |
Do Safety and NeuroCog Screens |
| I. |
Push [Submit form] at the bottom |
| J. |
Record the HSPC# for the subject
on the consent form and in the logger box. |
| K. |
Make sure not to Quit Netscape
|
2. Consent the Subject
| A. |
Make sure the subject has completed
the metal screen form (with special attention to the questions
re: any history of having gotten any small fragments of metal
in their eyes and attention that all earrings should be removed
and all HOOP TYPE earrings/body piercing MUST be removed). |
| B. |
Have ALL subjects read and sign
(in BOTH places) the STRUCTURAL & FUNCTIONAL MRI consent form
(HSPC#97-01-007-02) |
| C. |
Leave the STRUCTURAL & FUNCTIONAL
MRI form consent form in the lab (for signature by one of the
MRI PI's), include HSPC# for the subject. |
3. Register the Subject on
the Signa
Before you place the subject in the scanner you must register them
on the signa:
| A. |
On the Signa console (left),
select [New exam]
You must fill out the sign-in screen BEFORE you can place a
subject in the scanner. Note: if you place the subject in the
scanner first and THEN come out to the console and hit [new
exam], the Signa will require that you remove the subject and
re-landmark them before you can continue. |
| B. |
Choose [New exam]; If the New
Exam menu is not present on the left, hit [cancel] |
| C. |
Required fields: Signa ID, Subject
Name, Sex, Age, Weight, Description of Scan. Note: All EPI data
inherit the subject ID information. Do not use spaces, "!",
";", or other fancy characters. Also enter the signa ID on the
logger. |
| D. |
Press [Accept] |
4. Position the Subject in
the Scanner
| A. |
Have subject put in earplugs
|
| B. |
Position subject with their shoulders
not quite touching the head cradle |
| C. |
Have subject put on headphones
(hanging on the scanner) |
| D. |
Add lateral padding to reduce
movement (may be in pt. comfort cabinet). Supplement with masking
tape on the forehead. |
| E. |
Give subject the emergency alarm
bulb (black bulb hanging on the scanner) |
| F. |
Give subject the Goggles (sitting
on the counter). Adjust the visual correction lenses as need. |
| G. |
Give subject the button box.
Have the subject position the box on his leg. |
| H. |
Position the subject (before
goggles) |
| I. |
Press [Align On] on the scanner
itself |
| J. |
Move using [Fast in],[Slow out],
et al. |
| K. |
Move in or out to put light beam
cross just above the subject’s eye brow |
| L. |
Rotate head as needed |
| M. |
Press [Landmark] to mark position
|
| N. |
Put goggles on |
| O. |
Slide cage down over subject's
face |
| P. |
Press [Advance to scan] |
5. Confirm that the Subject
is O.K.
| A. |
Microphone to talk to subject
has an off-on switch in the console room. |
| B. |
Radio buttons control input (radio,
stereo, VCR, Mac) |
| C. |
Off-on switch for goggles is
in the scan room |
| D. |
Red button on top of the little
white box on top of the Signa console turns off the subject
'emergency' alarm if they have used the squeeze ball. |
| E. |
If problems with goggle display,
try Display Goodies Control Panel on the Mac. |
6. Run a Sagittal Scout
| A. |
Press [new series] on Signa console,
then press [list/select protocol] |
| B. |
A list of pre-programmed protocols
will come up, choose #1. 2 min Sag |
| C. |
Press [view protocol], select
the Sagittal scout |
| D. |
Select Head 1st, Supine, Nasion
and Head Coil |
| E. |
Press [scan ops] and wait for
scanning screen |
| F. |
Press [scan] (no need for pre-scan).
Warn about the noise. |
| G. |
When complete, the image should
appear on the right Signa Monitor. Look at the scans. This is
your best chance to find clinical data. If you suspect trouble
call an expert. Try Dr. Bookheimer or Dr. Cohen; their number
are listed at the end of this manual. |
| H. |
Press [cancel] when scan complete
|
7. Check that EPI Data will
be Placed on Correct APD Disk
| A. |
Open the APD II window on Instascan
console
Use the left mouse button to select Instascan APD II from the
pull down menu |
| B. |
Select FILE ---->Open database
If the database id correct (i.e.,apd3 when
you want to be scanning to apd3), select [cancel] and move on
to scanning.
If not, modify acquisition disk name by changing
the path in the open-database-sub-window and press [OK] |
| C. |
Modify shim disk
Open an X window on the Instascan console and type ‘pwd’
If you are on the correct disk, continue with scanning, if not,
type ‘cd /apdXX’ |
| D. |
Press [Accept] |
8. Shimming the Magnet
| A. |
Press [new series] on Signa console,
then press [list/select protocol] |
| B. |
Choose #12. Shim/ShimmerSeq. |
| C. |
Press [view protocol], select
the shimmer protocol |
| D. |
Press Review Screen to make sure
scanning in R-L direction. If not, go to Acq. Time, and select
R/L. |
| E. |
Select [scan ops], gets you to
the scanning window |
| F. |
Select [auto pre-scan], which
will likely fail. |
| G. |
Press [manual pre-scan], and
check amplitude and center, press [backup].
Adjust by entering -# for left, # for right. If necessary try
-40 or 40 to start. |
| H. |
On the Instascan console, select
the APDII window |
| I. |
Press the Scan Set-Up button
(upper left), this can be done before pre-scan. |
| J. |
On the Signa console, press [scan]
I f "IP device allocation fail" message appears on the bottom
of the Signa console, press the [cancel] on the lower right
half of the screen. |
| K. |
When the scan is complete "Image
process complete" message appears on the bottom of APDII window,
press [cancel] on the Signa window. |
| L. |
In the X window, type ‘shimmer’
Check to see that latest [I/Q] scan is followed by a name based
on your signa ID and exam number, e.g. sch001_02556_XXX….
Accept all defaults by pressing return.
response from program: SHIM
PROCESSING OPTIONS
0) go process image data
1) display frequency map with 'xds'
2) display frequency histogram with 'xgraph'
3) start the manual shim controller
4) select a shim volume? no
5) more options
6) quit
Type Return or 0 (to process the shim data you just acquired)
Look at shimmer images.
|
| If you
have problems with shimming: Look
at Brainmapping's Shimming Page |
9. Acquire a High-Resolution
T2 Weighted Image
| A. |
On the Signa console, press [new
series] |
| B. |
Select [list/select protocol]
|
| C. |
Choose Basic Functional III (This
is protocol specific and may change per experimenter.) |
| D. |
Select [view protocol] |
| E. |
Choose High-Resolution Co-Planer
— Oblique (With oblique you can change the angle of acquisition
and select the AC-PC.) |
| F. |
Choose [scanning range] from
the bottom buttons and:
Select the mid-sagittal slice from the prior
image
Position cursor at bottom of the brain,
Press [start] on the Graphics Rx line
Roll cursor to other extreme to include whole
brain
Adjust to subjects AC-PC line with tract ball.
For help, see AC-PC
page.
Use [erase slice] or [adjust]; [adjust] moves
the whole grid upward
Make sure vertical line is centered on head
to avoid wraparound
Press [end]
Select [Save Screen] to save Rx
We are trying for 16 slices, 64 x 64 x 4 with
1 mm blanks |
| G. |
Press [Scan ops], [Auto pre-scan],
[manual pre-scan], [backup] |
| H. |
On the Instascan console, press
Scan Set-Up button on the APD II window |
| I. |
On the Signa console, press [scan]
|
| J. |
When scan is complete, press
[cancel] |
10. Acquire Functional EPI
Images
| A. |
On the Signa console, press [new
series] |
| B. |
Select [view protocol] |
| C. |
Choose an oblique EPI series |
| D. |
If you need to erase slices:
Move to the [scan range] window
Press the plus (crosshair) button on the Singa
console
Move cursor above the top or below the bottom
of the lines
Hit [erase slice] on the signa console
Press [end] |
| E. |
Select [User CV] button from
the bottom, set number of acquisition (SCAP=208) Need
to change User
CV? |
| F. |
Select [Scan Timing] button from
the bottom, set TR = 3000 ms, TE = 45 ms |
| G. |
Select [scan setup] button from
the bottom, set [water] |
| H. |
Frequency R/L to avoid shocking
subject |
| I. |
Select [Acq time] button from
the bottom and check matrix size (64 x128) |
| J. |
Select [Acq time] button from
the bottom and check matrix size (64 x128) |
| K. |
On the Instascan console, press
Scan Set-Up button on the APD II window |
| L. |
Set up Mac stimulus delivery
system
Note when starting EPI sequence, there are
4 junk scans to allow for magnetization. With TR=3, subtract
12 seconds from scan time and start the stimuli when the counter
reaches this time. |
| M. |
On the Signa console, press [scan]
|
| N. |
When scanning complete, press
[cancel] |
11. Acquire the T1 Structural
Scan
| A. |
On the Signa console, press [new
series] |
| B. |
Select [list/select protocol]
|
| C. |
Select msc 9minT1, (3D volume
scan) |
| D. |
Select [view protocol] |
| E. |
Choose the coronal scout (8sec)
|
| F. |
Select [scan ops], [auto pre-scan],
[scan] |
| G. |
When coronal scout complete,
select [view protocol] |
| H. |
Choose 3D T1 (9 min) |
| I. |
Select [scan range], from the
bottom buttons
On the far right Signa window, move the rectangle
to include the entire head from ear to ear. Change the scan
thickness to make the head smaller, if necessary, so that it
will fit into the box.
Leave 3 to 4 cm of blank on the top to combat
rap-around artifact.
When satisfied press [deposit] to lock box.
|
| J. |
Press [Scan ops], [Auto pre-scan],
[scan] |
12. Liberate the Subject
| |
Press [home] on the table movement
panel in the magnet room |
13. Extracting the Structural
Scans
| A. |
On the right Signa window, press
[utilities] |
| B. |
Select [mr tools], select [gshell
tools] and a window will appear on the left |
| C. |
Place cursor in the new window
|
| D. |
Type ‘ximg —i EexamnumberSall
—t —s, For example, type:
ximg —i
E2556Sall —t —s |
| E. |
Data will be written in 3Tmr.loni.ucla.edu/usr/g/insite/tmp
|
14. Log out of the fMRI
Logger
| |
Press Accept on the Netscape
window |
15. FTPing data from HBM
| A. |
Call 5-9142 to see if anyone
is on the scanner |
| B. |
For EPI images:
Log into porkpie.loni.ucla.edu
cd apd/#/anmr_scans/image
nice ftp hirisk (bin, prompt, mput) |
| C. |
For structural image:
From porkpie, log into ###.##.###.## as genesis
cd usr/g/insite/tmp
ftp hirisk (bin, prompt, mput)
remove images from Signa |
Emergency Numbers
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