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How to Learn MRI
An Illustrated Workbook
Exercise 3: Scanning a Human
Using a Protocol
Teaching Points:
• How to run a pre-programmed protocol.
• How to scan the knee.
1
Exercise 3: Scanning a Human
using a Protocol
You have mastered the art of scanning the phantom,
now it is time to move on to a live person. The main
goal of this exercise is to show you how to use a
protocol to scan a patient. What’s a protocol? A
protocol is a set of scans designed to image a specific
anatomy. Protocols usually consist of scans that show
different views and weightings. To begin this exercise,
you need to first recruit an MRI compatible friend that
has some knee pain and would like a free MR scan.
Exercise 3a—Patient Prep
The following should be done every time you scan a
volunteer/patient/research subject.
STEP 1: Have your Friend Sign the
Appropriate Forms
If you are scanning a patient for research you will have
to have them sign a consent form to participate in the
study as well as an IRB form. Here we are still scanning
for QA though, so they do not have to sign the IRB
forms this time. You should have them fill out the
safety screening form and proceed on to step 2.
STEP 2: Safety Screen your Friend
Begin safety screening your friend to see if they are MR
compatible by reviewing their signed safety screening
form (exercise 2b). It is important that you verbally
review each item on the form with them to make sure
that nothing was overlooked. Be sure that they have
no metal in them (i.e. aneurysm clips, pacemakers, or
any other metallic implanted device), that they do not
have any scraps of metal in their eyes, and that they
have removed all credit cards, cell phones, and metal,
before entering the magnet room.
STEP 3: Have your Friend Change
Clothes
Although this is only needed if your friend is wearing
clothes containing metal, it is a good habit to have them
change because sometimes there is metal that you are
not aware of. Give them a clean gown and direct them
to a changing room. Also instruct them where they can
safely leave their belongings during the scan, such as
credit cards, cell phone, jewlery, etc. Gold and sliver
wedding rings are ok to leave on beacuse they are nonmagnetic. Who wants to be responsible for loosing a
friend’s wedding ring?
STEP 4: Prepare the Scanner for your
Friend
Place a clean disposable sheet down on the scanner bed.
Also, put a new disposable pillowcase on the pillow and
leave it on the scanner bed.
STEP 5: Enter Relevant Information in
the Computer
Go to the computer and create a new patient. Again,
don’t worry about accession or patient number. Type
in your friend’s name and relevant information. Be
sure to include your friend’s weight . Weight is used to
determine the maximum RF exposure and if weight is
too low, FDA regulations may not allow sufficent RF to
scan. For operator, type in your initials, and for exam
description enter QA-Knee Exam.
2
Exercise 3b—Scanning the Knee
with a Protocol
STEP 1: Prepare the Knee Coil in the
Scanner Room
Fig 3.1 Knee coil positioning
Find the knee coil in the scanner room and place it on
the table approximately where your friend’s knee will
be when they are lying down. Be sure to orient it so that
the knee coil is on the same side of the table as will be
the knee you want to scan, with the patient going in feet
first.
STEP 2: Place your Friend on the
Scanner Table in the Home Position
Fig 3.2 Centering the patella
First, lower the table by using the down pedal as noted
in exercise 2a. Now, have your friend get on the table
and lay down with their ailing knee in the coil. The knee
should be placed such that the foot is pointing slightly
outward toward the wall of the room (figure 3.1). This
is so that the cruciate ligaments will be under tension
making them more visible in the image. Also, the inferior
edge of the patella should be in the center of the coil,
when the patient is laying down (figure 3.2). You will
have to support the opposite knee using foam padding,
and ensure that the knee in the coil will not move using
foam shims (figure 3.3).
Next, place a piece of foam under your friend’s feet to let
them rest comfortably while in the coil. Once everything
is set with the coil, ensure your patient’s comfort. Ask
them if they want a blanket and if they want the fan and
lights on in the scanner, and adjust accordingly. Be sure
to give them ear plugs. Give them the squeeze-ball so
they can let you know if they are in distress and want to
come out of the scanner.
Note: It is important during this step to get a sense of
the patient’s comfort within the scanner. Try and see by
their gestures and what they say, if they seem nervous.
This may mean that they are claustrophobic and need
more attention while in the scanner. Be comforting
during this stage, and let them know that you will be
close by.
Fig 3.3 Cushion support
3
Fig 3.4 Protocol menu
STEP 3: Landmark the Knee
Patient Protocols
Now raise the table up to the scanner level and plug
in the coil to the scanner. Turn the align-on lights and
landmark the knee in the center of the coil at the inferior
edge of the patella. Shut off the align on lights—this is
especially important if you are using a scanner with laser
alignment, since you don’t want your patient accidentally
looking into the laser as they advance to scan. Then
press advance to scan and leave the MRI room, shutting
the door behind you.
Site
Head
Neck/Cervical
Chest Thoracic
Upper Extremities
Abodomen/Lumbar
Pelvis
LowerExtremities
Other
Protocol
STEP4: Choose Protocol
Go back to the computer. For this exercise, we are going to be using a knee protocol. This is a series of scans that has
already been setup for you. On the computer screen, choose Lower Extremity from the protocol menu (figure 3.4) .
Choose the KNEE (ROUTINE) protocol from the popup menu (figure 3.5). A series of scans will appear in the Rx manager
window (figure 3.6). Protocols are generally setup with the following basic structure. First, there is a three-plane
localizer so you can see the anatomy in the three normal planes. Next, are the large FOV images, and finally the smaller
FOV images. Also, usually the most important sequences are put first in the protocol, since patients usually tire as the
scan wears on, and at any moment can demand to be taken out of the scanner.
Be sure to shut off automatic scan sending to the central computer before scanning by clicking the Scan Modes on the
Rx Manager and Turning off Auto Transfer.
Patient Information
Patient Protocols
Patient Protocols
Site
Accession 0000
Number
Patient
Position Supine
Head
Patient ID 0000
Coil
Chest Thoracic
Upper Extremities
Auto Start
Rx Manager
Patient
Entry Feet First
Neck/Cervical
Patient Name MR PLASTIC
HEAD
Series MY THIRD SCAN
Description
Abodomen/Lumbar
Protocols
L1-ANKLE (routine) 4.07
L2 - FOOT (routine) 4.07
L3 - FOOT (
) 4.07
Full
L4 - KNEE (routine)
4.07
Info
L5 - MRV LEGS - DR.P 4.06
L6 - KNEE (ROUTINE)
L7 - BOLUS CHASE 9.07
L8 - BOLUS CHASE 10.07
L9 - TRICKS
Series
Plane 3-PLANE
Pelvis
LowerExtremities
Protocol
Pulse Seq Gradient Echo
1.3
PLANE LOCImaging Seq, Fast
Other
Options
2. Calibration
Psd
Name
3. AXL PD
4. SAG PD FREQ
A/P
Protocol
5. SAG PD FSAT FREQ A/P
6. COR PD FSAT FREQ R/L
7. COR PD FREQ R/L
Mode 2D
Grad
Mode
HIS/RIS
Scan Modes
Gating Control
New Series
End Exam
State # Series Description
SCND 1
SCND 2
SCND 3
SCND 4
SCND 5
SCND 6
ACT 7
3 PLANE LOC
Calibration
AXL PD
SAG PD FREQ
SAG PD FSAT
COR PD FSAT
COR PD FREQ
Selection
site/lower/KNEE(ROUTINE)/
View Edit
Accept
Backup
Download
Save as Rx Protocol
Fig 3.5 Protocol Pop-up menu
Fig 3.6 Rx Manager window
4
STEP 5: Three-Plane Localizer
We will start with the 3-plane localizer. Before choosing the localizer, be sure that the current coil is the knee coil. If
not change the coil to the currently connected coil and Apply All. Select the 3-plane from the RX manager and hit
View Edit. Then Save Series, Download and Scan.
During the exam, intermittently talk to your friend through the microphone to open up a line of contact with them.
Note: You can adjust the volume on the speaker and the microphone, so you can hear the patient better. Just don’t turn this
too low though, or else you won’t hear the patient. Also, sometimes during the scan, the RF noises come out very loud on the
speaker. There is usually a small pad you can put over the speaker to muffle these noises. Before each scan, you should make
a habit of telling the patient over the microphone, what the scan is, and what its duration will be.
You have to wait for the three-plane to finish before you can go on to graphically prescribe the rest of the scans.
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Disk 32% full
The patient comfort level has
returned to normal
Patient Information
Patient Protocols
Site
Accession 0000
Number
Patient
Position
Patient ID 0000
Patient
Entry
Head
HD TRknee PA
Coil
Chest Thoracic
Series
Description
Upper Extremities
Auto Start
3 PLANE LOC
Abodomen/Lumbar
Plane
iLinq
Axial
LowerExtremities
Imaging
Options
Protocol
Sent: 4236/10
(DYNACAD61)
Rx Manager
Scan Modes
New Series
# of TE(s)
per scan
Gating Control
TE2
Additional Parameters
TR
State # Series Description
Max
1.0
2.0
1.0
Inv. Time
TI2
Flip Angle
Graphic RX
1.5
6000.0
0
100000
50
4000
1
90
0.0
Freq DIR Unswap
256
Phase
126
Flow Comp
Direction
NEX
1.00
Shim
Users CVs
Screen
1.00
Contrast
View Edit
Download
Save as Rx Protocol
Auto Scan
Auto Step
Save Series
# of Acqs.: 1
dB/dt: First Level
SAR: First Level
Research
Operations...
Fig 3.7 Three plane localizer selection
ml
Amf
Agent
Scanning Range
Slice
Thickness:
250.0
250.0
24.0
Min.
Max
9
48
3.0
S/I
Max # of slices: 32
Rel. SNR(%): 100
(Drive FPS:< 1
P/A Center
0.0
170.0
A10.0
End
1.0
1.0
1.0
9
9
9
# of
Slices:
Spacing
L/R Center
Start
Actual
End
Rx Scan Time 0:22
Auto
Phase Correct
Acqs Before
Pause
FOV
Bandwidth2
Image
Enhance
1.0
5.0
2.0
OFF
Aquisition Timing
Freq
Phase
FOV
Echo Train
Length
Bandwidth
HIS/RIS
Protocol KNEE (routine) 4.07/1
Min.
1.5
TE
End Exam
3 PLANE LOC
AXL PD
SAG PD FSAT
SAG PD FREQ
COR PD FSAT
COR PD FREQ
1
Seq. Fast
Psd Name
Full
Info
Scan Timing
2D
Grad
Mode
Pulse Seq Gradient Echo
Other
Removed
Series 4234/9
Mode
3-plane
Pelvis
4237/4/26
28/28
ACT
NEW
NEW
NEW
NEW
NEW
Feet First
Neck/Cervical
Patient Name MY FRIEND
Idle
Supine
Est. SAR: 0.6
Peak SAR: 1.6
Table
Delta
Reset Values
Total # slices: 32
Exam Series 0000, Series 1 - scanned
Scan Time 0:22
dB/dt: 100%
0.00
dB/dt: First Level
SAR: First Level
Scan
Auto Prescan
Manual Prescan
Prep Scan
5
Fig 3.8 Three plane localizer
STEP 6—Calibration Scan
Some knee protocols have a calibration scan that is part
of the routine exam. The purpose of this scan is twofold. One is to provide a homogenous image over all
coils. Since one MR image is produced from the various
coil images taken from the coil array, the final image is
sensitive to the proximity of the coils to the anatomy
they are scanning. Each coil contributes a coil image
that has high intensity in locations closer to the coil and
less intensity in locations further from the coil. When the
coil images are assembled into the final image, these
variations can carry through. The calibration helps to
smooth out these variations over all coils to provide a
more homogenous image. The second purpose of the
calibration scan is to provide coil sensitivity maps that
can be used for parallel imaging algorithms such as GE’s
ASSET (which is an implementation of SENSE).
To setup the calibration scan, highlight it in the RX
manager and select View Edit. It should open in the
graphic RX screen, but if it doesn’t click on the graphic
RX button. The goal for this scan is to prescribe the slices
to be far above and below the field of view. Do this
by pulling down the slices, extending them, and then
pushing them way up beyond the field of view. Do the
same for the bottom part of the slices. You only need to
do this in one plane—the others will adjust accordingly.
Now click save series, download, and scan, begin the
calibration scan.
Fig 3.9 Calibration scan
6
Fig 3.10 Axial pd
STEP 7—Axial Proton Density Scan
Once the calibration scan is done, you can then go to
the Rx manager and View Edit the axial PD scan. Adjust
the localizer to 3 slices in the graphic Rx window (fig
3.11)
Once the slices are arranged for the axial scan on the
planes in the screen, click Save series, Download, and
Scan. Remember to tell your patient the length of the
scan! Go on to Step 8 while the current scan is running.
Fig 3.11 Graphic Rx for axial pd
X
Graphic Rx
Erase Selected
Erase All
Reset
Center
Fallback
to SO
Loc Ref
Lines
Report
Cursor
Update All
Keep W/L
2
3
1
3
1
2
Display
Normal
1.0
ZOOM
Copy Rx...
Select Series
Select image
SAT
...
Scan Plane: Oblique
Graphic Rx
*
FOV: 14.0
Localized image - 2 , 5
Phase FOV
Fat
Accel.
Bar:
Slice
Water
Freq DIR: A/P
Acqs Before
Shim FOV:
Pause:
Shime Vol
TR: 3325.0
Numbe of 1
Radial Slices
CW
CCW
Start:
R76.7
P5.8
I37.8
End:
R70.0
P9.4
S36.8
Rx Scan Time 3:13
# of Acqs.: 1
dB/dt: First Level
SAR: First Level
Research
Operations...
Minimum TR: 134.0
Hide Shim
Partial Radial 0
Spacing
Save Series
0.0
Spacing
SPECIAL
Radial
Direction
3.0
Thickness:
Fat Classic
Max # of slices: 3
# of
Slices
3
Rel. SNR(%): 100
(Drive FPS:< 1
Total # slices: 3
Est. SAR: 0.0
Peak SAR: 2.8
Avg. Coil SAR: 1.1
dB/dt: First Level
SAR: First Level
Reset Values
Exam Series 0000, Series 1 - prescanning.
Scan Time 5:36
dB/dt: 100%
Scan
Auto Prescan
Manual Prescan
Prep Scan
7
Number of Acquisitions and Why it
Matters
The number of acquisitions plays an important role in
scan length—it can sometimes double or triple the scan
time in trade for extra slices, if you are not careful. You
can see the number of acquisitions at the bottom of
the screen near the save series button (figure 3.12). To
the right of the # of Acquisitions, you will see two other
numbers: Max # of Slices and Total # of Slices. Max #
of slices tells you how many slices you are allowed per
acquisition with your current scan parameters. Total #
of Slices tells you how many slices you currently have
prescribed. The number of acquisitions is dependent
upon the number of slices you are taking. Therefore, if
Total # of Slices > Max # of slices, then you will have more
than one acquisition.
It can be very frustrating if you really want 30 slices, but
only have a maximum number of 29 slices allowed. You
don’t want to make your patient stay in the scanner for
double the scan time, but it is essential to get that extra
slice. What can you do to fix it? One quick way is to bump
up the TR by a small amount, so that you don’t really
change any of the weighting parameters, but you have
a longer repetition time. Let’s look at this for a Spin Echo
Sequence.
Fig 3.12 Number of acquisitions
Rx Scan Time 3:13
Save Series
In a spin echo you have the following:
90 0 pulse
Echo
TE
Where in the above, TE is time to echo and TR is time to
repetition. During TR is when the slices are collected.
Therefore, you can see that a longer TR will allow for
more slices! So, if you need a few more slices, just
bump up the TR by a tiny bit to keep your scan at one
acquisition.
Total # slices: 26
Fig 3.13 Spin echo pulse sequence
TR
1800 pulse
# of Acqs.: 1
Max # of slices: 28
8
STEP 8—Prepare the final four scans and
auto-scan your friend.
Time is of the essence when working on the MRI scanner
both for your patient’s benefit and because of the busy
hospital schedule. Therefore, normally when scanning a
protocol, after getting through the first setup scans (i.e.
3-plane and calibration), while your first scan is running,
you can prescribe the rest of the scans and then click
auto-scan. Auto-scan will automatically and continuously
run the rest of the scans, so there is no down time inbetween scans.
We will setup for auto-scan while the axial-pd scan is
running. Go to the RX manager and click on the sag PD
freq. Click View Edit and go to the graphic rx. Prescribe
the slices for the saggital orientation by moving the slices
on the views to match those in figure 3.14. When you are
all set, click Save series.
What’s the difference between PD Freq and
PD FATSAT?
These are different sequences that are used to
highlight different portions of the anatomy. PD
(Proton Density) is just as its name describes—a
sequence that utilizes the ‘proton density’ of
hydrogen atoms in tissues. Fluids have the highest
Proton Density. PD FATSAT is a PD weighted
sequence that suppresses the fat signal. This is
done by giving a selective RF pulse to fat protons
just before an imaging sequence. Therefore,
the fat protons cannot recover to their normal
magnetization and their signal is suppressed during
the imaging scan.
Fig 3.14 Graphic RX for saggital pd
X
Graphic Rx
3
1
Erase Selected
Erase All
Reset
Center
Fallback
to SO
Loc Ref
Lines
Report
Cursor
Update All
Keep W/L
Display
Normal
1.0
2
ZOOM
Copy Rx...
Select Series
Select image
SAT
Graphic Rx
Scan Plane: Oblique
*
FOV: 16.0
Localized image - 2 , 14
Phase FOV
Fat
Accel.
Bar:
Slice
Water
Freq DIR: A/P
Acqs Before
Pause:
TR: 4825.0
Numbe of 1
Radial Slices
Minimum TR: 217.0
Hide Shim
Start:
R112.3
P7.4
S0.2
End:
R25.5
A22.7
I2.4
Rx Scan Time 4:15
# of Acqs.: 1
dB/dt: First Level
SAR: First Level
Max # of slices: 3
# of
Slices
2
CW
CCW
Partial Radial 0
Spacing
Research
Operations...
0.0
SPECIAL
Spacing
Shim FOV:
Save Series
4.0
Thickness:
Fat Classic
Shime Vol
Radial
Direction
3
1
...
3
Rel. SNR(%): 100
(Drive FPS:< 1
Total # slices: 3
Est. SAR: 0.1
Peak SAR: 4.8
Avg. Coil SAR: 1.8
dB/dt: First Level
SAR: First Level
Reset Values
Exam Series 0000, Series 1 - prescanning.
Scan Time 7:57
dB/dt: 100%
Scan
Auto Prescan
Manual Prescan
Prep Scan
State # Series Description
That was simple enough, now lets move on to
the sag PD fatsat. Click View Edit, and go to the
graphic RX. In clinical scans, it is important that
within the same view, you get the same slices
for different scan types. To do this, you want
the same slices that you already choose for
the Sag PD Freq. Click on Copy Rx (figure 3.15)
and choose the Sag PD Freq RX to copy. The
slices will appear on the screen as you already
prescribed them for the previous scan. Click
save series.
3 PLANE
LOC all of your
Now,ACT
you have
prescribed
NEW
AXL PD
scans.
Click on
the Auto Scan box at the
NEW
SAG PD FSAT
bottom
RXPD
manager
NEWof the
SAG
FREQ (figure 3.16).
YourNEW
scans will
now
continue
to run until
COR PD FSAT
NEW
COR
PD
FREQ
they are finished. You do not have to
press anything. Just continue to watch
the patient and update them on the
scan timing before each scan starts.
Fig 3.16 Auto-scan button
View Edit
Now, let’s go on to prescribe the coronal freq,
and coronal fatsat. You are going to do exactly
what you did for the saggital views, only
prescribe different slices on the first coronal
scan, to match the coronal orientation (figure
3.15) and then copy those to the second
coronal scan. When you prescribe each scan,
remember to save the series.
Download
Save as Rx Protocol
Auto Scan
Auto Step
Fig 3.15 Graphic Rx for coronal pd
X
2
Graphic Rx
Erase Selected
Erase All
Reset
Center
Fallback
to SO
Loc Ref
Lines
Report
Cursor
Update All
Keep W/L
Display
Normal
3
1
1.0
ZOOM
Copy Rx...
Select Series
Select image
SAT
...
Graphic Rx
Scan Plane: Oblique
*
Phase FOV
Fat
Accel.
Bar:
Slice
Spacing
Water
Freq DIR: R/L
Acqs Before
Pause:
TR: 3325.0
Numbe of 1
Radial Slices
Minimum TR: 134.0
Hide Shim
2
CW
CCW
Partial Radial 0
Spacing
Start:
R81.6
A44.2
0.0
End:
R64.9
P28.9
0.0
Rx Scan Time 3:13
# of Acqs.: 1
dB/dt: First Level
SAR: First Level
Research
Operations...
0.0
SPECIAL
Shim FOV:
Save Series
6.0
Thickness:
Fat Classic
Shime Vol
Radial
Direction
3
1
FOV: 14.0
Localized image - 2 , 5
Max # of slices: 3
# of
Slices
3
Rel. SNR(%): 200
(Drive FPS:< 1
Total # slices: 3
Est. SAR: 0.0
Peak SAR: 2.8
Avg. Coil SAR: 1.1
dB/dt: First Level
SAR: First Level
Reset Values
Exam Series 0000, Series 1 - prescanning.
Scan Time 7:57
dB/dt: 100%
Scan
Auto Prescan
Manual Prescan
Prep Scan
9
10
STEP 8—Take your friend out of the scanner
After the last scan has finished, go into the MR room and press the home button on the scanner to
bring your friend out of the magnet. Open the coil so they can take their knee out of it, unplug the
coil, and lower the table so they can get down. Clean up the room and restore it back to its original
state.
STEP 9—Show your friend the images on the screen and burn them a CD
Your friend was very generous to let you test out your MR skills on them for the first time. So it’s time
to give them something in return. First, open up their scans in the browser window and walk them
through their anatomy. Second burn them a CD so they can take the images home with them. To burn
a CD, in the browser window click CD/DVD. Insert a blank CD into the CD drive of the computer. Go
to select the series you want to add on the list of scans. You can only select one series at a time. After
you select the series you want, open up the CD/DVD burner window, by clicking the CD/DVD button
on the right panel of the browser. In the CD/DVD burner window, hit Add Series. Do this for all of the
series that you want to add to the CD, and then click Copy.
This will burn all of the images to the CD in a dicom format. The burner also automatically adds a
dicom viewer to the disk so your friend can view the images on any computer.
CD/DVD Composer
Add Exam
Selected Drive:
_
Clear
Add Series
DICOM CD 1
Ex: 0000
+
Se: 1
+
Se: 2
Se: 3
Application: Selection: Remove Sort: Network Archive: PPS Queue Utilities Services Messages
+
Examinations :
Exam
| Name
4238/MR55|
| MR PLASTIC
| Date
Exam no 4238. Mar 04 09, MR PLASTIC
| Description | Mod| PPS | A |
| Mar 04 09 | QA
| MR | -
Ser
| Type
1
2
| N |
| Imgs
| PROSP |
| PROSP |
| Description| Mod| PPS | Manf |
32 | MY FIRST S | MR | 32 | MY SECOND | MR | -
| GEMS |
| GEMS |
Add/Sub
CD/DVD
CIET
Clariview
Data Export
Edit Patient
Film Composer
Functool
Used Space: 8.12 MB
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Series no 1 - PROSP MY FIRST SCAN
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FOV
(cm)
24x24
24x24
24x24
24x24
24x24
24x24
24x24
24x24
24x24
24x24
24x24
24x24
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2 series
Matrix | NEX
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128x128 | 1.00
128x128 | 1.00
128x128 | 1.00
128x128 | 1.00
128x128 | 1.00
128x128 | 1.00
128x128 | 1.00
128x128 | 1.00
128x128 | 1.00
128x128 | 1.00
128x128 | 1.00
128x128 | 1.00
Eject
| Archive |
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No
No
No
No
No
No
No
No
No
No
No
No
Options
Quit
IVI
Mini Viewer
PACC
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ProtoCopy
ProtoExchange
Reformat
SR Viewer
SWIFT
Viewer
32 images
Fig 3.17 CD/DVD window
11
You’re done now! Congratulations on your first successful human scan! You are now ready for more
interesting anatomies! Next we will go on to the brain!
Fig 3.17 Coronal Fatsat
Fig 3.18 Coronal freq
Fig 3.19 Saggital Fatsat
Fig 3.20 Saggital Fatsat