Revision Date: 3/6/2025

Siemens Prisma 3T MRI Scanner

User Guide

Ahmanson-Lovelace Brain Mapping Center

University of California, Los Angeles
 Revision Date: 3/6/2025

BMC Contacts ............................................................................................................................... 1

Scanner Operation ........................................................................................................................ 2
• How to do a “Restart System” Reboot .................................................................... 2
• How to Turn Off the MRI Scanner/Computer (Full Shutdown)............................. 3
• How to Turn on the MRI Scanner/Computer ......................................................... 3
• MR Scanner Error Save Log ................................................................................... 4
Re-import DICOM Data .............................................................................................................. 5
• How to Map a Dicom Network Folder on the Scanner Console to Re-import a
Scan ......................................................................................................................... 5
Export and Save Raw Data Files (.RDA and TWIX Raw) ....................................................... 8
• How to Map a Non-Dicom Network Folder on the Scanner Console .................... 8
• How to Create a Spectroscopy .RDA File .............................................................. 8
• How to Transfer Raw Data Using TWIX Software .............................................. 10
How to Burn a CD/DVD From the Scanner Console .............................................................. 11
Prisma Cleanup Procedures....................................................................................................... 12
• General Cleanup Guidelines ................................................................................. 12
Squeeze Ball/Button Alarm ........................................................................................................ 13
• What to do when the Squeeze Ball/Button Alarm Goes Off ................................ 13
• Reset the Table ...................................................................................................... 13
How to Run the ABCD Phantom QA........................................................................................ 14
• Setting up the Phantom ......................................................................................... 14
• Register the Phantom ............................................................................................ 15
• Registration Pictures ............................................................................................. 15
• Running Scans ...................................................................................................... 17
How to Trigger Test Stimuli/Tasks ........................................................................................... 18
• Setting up the Phantom ......................................................................................... 18
• Register Phantom .................................................................................................. 18
• Click for registration Pictures ............................................................................... 18
• Running Scans ...................................................................................................... 18
Quality Assurance: How to Check Your Scan Data ................................................................ 19
• Check Your Localizer ........................................................................................... 19
• Verify Full Coverage of the Brain ........................................................................ 19
• Check for Dropout in Your Slices ........................................................................ 21
• Check to Make Sure Your Head Coils Are Attached ........................................... 21
• Check That the Table is at Isocenter ..................................................................... 21
Coil Warnings - Protocol Was Fixed......................................................................................... 22
• Main Reasons for Coil Warnings .......................................................................... 22
• Anterior or Posterior Protocol Fixed Warning Messages ..................................... 22
• Coil Issue Resolution ............................................................................................ 22
• Wrong Coil Protocol Fixed Warning Messages ................................................... 22
Prisma XA30 Software Bugs ...................................................................................................... 23
• AP/PA Copy Reference Issue ............................................................................... 23
Prisma XA30 Scanner Warnings/Messages/Errors ................................................................. 24
• Adjustment Measurement Was Aborted ............................................................... 24
• Gradient Power Amplifier Warning...................................................................... 24
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• Participant Registration Errors .............................................................................. 25

Preparation Scans (aka dummy time)....................................................................................... 26
• Preparation Scans (dummy time) for CMRR/HCP Multiband Sequences ........... 26
• Preparation Scans (dummy time) for Regular BOLD Sequences ......................... 26
• Slice Timing for BOLD Sequences and other BOLD Questions ......................... 26
• How to Manually Trigger Stimuli......................................................................... 27
Current Designs Button Box and Trigger Setup (FORP 932) ................................................ 28
• Device Selection ................................................................................................... 28
• Response Settings ................................................................................................. 28
• Troubleshooting .................................................................................................... 29
Siemens Talk Box Setup ............................................................................................................. 31
Optoacoustics Headphone and Microphone Setup .................................................................. 32
• Positioning the Participant .................................................................................... 32
• Setting up the Opto Console ................................................................................. 32
• Using Active Noise Cancellation .......................................................................... 33
• Troubleshooting Tips ............................................................................................ 34
BOLDScreen LCD ...................................................................................................................... 36
• Specifications ........................................................................................................ 36
• Turning on the LCD .............................................................................................. 36
• Positioning the Participant .................................................................................... 36
• Troubleshooting Tips ............................................................................................ 37
How to use E-Prime with the Desktop Computer and LCD ................................................... 38
• Duplicate/Mirrored Display with E-Prime............................................................ 38
• Extended Display with E-Prime............................................................................ 38
• Switching from Extended Display to Duplicate/Mirrored Display ...................... 38
Siemens Physiological Device Setup .......................................................................................... 39
• ECG/Respiratory Setup ......................................................................................... 39
• Pulse Setup ............................................................................................................ 39
How to Use the MR Camera ...................................................................................................... 40
• Quick Overview .................................................................................................... 40
• Equipment ............................................................................................................. 40
• Camera Setup ........................................................................................................ 40
• Participant Setup ................................................................................................... 40
• Camera Cleanup .................................................................................................... 41
• Troubleshooting Tips ............................................................................................ 41
Equipment Manuals.................................................................................................................... 42
• Current Designs Button Box and Trigger Manual - Forp 932 .............................. 42
• Optoacoustics Manual ........................................................................................... 42
• MRI Safety Manual............................................................................................... 42
Movie List .................................................................................................................................... 43
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BMC Contacts

1. Ludmila Budilo Building Manager x52699

2. Mary Susselman PET/MRI Tech x64291
3. Trent Thixton Lead MRI Tech x59217
4. Dr. Roger Woods Center Director x44057
5. BMC Techs BMCTechs@[Link] (424) 652-6290
6. BMC Emergency ONLY Line: 323-999-1593

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Scanner Operation

How to do a “Restart System” Reboot

This type of reboot clears most errors and takes approximately 6 minutes

1. Make sure the scanner bed is at the home position (all the way up and all the way out)
2. If a coil is on the table, all elements should be plugged in
3. Go to the home screen and you will see a Power Button icon at the bottom right of screen
4. Click on “Restart System”

5. You’ll get a pop-up box, click “Restart” - the computer screen will stay on for a bit &
then turn black.

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How to Turn Off the MRI Scanner/Computer (Full Shutdown)

This type of full shutdown takes approximately 20 minutes – try this method if a "Restart” reboot
did not clear the issue.

1. Make sure the scanner bed is at the home position (all the way up and all the way out)
2. If a coil is on the table, all elements should be plugged in OR all unplugged
3. Go to the home screen and you will see a Power Button icon at the bottom right of screen
4. Click “Shut down system”
5. You’ll see a pop-up box, Click “Shut down”

6. It will take approximately 6 minutes before you’ll hear a clunk sound AND the LCD
monitor ON the scanner will turn black
7. Note – the console computer will still look like it is on - you will see the mouse on a
black screen
8. Press the blue “system off” button on the Siemens scanner control box located on the
wall next to the MR Scanner window

9. Wait 5min before turning the system back on

How to Turn on the MRI Scanner/Computer

1. You must first press the “system on” button on the Siemens scanner control box located
on the wall next to the MR Scanner window

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2. It will take approximately 10 minutes for the system to completely boot up

3. After a successful reboot you will hear 3 small beeps and the LCD will come back on
4. If the console computer does not come back online, you may need to do a “hard off” on
the Prisma Scanner console computer just to the left of the operator’s console. Then turn
it back on.

MR Scanner Error Save Log

1. Only do this if an engineer or tech tells you to make an MR save log.
2. This log entry helps the Siemens engineer isolate the scanner problem and expedite the
system repair. To make a MR Save Log entry, you must do the following:
• At the top of the screen – look to the right and find the “cog wheel” icon & click
it
• Click on “SaveLog””
o You will see a box pop up, fill in the requested information about the
error as best as possible
o You must wait until the black pop box with script closes before you can
proceed to reboot, scan etc
3. Please email BMCTechs@[Link] with details of the problem

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Re-import DICOM Data

How to Map a Dicom Network Folder on the Scanner Console to Re-import a Scan

1. Click control and click escape key. You should see the PC computer menu/dashboard.
• If you do not see the PC computer menu/dashboard, you will need to access it by
holding 3 buttons at once: the Tab, Delete and Send buttons. This toggles you into PC
access mode.

2. Click “This PC”

3. It is possible that the BMC Techs have already logged into the PC side & to Dicom7. If
so, you’ll see one or both drives are ready to go & you can proceed to Step 5 below.
4. If the drives are not already logged in, you will need to map a drive
• After accessing PC side of computer as described above, Right Click on "This
PC” and then click, “Map Network Drive”
• When the box pops up choose an available drive, Z drive is the default, if it is
being used choose the next available letter (i.e. Y, X, W etc) – DO NOT use drive
M
• Under “Folder” choose the path \\[Link]\DICOM7 (or whichever dicom you
are trying to access dicom7 is the current data directory)
• Click on “Connect using different credentials" then click finish
• Log in with your NRB credentials (don't forget the \bmap) before your name
• bmap\username
• Password
5. Navigate to your group folder and choose the participant folder that you want to import
6. Right click on the folder and click Copy
7. Now, open up Computer – then, Med System C: Temp/_User_Data (select a temp folder
or create a new one)
8. Paste the copied files into the Temp folder

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9. Now go to the Patient Browser – Look to the right of the screen and click “Import”

10. A box pops up, select from the left side of box: Medsystem(C):-TEMP-_Userdata

11. Select your Temp folder (i.e. C: Temp/_User_Data/Woods)

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12. Select scan folder that you want to import & click “Import”

13. This loads the images/sequence to the patient browser

14. You can now export raw data or import sequences into MR view and go

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Export and Save Raw Data Files (.RDA and TWIX Raw)

How to Map a Non-Dicom Network Folder on the Scanner Console

1. Click control and click escape key. You should see the PC computer menu/dashboard.
• If you do not see the PC computer menu/dashboard, you will need to access it by
holding 3 buttons at once: the Tab, Delete and Send buttons. This toggles you into
PC access mode.

2. Click “This PC”

3. It is possible that the BMC Techs have already logged into the PC side & to MRIFile. If
so, you’ll see one or both drives are ready to go & you can proceed to Step 5 below.
4. If the drives are not already logged in, you will need to map a drive
o After accessing PC side of computer as described above, Right Click on "This
PC” and then click, “Map Network Drive”.
o When the box pops up choose an available drive, Z drive is the default, if it is
being used choose the next available letter (i.e. Y, X, W etc) – DO NOT use drive
M
o Under “Folder” choose the path \\[Link]\MRIFILE or enter the path name
manually if this is your first time mapping the drive
o Click on “Connect using different credentials" then click finish
o Log in with your NRB credentials (don't forget the \bmap) before your name
▪ bmap\username
▪ Password
5. Choose your group folder
6. This drive will allow you to save raw data etc into the network folder instead of on a usb
drive
7. When you are done close the non-dicom folder windows
8. If your non-dicom NRB account is not working – save the raw data on the C: Drive in
Temp/_UserData/LabName/ParticipantID folder
9. Note – please remember to delete saved data from your non-dicom folder and
scanner console temp folder as soon as possible – data is not meant to stay in these
folders indefinitely as there is limited space

How to Create a Spectroscopy .RDA File

1. Go to Patient Browser
2. Select MRS sequence

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3. At top of the screen, click “Open with MR Spectro”

4. While in MR Spectro application, look to left of the screen and select “Raw-Export
Selected”

5. You’ll see a Pop-Up box where you will select the folder to save too. Typically this is:
MedSystem C: - Temp – _User_data – BMCGroup OR you can save directly to your
MRIFile folder.

6. Your group should have their own temp folder & Non-dicom MRIFile folder setup prior
to this step
7. Then click "OK”
8. This data does not get overwritten as long as you have the scan data

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9. Data needs to be manually deleted from the temp folder and non-dicom folder as
soon as possible due to limited space.

How to Transfer Raw Data Using TWIX Software

1. Click control and click escape key. You should see the PC computer menu/dashboard.
o If you do not see the PC computer menu/dashboard, you will need to access it by
holding 3 buttons at once: the Tab, Delete and Send buttons. This toggles you into
PC access mode.

2. Open the Command Prompt

3. Type: TWIX - then press enter
4. All raw data will be listed
5. Select the raw data you wish to save by choosing the correct participant ID and
sequence(s)
6. Hold down control if selecting multiple files then right click on one and choose the top
option "copy total raid file"
7. Copy and paste these files into your non-dicom folder (preferred method) or to a temp
folder on the C drive (typically your group will have their own temp folder)
o Temp files can then be copied to a non-dicom folder
8. Data needs to be manually deleted from the temp folder and non-dicom folders as
soon as possible due to limited hard drive space.

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How to Burn a CD/DVD From the Scanner Console

1. Get USB key from upper left cabinet above Techs desk in the Prisma Control room
2. Unlock one of the USB drives on the Prisma tower computer to the left of the Prisma
operator’s console
3. Plug the external CD/DVD drive into the open USB port you just unlocked and insert a
blank DVD or CD
o Disks that can be used to burn data:
▪ DVD’s
• 8x DVD + or -R
• 8x DVD + RW
• 6x DVD – RW
▪ CD’s
• 24x CD-R
• 24x CD-RW
4. Open the patient browser on the console once the blank CD/DVD has loaded. You may
need multiple CD’s or DVD’s depending on the size of your dataset
5. Highlight the participant's parent level folder for the whole scan or any individual
sequences you want to burn (use CTRL to highlight multiple seq at once)
o Must burn all sequences in one setting – you cannot add more later as the disk
gets finalized
6. Near the top of the screen, select “Export”, this will open up another field
7. Select “Optical disk”
8. Input at least 3 digits in the field “Media label”
9. Select “Include image viewer on disk”
10. "Action” should be set to “Burn”
11. Click “Export”
12. When the disc is done burning, it will automatically eject the disc from the drive
13. Put everything back the way you found it

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Prisma Cleanup Procedures

General Cleanup Guidelines

CLEAN ANYTHING THAT YOU OR THE PARTICIPANT TOUCHED
1. Put the head coil away in the coil cabinet with the top attached
2. All cables should be untangled and placed on the appropriate hooks completely off the
ground to prevent being stepped on (please see below pictures)
3. All equipment (headphones, button box, squeeze ball, coil etc) that you used should be
wiped down with Saniwipes to disinfect
4. The button response box should be disconnected and store in the appropriately labelled
drawer
5. The squeeze ball should be coiled at the end of the bed
6. One sandbag should be left on the white cart
7. The white head cushion should be left on the bed or cart
8. The Opto box should be turned off at back of box
9. The Opto audio cable should be unattached from audio source and coiled up in the bungie
hook
10. The trigger, LCD HMDI and EPI cables should be coiled and stored
11. The LCD switch box should be turned off
12. Everything is labelled for your convenience
13. Note: the top of the cart is a suitable place to set the top of the coil and/or mirror when
you are setting up your participant

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Squeeze Ball/Button Alarm

What to do when the Squeeze Ball/Button Alarm Goes Off

1. Stop the scanner using the mouse and clicking the stop icon in the lower left on the
console screen
2. To clear the alarm, press the talk button on the intercom associated with the squeeze ball
- Siemens (#2 talk or #3 alarm
3. Talk to your participant through the intercom system associated with the headphones you
gave your participant (opto or siemens)

4. DO NOT press the “Stop” button (#1) on the Siemens Talk Box
5. If you press this, you will need to reset the table
6. To reset the table follow the below instructions

Reset the Table

1. Press the (#7) button on the side of the intercom box
2. Go into the scanner room and simultaneously press the Table Up and Table Down button

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How to Run the ABCD Phantom QA

The ABCD phantom should be run at least once per week. The full version takes 29min and the
quick version takes 16min.

Setting up the Phantom

1. Place the spherical ABCD phantom inside 32 (ABCD/HCP protocols) or 64 (Other) head
coil on top of the white cushion
2. Place the gray cushion in front to secure the phantom (32ch coil only)
3. Cushions are located next to the phantom in the bin
4. The cap of the phantom should be center as if it were the nose – it should line up with the
laser landmark line on the coil
5. Secure the top half of the head coil by clicking it in and plugging in cable(s) if necessary
6. Raise the table
7. Turn on the laser light and set the landmark to run through the cap
8. Slide the table fully into the scanner
9. Close and flip the air seal on the scanner door

32 Ch Coil

64 CH Coil

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Register the Phantom

1. Press the “little person” key on the keyboard to bring up the registration screen
2. Enter phantom information (all required fields are indicated in bold except required data
destination= Referring physician)
• Last Name = ABCDPhantom017_32CH or ABCDPhantom017_64CH
• Patient ID = copy the information from the Last Name field to the Patient
ID field.
• Sex = “other”
• Age = “18”
• Height = “5ft”
• Weight = “100 lbs”
• Referring Physician = select “ABCDPHANTOMGROUP”
• Patient Position = select “Head First Supine”
3. Click “Exam”
4. Another box will pop up
• Under ABCD choose the appropriate protocol:
o ABCD_QA_full__32ch (29:04min)
o ABCD_QA_quick__32ch (15:36min)
o ABCD_QA_full__64ch (29:04min)
o ABCD_QA_quick__64ch (15:36min)
• Click “Confirm”

Registration Pictures

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Running Scans
1. Press the green play button to start the first localizer
2. Set up sequence #3: SNR_Map by centering the yellow box on the phantom – it should
be placed right through the cap (the cap is circled in red below) then click the orange go
(green circle)

3. Set up sequence #4 by centering the yellow box on the phantom – click the orange Go
4. Press ok to the “Stimulation Monitor Warning” that will pop up after #3 finishes running
– you can step away to let the sequences auto run after this step
5. The rest of the sequences will automatically copy the slice locations from #4 and run
automatically
6. When scanning is complete, remove the phantom/cushions and place them securely in the
phantom cabinet bin

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How to Trigger Test Stimuli/Tasks

Setting up the Phantom

1. Place the phantom and phantom cushion inside the 20ch head coil (round end at top of
coil)
2. Secure the top half of the head coil by clicking it in and plugging in cable(s) if necessary
3. Raise the table
7. Turn on the laser light and set the landmark
8. Slide the table fully into the scanner
9. Close and flip the air seal on the scanner door

Register Phantom
1. Press the “little person” key on the keyboard to bring up the registration screen
2. Enter phantom information (all required fields are indicated in bold except required data
destination= Referring physician)
• Last Name = TriggerTest
• Patient ID = copy the information from the Last Name field to the Patient
ID field.
• Sex = “other”
• Age = “18”
• Height = “5ft”
• Weight = “100 lbs”
• Referring Physician = select “QC Group”
• Patient Position = select “Head First Supine”
3. Click “Exam”
4. Another box will pop up
• Choose Study = TriggerTest
• Click “Confirm”

Click for registration Pictures

Running Scans
1. Double check the sequence to open and then click the “the orange Go” to start the shim
2. When you are ready to trigger your task please the continue button
3. Don’t forget to plug the trigger cable into your computer
4. When scanning is complete, remove the phantom and place it securely in the phantom
cabin

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Quality Assurance: How to Check Your Scan Data

EVERY sequence should be checked after completion for quality assurance. They can be opened
in the viewing tab or 3D tab for T1 and T2 sequences.

The techs will try to show everyone how to properly QA data as it is collected. Next time you are
scanning please feel free to ask for a lesson. Good scanning technique means reviewing every
sequence as you collect them!

Check Your Localizer

1. If you are running HCP/CMRR localizers, it is very helpful to review the first localizer
(not the one called localizer aligned) to confirm a good head position within the magnet.

2. If you think of the brain as a full circle, the cross hair should be roughly in the middle. A
little off top to bottom is ok, but it should not be outside of the brain
3. If it is outside the brain, then the participant was not “landmarked/lasered” properly
4. If this happens stop the scan as soon as you see the issue (should be within first min of
scanning), re-laser (do not remove coil), click re-run from here on the first localizer to
start over
5. The laser line should be roughly at the participant’s eyebrows
• This position should correlate, if possible, with the line on the side of the coil
• If the participant’s anatomy can’t be matched up with the line due to a short neck
etc, then laser to the participant’s eyebrows only (not to the coil line)
• BUT do your best to match them both up by having participant move up or down
accordingly if possible

Verify Full Coverage of the Brain

1. After you load the sequence into MR View and Go click the tile with the sequence you
want to review and then click the mosaic icon (bottom left)
2. Press the 9 on the keyboard to auto window the contrast
3. Verify that you have full brain coverage from the top of the head to cerebellum
4. To do this review the first and last slice

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• If the participant moved up or down too much you will start to lose either the top
slices of the brain or the bottom slices (cerebellum)
• If the participant moves to the point where you are cutting off the top or bottom
structures, stop scanning and fix the positioning
• If the position is only slightly off, you can just rerun your ‘localizer block’ to
update autoalign
• If they have moved a lot, then you will need to go in the scanner room and
reposition/re-laser them in the coil
• After you re-laser repeat all 5 localizer scans if using HCP/CMRR sequences (loc,
autoalign, loc aligned and 2 spin echoes)
• Then delete any sequences you have successfully completed and continue where
you left off
• In this picture, you will see the bottom slice (red circle) still has a little bit of
cerebellum in it
▪ Ideally there would be only brain stem showing, but this is usable
▪ The top slice (green circle) should be basically empty

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Check for Dropout in Your Slices

1. Verify there is no dropout/fading throughout
your slices
2. If using CMRR/HCP sequences always
check your SBref for dropoff and stop and
repeat the scan if you encounter dropout
• A bad sbref scan will contaminate the
rest of the sequence

Check to Make Sure Your Head Coils Are

Attached
1. 32 ch: HEA HEP
2. 64 ch: HC1-7 or HC1-7;NC1,2 if using neck
elements
3. 20ch: HE1-4
4. More info on head coil warnings

Check That the Table is at Isocenter

1. It should say TP 0

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Coil Warnings - Protocol Was Fixed

If you see warning messages while scanning, please read the message and address the issue. DO
NOT just click “OK”. Ask a tech for help if you are uncomfortable with resolving the issue on
your own. Please be vigilant, as we do not refund scans for this type of error.

Main Reasons for Coil Warnings

1. The coil wasn’t plugged in at all or properly
2. The participant was registered and the protocol was loaded
Anterior (HEA)
into the exam card before plugging in the coil
portion of 32ch
3. You put the wrong coil on the table
coil not active
Anterior or Posterior Protocol Fixed Warning Messages
1. The pop-up message will let you know that it is turning off
the elements that are not plugged in properly
2. If you click “OK”, you will be approving this change and
you will lose signal from that part of the coil
3. Data collected in the manner will be suboptimal and most
likely unusable!
Anterior (HC1,3,5,)
Coil Issue Resolution portion of 64ch coil
1. Check the coil plugs not active
2. Reseat the plug if necessary
3. Make sure the LCD screen displays the anterior and
posterior elements
4. Close your patient
5. Resume registration and try again

Wrong Coil Protocol Fixed Warning Messages

Coil changed
1. The wrong coil was put on the scanner bed from 32ch to
• The message will let you know that it is changing 64ch
the coil to the one you put on the scanner bed
• Your data will not be “bad” per se, but you won’t be
using the proper coil for your study
• Resolution: change the coil, close and resume
registration for your participant
2. The protocol was not setup for the correct coil
• The message will let you know that it is changing
the coil to the one you put on the scanner bed
• Resolution: this is the only scenario where it is ok to click “OK” and proceed
• Let a tech know your protocol is setup with the wrong coil so it can be fixed
• Check which coils are turned on in the system card of the sequence after the
system auto detects the new coil to make sure they are correct
• Note – if you are using the 20ch or 64ch coils the neck elements “NC” do not
need to be on unless your study requires neck imaging

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Prisma XA30 Software Bugs

This is a list of known software bugs/glitches. If you encounter any other suspected issues,
please report them to bmctechs@[Link] and during study reporting.

AP/PA Copy Reference Issue

If you are using Siemens product sequences with different phase encoding directions (e.g. AP
then PA), you MUST NOT use the copy reference option. This glitch will change your second
PA sequence to RL. This glitch does not affect CMRR, HCP or ABCD sequences as the phase
encoding direction is controlled on the special card instead of the routine parameter card.

Workaround:
1. You must manually input the angle for each sequence if you are manually prescribing
your FOV
2. If you use autoalign and DO NOT manually adjust your FOV in any way, then your scans
will not be affected and there would be no need to use copy reference

***This glitch has been reported to Siemens, but there is no way to know when and if
there will be a fix.

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Prisma XA30 Scanner Warnings/Messages/Errors

Adjustment Measurement Was Aborted

• If you ever encounter any kind of adjustment
error try to see if the scanner will let you
continue scanning by clicking ok on the error
and re-running the sequence
• You can also try running a simple sequence
like a localizer first, removing and re-plugging
the coil and then re-lasering the participant
• Make sure you close the patient and resume
registration after if you try these methods
• If you still can’t continue then perform a
restart which takes about 7-10 min
• Some examples are show below
• Please submit the issue as an equipment failure during study reporting
o Critical if you couldn’t collect some or all of your data and
o Minor if you were able to complete the scan after fixing the issue

Gradient Power Amplifier Warning

If you ever seen the below warning/orange FOV box,
1. Check your first localizer to ensure the participant’s brain is positioned correctly at
isocenter – the cross hair should be center in the brain in the head to foot direction (see
below pic)
2. If it is, then it is safe to continue scanning as is, but please alert
bmctechs@[Link]
3. If it is not, stop scanning, re-laser your participant to their eyebrows, close the patient,
resume registration

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Participant Registration Errors

1. You cannot confirm your registration due to the below error

• This happens when there are still active sequences in the Exam Card
• Go back to the Exam card and stop (red square) or Skip (>|) the remaining
sequences in the queue
• This happens when a participant aborts a scan early or the group runs out of time
and stops scanning before their protocol is complete
• Also note, you will not be able to close the patient on the Exam card until the
sequences are stopped, skipped and/or deleted

2. You press the registration exam button & fields turn yellow on the registration page
• This means you have forgotten to complete a required field
• Required fields have an asterisk next to them & will turn yellow if no information
is listed. Fill these fields out and proceed as normal
• NOTE: “Date of Birth” is bold, but we use “Age” instead – please do not input a
DOB – once you input the age a general DOB will be generated
• NOTE: Referring Physician is not bold but is required to access your data

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Preparation Scans (aka dummy time)

Preparation Scans (dummy time) for CMRR/HCP Multiband Sequences

Dummy time for CMRR/HCP MB sequences is always 10 sec

Preparation Scans (dummy time) for Regular BOLD Sequences

1. To ensure that a steady-state magnetization is achieved when multiple averages or
measurements are acquired, a number of preparation scans are performed at the start of
the measurement
2. The number of preparation scans is set within the sequences, and chosen so that the
preparation time is longer than 3 seconds

• TR = 500 ms 7 preparation scans

• TR > 501 ms 6 preparation scans
• TR > 601 ms 5 preparation scans
• TR > 751 ms 4 preparation scans
• TR > 1001 ms 3 preparation scans
• TR > 1501 ms 2 preparation scans
• TR = 2000 ms 2 preparation scans
• TR = 2500 ms 2 preparation scans
• TR = 3000 ms 2 preparation scans
• TR > 3001 ms 1 preparation scan

3. The preparation scans result in a longer scan time for the first measurement in a time-
series acquisition, which should be taken into account when performing BOLD imaging
4. The sequence does not send external trigger pulses when performing these preparation
scans, so that they do not have to be considered when triggering external devices for
stimulus presentation in BOLD imaging studies
5. This formula does not apply to multiband bold sequences
6. Turning iPAT on will add 1 additional prep scan
7. Turning introduction “on” will add 1 additional prep scan

Slice Timing for BOLD Sequences and other BOLD Questions

1. When EPI slice are collected in a mosaic/volume, are they interleaved or sequential?
• Interleaved (that is the default)

2. When collected interleaved, are all the odd numbered slices collected first?
• It depends on the number of slices in the group
• If there are an even # of slices then even numbered slices are collected first
• If there are an odd # of slices then odd numbered slices are collected first

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3. Is slice #1 always at the “lowest” part of the brain and the last slice at the top?
• The default “image numbering” in the transversal/axial plane is F>H - so the
bottom slice is acquired first

4. Regarding the timing of slices, is the scanner set to collect slices in an equidistant fashion
within the TR time or as fast as possible?
• Within the TR time

How to Manually Trigger Stimuli

The below video will show you how to manually trigger your stimuli if the auto trigger fails to
work.

[Link]

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Current Designs Button Box and Trigger Setup (FORP 932)

There is no on/off switch and this device does not need to be unplugged

Device Selection
1. DO NOT set the interface settings until you plug in the button box inside the scanner
room – the button responses will not work
2. Note - you do not need to plug in a box if you only need a trigger – just choose your
interface setting with appropriate trigger (5s or Ts)
3. Click dial in once and scroll to yes in “change modes” menu and click dial once
4. Scroll to “autoconfigure” and click dial once
5. Scroll to “usb” and click dial once
6. Below is a list of available devices – autoconfigure will automatically choose the box that
is connected in the scanner room
• HHSC - 1X4-L - buttons straight in a row
• HHSC - 2X2 - split boxes, you may use just one box if applicable
o Left box sends dnwe or 9876
o Right box sends bygr or 1234
• HHSC – 2x4 - curved row of buttons, you may use just one box if applicable
• HHSC Joy-1 joystick (older model than what is on the current designs website)
• HHSC TRK-1 trackball
7. You may see other devices listed that are not available, contact BMC Techs for more info
8. Once you have selected your device, you will see the “Response Settings” menu

Response Settings
1. Scroll to applicable setting and click dial once
2. "KEY" sends the button press signal as soon as the button is pressed but stops sending
the button press signal immediately after sending it once
1. HID KEY BYGRT - use this for letter responses and T is the trigger
o this is the same as 0 setting on previous interface box
2. HID KEY 12345 - use this for number responses and 5 is the trigger
o this is the same as 4 setting on previous interface box
3. "NAR" sends the button press signal as soon as the button is pressed but keeps sending
the button press signal until the button is physically released
1. HID KEY NAR BYGRT - use this for letter responses and T is the trigger
o this is the same as 2 setting on previous interface box
o this setting is often required for psycho tool box in matlab
2. HID KEY NAR 12345 - use this for number responses and 5 is the trigger

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4. HID KEY 1-9 No 5 - for MacStim users: no trigger will be sent, must manually start scan
5. On the small screen you will see the “setting description” which includes
the device selected as well as the response setting selected
6. Be sure to plug in the trigger cable before starting your stimuli
7. Set the interface back to the “autoconfigure” menu after scan

Troubleshooting
Button Response and Trigger Interface Box

Response Lights

12345 Trigger Light

BYGRT

A. Button responses are not coming through

1. If the button response lights (red circle above) on the interface are visible, but your
computer is not receiving the responses then
• Check to make sure the trigger cable is plugged into your computer
• Check to make sure you have chosen the correct response setting (12345 or bygrt)
2. If the button response lights (red circle above) are not visible on the interface
• Check to make sure the correct button box is plugged in inside the scanner room
• Make sure your participant is pressing the buttons
• Reset the interface box – you may have set it before the box was plugged in inside
the scanner room

B. The task is not triggering

1. Make sure the trigger cable is plugged in to your computer
2. Make sure the interface is set to the appropriate trigger value for your script (5 or T)
3. Make sure you started the scan and waited long enough for the dummy time to complete–
the trigger light (green square above) on the interface will blink when triggers are being
sent so you can watch for the signal
4. Make sure you are on the correct screen on your computer for the task to begin
(sometimes you may need to advance to another screen)
5. Check your script
6. Check the trigger cable connection on the interface box to
make sure it is secure
• the blue circle on the below picture shows where it
connects in the back of the interface box – it does
not lock in place or screw in, so just push on it
gently to make sure it is seated on the connector
• the yellow square is the other end of the
connection – this should not come loose as it screws in, but you can also check it
to make sure it is connected

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• BE VERY careful not to unscrew/loosen anything else – DO NOT remove box

from velcro

C. USB is flashing on the interface LCD screen

1. This indicates the USB trigger cable is not plugged into your computer or the computer
doesn’t see it
2. Plug or Re-plug or
3. Reset interface box or
4. Reboot computer if that doesn’t work

D. It looks like buttons are being held down because the button interface lights are on
1. Check the interface settings first – it is likely that the interface is set for the wrong box
(i.e. 2x2 instead of 1x4 etc)
2. Ask the participant if they are pressing/holding down the buttons
3. Check the actual button box to see if something is pressing against the buttons
4. Reset the interface box – you may have set it before the box was plugged in inside the
scanner room

E. Interface Menu Issues

1. If you get “lost” in the menu, just scroll down to “back” until you get to the proper menu

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Siemens Talk Box Setup

1. You must use the Siemens talk box to talk & listen to your participant if you are using the
Siemens headphones, inner ear headphones or no headphones
2. You must also make sure that the volume on the scanner’s control panel is turned up so
the participant can hear the stimuli computer
3. Press the “ear” button (#4) to hear the participant
4. This is the sound that comes from bore speaker - you should also use this to listen if you
are using the opto headphones
5. Make sure the sound is turned up
6. Press the “talk” button (#2) to talk to the participant
7. Make sure the sound is turned up
8. For music, plug in the extra audio cable (hanging in the bungie to the left and behind the
console computer) to the port labelled (#6)

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Optoacoustics Headphone and Microphone Setup

Positioning the Participant

1. You may use the Opto headphones with or without earplugs
2. Position the headphones on the participant and be sure to use pads or paper towels to take
up the extra space between the headphones and coil (this is especially important if you
are using the active noise cancellation feature)
3. Position the microphone if applicable - be sure it is almost touching the participant’s lips

Setting up the Opto Console

1. AFTER moving the participant into the bore, turn on the Opto control box
using the black switch on the back right side of the console
2. Touch the screen to continue
3. If you are playing audio (movie, music or an audio task) connect the audio
cable to either the green connection inside the white drawer for the desktop
computer or to a laptop port – the other end of this should be connected at the
back of the Opto console in “line 1”
4. The line 1 (#5) knob controls the volume of this audio
5. The left button (#4 FORMI NOISE CANCELLER) on the Opto console should always
be pressed down “On”
6. The right button (#3) should always be up (in the FORMI position) when talking to the
participant - otherwise feedback will be generated
7. During the movie or task you can press the right button down (#3 headphones position) to
hear what the participant is hearing – just don’t forget to put it back up before talking to
the participant
8. To talk to the participant press the bottom silver button (#2)
9. Use the Siemens talk box to listen to your participant’s responses

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10. The speaker knob (#8) controls the volume that you hear in the control room
11. Note: there is no volume control for the volume of your voice to the participant – please
manually adjust your voice volume if need be

Using Active Noise Cancellation

1. Only proceed to the below steps if you are using the active noise cancelling (ANC)
feature
2. Press “Start” then “Calibrate” – you should get two green check shields – participant
must be inside the bore during this step and there should be no sound playing or talking

3. When you are ready to calibrate for your BOLD runs, press the red “ANC” button in the
top right corner
4. Unplug the audio cable – this eliminates the possibility of accidentally transmitting
sounds during the calibration step
5. Press “Learn” then start your calibration scan – this takes 16 sec – it is very important to
not transmit any auditory stimuli/movie during the learn mode

6. NOTE: if you remove you participant from the bore for any reason you will need to
repeat steps 2-5
7. You are now ready to start your task

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Troubleshooting Tips
1. If you are using the active noise cancellation and get a “out of range” error this means
your volume was too high – press the “Stop” wait a couple seconds and then press
“ANC” again to reactivate the noise cancellation
2. To reboot the system, turn off the power switch on the back of the console – wait at least
20s – then turn it back on
3. If the participant can only hear out of one ear, check the balance nodes (#11 and # 13) on
the back behind the line 1/line 2 knobs – make sure it is balanced in the middle
4. If the participant can’t hear the movie or auditory stimuli check the following:
a. the correct audio cable is connected to the correct port/computer
b. the sound on the computer is not muted in VLC player or system volume
c. there are no faults on the opto box (see #5 below)
d. line 1 on the opto dial is turned up
e. volume output is set to speakers/headphones. Sometimes the audio defaults to
BOLDscreen 24 instead of speakers/headphones – BOLDscreen 24 is the
WRONG setting! If it is wrong:
▪ Go into sound settings and change it back to speakers/headphones
o On PC left click on the volume icon in bottom left corner – click the
up arrow and choose speakers/headphones
o On Mac go into settings – click sound – click output – choose
MacBook Pro Speakers
5. If everything is ok reset the system (step #2) to try to resolve the issue
6. If the participant can’t hear you, you will see a “Laser Fault” icon (see icon list below)
on the screen that says “Start” – this is the first screen after “touch screen to continue”
– try to reset the system (step #2) to resolve the issue
7. If the participant can’t hear you but there is no laser fault, the opto box is on and the
participant has the headphones – then check the mic volume
a. It is a small knob on the back left side of the opto console if you look at it
from the top. It should only be turned up a little as it is very sensitive.

8. If the participant can hear “talking” during the scans (not from the movie) there was
probably sound playing or talking during the calibration setup – any noise during this step
will be dubbed into the headphones during scans – rerun calibration

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BOLDScreen LCD

Specifications
1. Resolution: 1920 x 1200 (60Hz)
2. 24” screen
3. 52cm wide
4. 151cm from the participant’s eyes to the screen

Turning on the LCD

1. For laptops: plug the LCD HDMI cable into the laptop using an adapter if needed (the
desktop is always plugged in and active)
2. Flip the power switch (red circle on picture) on the front of the black “LCD” switch box
to turn the system on
3. Use the select button (green circle on picture) to choose “L” for a laptop computer
4. Use the select button (green circle on picture) to choose “D” for the Dell Desktop
computer
5. The monitor labelled “LCD” is a duplication of what is being projected to the
participant’s screen
6. Note - the LCD takes a couple seconds to display after the switch box is turned on – it
will also start dark and lighten up automatically within seconds
7. You MUST turn off the switch box after your scan to allow the screen to go to sleep so
the static computer image does not “burn” into the display
8. Note – after turning off the LCD switch box the LCD screen will stay on for about 5 min
before going into sleep mode – this is normal

Positioning the Participant

1. Select the mirror frame and mirror for the coil you are using
2. Place the mirror frame onto the anterior portion of the coil
3. Snap the mirror onto the frame – the curved side of the mirror should point in the
direction of the participant’s feet
4. Position the mirror so that the participant can see the whole LCD screen without straining
their neck or eyes
5. Laser landmark the participant per usual (if you have trouble marking the laser with the
mirror on you may laser the participant before attaching the mirror – be sure you have the
participant close their eyes)

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6. Prescription lenses are available if needed – they range -6 to +6 and are kept in the
cabinet next to the control room door

Troubleshooting Tips
A. The LCD is not displaying the laptop screen, but you can see the desktop computer screen
1. Select “L” on the black LCD switch box
2. If the switch box will not let you select “L” that means the laptop is not plugged in
properly
3. Check the HDMI connection cable
4. If you are using a mini displayport adapter ensure it is not plugged in upside down

B. The LCD is not displaying the laptop or desktop computer

1. Make sure you turned on the black LCD switch box
2. Make sure the connections at the back of the LCD box are plugged in and not loose –
there should be 4 cables plugged in
3. Reboot the black LCD switch box
• Turn off the power - wait 5 sec then turn it back on
• Use the select button to choose “D” or “L”
4. If you are using the desktop, switch to the BMC laptop to see if it is working
• If the laptop is working, then check the HDMI cable in the back of the dell
desktop tower
▪ please be careful not to unplug anything
▪ do not pull the tower out, but rather look behind it in its current position to
avoid unplugging cables
5. If you are using a laptop, switch to the BMC desktop to see if it is working
• If the desktop is working, then check the HDMI connection on the laptop (see A
above)
C. The The LCD control room Dell monitor is displaying random colors or a solid color. The
LCD BOLDscreen in the scanner room may look fine or be out as well.
1. Cycle the power to the control room LCD Dell monitor by unplugging its power cable
2. The power cable is located in the power strip to the left of the BMC MAC laptop next to
the shelf - it is labelled LCD monitor in orange label tape
3. Simply unplug it and then plug it back in – the computer screen should appear within a
few seconds
`

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How to use E-Prime with the Desktop Computer and LCD

Duplicate/Mirrored Display with E-Prime

1. Setup the display to work with a duplicate display E-Prime task
• Turn on the black LCD switch box and use the select button to choose "D"
• The LCD and the “LCD” monitor should turn on
2. Plug in Cables
• Plug the audio cable into the port labelled "AUDIO TO
DESKTOP"
• Plug the trigger cable into the port labelled "TRIGGER TO
DESKTOP"
3. Run task
4. After tasks, unplug the “Trigger”

Extended Display with E-Prime

1. Setup the display to work with an extended E-Prime task
• Turn on the dell desktop monitor (lower right corner)
• Turn on the black LCD switch box and use the select button
to choose "D"
• The LCD in the scanner room and the “LCD” monitor should
turn on
• Change to extended display using the extend shortcut on the desktop or
• Right click on the desktop and click "Display settings"
• Under "Multiple Displays" choose "Extend these displays"
2. Plug in Cables
• Plug the audio cable into the port labelled "AUDIO TO DESKTOP"
• Plug the trigger cable into the port labelled "TRIGGER TO DESKTOP"
3. Run task
4. After tasks, unplug the “Trigger”

Switching from Extended Display to Duplicate/Mirrored Display

1. Turn on the black LCD switch box and use the select button to choose "D"
2. Turn on the dell desktop monitor (lower right corner)
3. Use the duplicate shortcut on the desktop or
• Right click on the desktop of the EXTENDED monitor and click "Display
settings"
• Under "Multiple Displays" choose "Duplicate these displays”

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Siemens Physiological Device Setup

ECG/Respiratory Setup
1. The gray strap should be placed velcro side down on the bed roughly where the
participants ribs/diaphragm would go
2. Wrap the strap around your participant when they lay down and adjust the position as
needed. Have them suck in a little as you do it, so it is snug. Make sure to ask them if it is
okay (not too tight).
3. Tuck the respiratory “pillow” under the strap
4. Plug the clear cord from the pillow into the respiratory device
5. The ECG/Respiratory device MUST be placed into the gray holder for safety reasons–
this module should never directly touch the participant’s skin as it can heat up
6. A washcloth (located in the bottom shelf of linen cabinet) must be wrapped around the
loose cables

Pulse Setup
1. The finger pulse device should be placed on the left ring finger with the red light side on
top of the nail – nail polish remover is available in the scanner room drawer labelled HCP
if needed (note the remover will not work on gel nail polish)
2. The pulse device should be placed in one of the gray holders – this holder is not a safety
requirement, but rather a stability aid
3. If the pulse is not working properly (e.g. there is no pulse signal or it is erratic) check the
signal and receiver elements inside the finger cuff – these elements sometimes get twisted
so they are not showing properly through the cutouts

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How to Use the MR Camera

Quick Overview
Open VLC → Press Ctrl+C → Play

Equipment
1. Head coil
2. Head coil mirror frame
3. MReyes cameras (mounted in the back of the bore)
4. Desktop Computer

Camera Setup
1. Turn on the monitor (small button on bottom right corner of monitor)
2. Click the VLC icon on the bottom task bar of the desktop computer or click the
windows button in the bottom left corner then scroll to find VLC in the program list
3. Pres Ctrl+C (shortcut) OR click Media then Open Capture Device
4. Make sure you are in the Capture Device tab
5. Click Play

6. If you use the desktop computer for movies or fixation – you must switch it to extended
display to use the camera – use the extend desktop shortcut or
• Right click on the desktop and click Display settings
• Under Multiple Displays choose Extend these displays
• Drag your fixation cross or movie to the LCD monitor so you can display the
camera on the extended monitor
7. Note – the camera cannot be used during your task if you use the desktop computer for
the task in duplicate display mode

Participant Setup
1. Position your participant
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2. Position the mirror so the participant can see the whole LCD screen
3. Landmark the participant and move them into the bore
4. Verify camera positioning
5. If needed, get a tech to adjust the camera (in the back of the bore) to see the participant’s
eyes through the mirror – this step should not need to be done unless someone has
accidentally moved the camera
6. Turn the room lights to the HCP LED setting

Camera Cleanup
1. Close VLC
2. Turn off the dell monitor (lower right corner)

Troubleshooting Tips

1. If the camera will not stream through VLC and you get the below error then:
• Unplug and replug the USB cable in the back top right side of the PC desktop
tower – labelled MREyes
• Close VLC and try again

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Equipment Manuals

Hard copies of manuals are located on the Prisma tech desk

Current Designs Button Box and Trigger Manual - Forp 932

Optoacoustics Manual
MRI Safety Manual

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Movie List

• Planet Earth – Saving Species, Into

• A Bug’s Life
Wilderness, Living Together
• Almost Famous • Predator

• Big Hero 6 • Princess Bride

• Cheaper by the Dozen • Princess Mononoke
• Corpse Bride • Riding Giants
• Crouching Tiger Hidden Dragon • SNL Chris Farley
• Daddy Daycare • SNL Will Farrell
• Despicable Me • Sandlot
• Elf • Seinfeld
• Endless Summer II • Shrek
• Finding Nemo • Shawshank Redemption
• Forrest Gump • Sisters
• Frozen • Sponge Bob
• Harry Potter and the Sorcerer’s
• Stars Wars - The Phantom Menace
Stone
• Howl’s Moving Castle • Tangled
• In Search of Santa • Timeline
• Incredibles • Total Recall
• Inside Out • Toy Story
• Lion King • The King’s Speech
• Lord of the Rings Fellowship • The Matrix
• Maleficent • The One Jet Li
• Napoleon Dynamite • The Rock
• Planet Earth – Caves, Deserts, Ice • The Wizard of Oz
Worlds
• Planet Earth – Seasonal Forests and
• Up
Deep Ocean
• Planet Earth – Pole to Pole, • Winged Migration
Mountains, Fresh Water
• Planet Earth – Great Plains, Jungles,
ALSO ON THE BMC MAC LAPTOP
Shallow Seas

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