Q. Who is my experiment coordinator? What does he do?
To save your time on mastering the detail features of the scanner, and
enforce the high magnetic field safety and all concern about
subject safety issues, we always assign a qualified
BITC staff,
in most case
Robert Smith, to
work with you through your assigned machine time. He is your
experiment coordinator and is supposed to perform required
safety survey and to help you solve and issues and concerns about
the scanner and the experiment procedure, or at least help to
to contact the most experienced BITC staffs about certain issues.
You are recommented and encouraged to discuss any unsure issues
and should report and abnormal to him as soon as possible.
When Robert is not available or at nights or weekends, another
BITC executive member will be assigned as your experiment coordinator.
[TOP]
Q. What's your new fixes and features of the facility?
Pending new features:
- Aug. 2006 - Cluster master node is to be upgraded for better data transfer spped and x-windows performance.
- July. 2006 - mirror for 12-channel and TEM coil is being made.
- July. 2006 - 2-coil CASL project started.
- June 2006 - Optical trigger is to be made.
- Dec. 2005 - Liquid/scent stimulation delivery subsystems
are put on the wish list.
New feature log:
- Aug. 07th, 2006 - SimMeasData is now stored on drive P: and automatically backed up to /data2/meas on the cluster
- Jun. 21st, 2006 - Alternative subject voice recording option available.
- Jun. 04th, 2006 - New Joystick installed.
- Jun. 01st, 2006 - TIM is ready for public use.
- Feb. 08th, 2006 - New cabinets installed. Frequently
used coils are relocated in the in-scanner-room cabinet.
Rarely used coils and phantoms are relocated in the
cabinet at the hallway in between the scanner room and
the control room.
- Oct. 12th, 2005 - BITC_archive storage disk array
udgraded.
- Aug. 22nd, 2005 - Belt respiration monitor is released.
Previously the respiration belt can only be hooked on the
scanner and cannot provide recordible digital output. The
SPCO_2 nostril respiration monitor suffers off
synchronization problem and cannot be successfully used
for gating. The new set up is supposed to do both.
- Aug. 21st, 2005 - Acoustic stimulation can now be heard
by investigators also.
- Aug. 17th, 2005 - User Protocols sorted.
- Aug. 1st, 2005 - most of user relevant cables and plugs
in the scanner control room labeled.
- June 2005 - Subject acoustic response recording available.
- May 2005 - Easy-single button available.
- April 2005 - New headset working with AVOTEC available
for more stable acoustic stimulation.
Pending fixes:
- Jul. 22th, 2006 - communication to MRIR drop issue triggered
user concern. This is expected to be fixed with the new
version of MRIR software.
- Jul. 22th, 2006 - T1-se, t2-FLAIR, DTI, and general EPI sequences are
forced to run with slightly different parameters. Siemens is investigating
this. It may be feature of the new scanner.
- Jun. 19th, 2006 - Image quality issue. Siemens service is
investigating this.
Fix Log:
- Aug. 03rd, 2006 - MRIR replaced by Siemens as an attempt of fixing the MRIR lost communication issue
- Jul. 22th, 2006 - Cooling water line purged.
- Jul. 17th, 2006 - Pump for sand bag cushion installed.
- Jul. 14th, 2006 - Some small adjusts to the back projection system.
- Jun. 26th, 2006 - DTI and T2-Flair sequence are now working properly.
- Jun. 22nd, 2006 - ACS over temperature issue cleared. Siemen chiller
clogging cleaned.
- Jun. 19th, 2006 - Scanner recovered from 'refuse to scan'
status after a system backup and the talking of doing a full
software reinstalltion. Real reason of failure still unknown.
Will keep a close eye on the consequence.
- Jun. 14th, 2006 - TxRx Head coil replaced for over-temperature issue.
- Jun. 07th, 2006 - eye tracker works.
- Jun. 05th, 2006 - trigger works.
- Jun. 01st, 2006 - Button box fixed.
- Apr. 11th, 2006 - BC RF power amplifier firmware upgrade.
- Apr. 11th, 2006 - Temporarily fixed the button box.
- Apr. 03st, 2006 - Fixed software confliction that causes
broken communication with imager.
- Mar. 27th, 2006 - Purged primary cooling water line.
Next service due: Sept. 2006.
- Mar. 25th, 2006 - Fixed software confliction that disabled
stimulation monitor.
- Mar. 01st, 2006 - Fixed software confliction that causes
temporary system down.
- Feb. 28th, 2006 - CCA radiator is replaced.
- Dec. 05th, 2005 - New button box installed.
- Oct. 10th, 2005 - A customer sequence that triggered
license inconsistency was fixed. And procedures for fixing
such license inconsistency are confirmed.
- Oct. 6th, 2005 - A license inconsistency was triggered
by tripped stimulation monitor. Faxed in 5 hours.
- Oct. 3rd, 2005 - MPU fixed. Now gating function is back.
- Aug. 26th, 2005 - Cooling water line repaired. Next
service due: Feb. 2006.
- Aug. 16th, 2005 - New CP Head Coil arrived. Expecting
better performance and less fMRI bad data incident.
- Aug. 4th, 2005 - helium compressor replace by Oxford.
The magnet cold shield is expected to get back to normal
by next Monday. Friday, Aug. 5th schedule is not cancelled
but the image quality may be not as good as usual. Cooling
water quality is proved very poor. A water inlet filter is
expected to be installed by the hospital facility management
as soon as possible.
- July 31st - Aug. 1st, 2005 - Hospital tri-phase power outage three
times in a row. Facility management changed a power breaker.
Displex compressor malfunction again. Schedule cancelled for
Aug. 1st to 4th. Oxford and Siemens service pending.
- July 28th, 2005 - Hospital tri-phase power outage, displex compressor
malfunction. Siemens services call put on. Some fMRI data bad.
- July 5th, 2005 - Eye tracker misplacement found and fixed.
- June 23rd, 2005 - Gradient spike fix. This is supposed to
reduce the chance of getting bad fMRI data.
- June 4th, 2005 - Gradient cooling pipe leaking fix.
- May 2005 - Gradient coil chiller cleaned - fixed gradient coil
warm up issue.
- May 2005 - Main magnet cold shield displex compressor replacement.
- Jan. 2005 - 3T Trio console upgrading. Baseline to V25. OS to Windows XP.
Error Log:
- Jun. 17th, 2006 - Scanner normally started but refused to scan.
Reason unknown.
- Apr. 01st, 2006 - Afternoon system down - connot start imager.
- Mar. 01st, 2006 - Afternoon system down - cannot scan.
- Feb. 03rd, 2006 - CCA cabinet temperature over threshold.
- Aug. 20th, 2005 - At noon, minor facility power failure interupted a
funded project. Scanner reboot forced.
Newest user protocol back up: Feb. 15th, 2006.
TIM upgrade diary
- 05/05/2006 - [OUT] Data backed up; magnet ramped down; customer attachments secured
- 05/06/2006 - [OUT] Skelecton disassembled and stored; cables removed
- 05/07/2006 - [OUT] Gradient coil and patient bed removed
- 05/08/2006 - [OUT] Instrument cabinet removed; [IN] Computers replaced; shipment of new
parts and electronics arrived
- 05/09/2006 - [IN] New gradient and body coil installed;
Instrument cabinet placed; cabling in progress
- 05/10/2006 - [IN] New patient table installed; New penetration panel installed;
cabling in progress
- 05/11/2006 - [IN] Cabling finished; Cover installation in progress
- 05/12/2006 - [IN] Cover installation finished; field clean up in progress
- 05/13/2006 - Field Clean-up
- 05/14/2006 - Break
- 05/15/2006 - Off-site software configuration
- 05/16/2006 - On-site software configuration
- 05/17/2006 - On-site software configuration
- 05/18/2006 - Energize magnet
- 05/19/2006 - Hardware tune-up
- 05/20-21/2006 - Break
- 05/22-24/2006 - Shimming
- 05/25/2006 - Software tune-up
- 05/26/2006 - Customer setups restoration
- 06/05/2006 - Trigger temporary solution works
Cluster storage upgrade diary
- 05/05/2006 - mkfs /data5
- 05/06/2006 - rsync /data3/ /data5
- 05/07/2006 - rsync /data4 /data5
- 05/08/2006 - keep going
- 05/09/2006 - keep going - super long warehouse directory slowed the
process significantly
- 05/10/2006 - umount /data5; umount /data3; mount /dev/sdb1 as /data3;
initialization of 320GBx11 volume; expanding /data3
- 05/11/2006 - keep going
- 05/12/2006 - 320GBx11 volume initialization failed. Restart 320GBx7. Looks working
- 05/13-17/2006 - Tried several firmware. Settled on multi-RAID version
- 05/18/2006 - Built 320Mx7 and 320Mx4 RAID groups, for /data2/rawdata and /data2
- 05/19-21/2006 - rsync /data2 /data4
- 05/22/2006 - Swap /data2 and /data4. rsync /data3 /data2
- 05/23-26/2006 - keep going
- 05/27/2006 - umount /data3; assign /data2/rawdata/data3 as /data3; create /data5; rsync /data /data5
- 05/28-29/2006 - rsync /data /data5
- 05/30/2006 - swap /data /data5; rsync -u /data5 /data; delete /data4; expand /data5
- 05/31-06/01/2006 - rebuild 250Gx15 RAID, split into 2G and 1.4G partitions; assign as /data4 and /data1
- 06/02-03/2006 - rsync /data /data4, except 10 chosen users, which are moved onto /data1
- 06/04/2006 - swap /data /data4; reassign /data4 as /data3; remove extras from /data3 and /data
- 06/05/2006 - rsync /data2/rawdata/data3/ /data3
- 06/06/2006 - rm -Rf /data2/rawdata/data3; rsync /data2/old-dicomWarehoses /data3
- 06/07/2006 - rm -Rf /data2/old-dicomWarehouse
[TOP]
Q. Why are my scanned images noisy?
- Please check if both the scanner room doors are properly shut.
MRI is an imaging method rely to very weak RF signals, which are
wide spreaded by all sorts of radio/video/wireless stations and
common electronics like TV/computer/vehicle/handhold digital
devices. The scanner room is constructed with a well grounded
metal wall to shield those RF noise out. An open door will void
the shielding and introduce enormouse noise into your images.
- If not the above mentioned cases, please check if the small LCD
monitor on top of the eye-tracker is turned off, which is mounted
behind the scanner on the wall as a black rectangle box, and can be
reached from the left side of the scanner.
As what mentioned above, LCD monitor is a potential RF noise source.
However, this monitor is required for tuning the eye-tracker, and
cannot be removed from the room. When scan is in progress, the
display of this monitor is neither visible nor a data source, and
has no influence to the normal function of the eye-tracker. It is
supposed to be turned off when you are not working on tuning the
eye-tracker.
We may work on making a door status interlock if complains related
with this issue increases.
- If not the above mentioned cases, please double-check if you have
brought in any foreign electronic devices or wiring into the scanner
room. If so, please consult your experiment coordinator
or BITC hardware person
We offer cabling and mounting services from the control room to the scanner.
- If not the above mentioned cases, and you are doing EPI,
you are possibly experiencing a unexpected shimming problem.
This can be either caused by the motion of the subject, or
an environmental shimming change. This may or may not be
corrected by invalid the shimming parameters and the scanner
will automatically re-shim before your next scan.
- If not the above mentioned cases, please ask
your experiment coordinator if this is
an existing unsolved issue, to decide if you will live with
it or postpone your experiment to the point this issue is solved.
[TOP]
Q. The images are OK at begining but get worse timely.
Is there anything wrong with the scanner?
The image quality of EPI sequence is very sensitive to the shimming
quality. Bad shimming not only reduces the brightness, but also
causes the image distortion, ghosts, too strong phase wrap caused
strips, and image displacement along phase encoding direction.
Normally, the Siemens scanner perform a series of automatic
adjustments when a laser helped table relocation or a FOV change
happens, including frequency adjustment, flip angle adjustment,
3D shimming, water suppression, etc. This is denoted by an about
half minutes delay in between the command and the normal scanning
noise. It can be heard as a series of short low tone noises.
The purpose of the automatic adjustment is to tune the scanned
to the optimized performance for the current subject and current
FOV.
Soon afterward, the system will assume that the adjustment parameters
are still valid if you adapt the FOV parameters in the protocols
thereafter, and won't perform another set of adjustments until
you change the FOV or re locate the subject.
However, though you can always remind the subject that it is
crucial to keep his head still in the scanner before each protocol,
there is actually no legal way to prevent subconscious head motion.
If your experiment coordinator is to locate
the subject for you, he will do his best to ensure the comfort
of the subject, to reduce his wish of head motion as much as
possible. If you are going to locate the subject, we recommend
you never omit asking the subject to adjust his body and head
position to the most comfotable status, not only for the health
of him, but also the quality of your data.
The in situ shimming is to correct the subject susceptibility
induced B0 distortion. This is to say, it is subject position
sensitive. If the subject moves, whatever a head shift, or
a rotate, or a body part shift without accompanying a head motion,
the shimming will no longer be valid. But the scanner won't
know and will still adapt the old parameters. In this case,
the ghost in your image will grow, the strips will develop in
the images, the signal intensity will drop, the image may be
misplaced along the phase encoding direction. And, a motion
going through one shot will cause universal strips in the image.
It is currently no technical solution to administrate this
kind of artifacts. So we highly encourage you to keep reminding
your subject to keep his head still and reduce the body motion,
especially when your protocol request the subject to stay in
the scanner for more than 1 hour. Certainly you should ensure
his comfort while putting him into the scanner.
[TOP]
Q. I was expecting visual cortex stimulation
result using the eight-channel head coil for stronger signal.
However, I got extremely flat time-course signal. What's the
problem?
The eight channel head coil is a receive-only parallel imaging
coil. It is constructed of eight surface coils grouped in two
selectable sets. It uses the body resonator for RF transmitter.
It is designed for obtaining enhanced visual cortex signal while
preserve whole brain SNR comparable with the standard CP_Head
coil.
However, for some sequence, some scan parameter set up, and/or
some subjects, the signal around the bottom of the coil (usually
the position of the visual cortex when the subject takes a face-up
position) could be so strong that it saturates the RF receiver
amplifier.
When this happens, though the image storage data format enables
intensity to take any value between 0 to 32767, the 12-bits
AD and consiquence software set up will only render the image
into 12-bit set up, i.e., it truncates all data to a value less
than 4095. This is to say, if your image has rigions potentially
brighter than 3500, you should think that if you have got a
saturated image.
If you have got saturated images, there are three things you
can do to administrate it.
- If the sequence is programmed by you, or say a customer
protocol, you should consider to reduce the gain in your
protocol
- If the above one doesn't work or is not applicable,
you should consider to put in more pads in between the
head of the subject and the coil's plastic head holder.
This is supposed to move the visual cortex farther away
from the most sensitive area, and reduce the signal
intensity.
- If this cannot be applied or still does not work, but
you are using a gradient echo sequence, you should consider
reducing the flip angle.
For best result, we highly recommend to limit the average
image intensity of your interested area in between 500 and
3000.
[TOP]
Q. How may I obtain whole brain BOLD coverage?
Using standard 64x64 base resolution GRE-EPI sequence over
a single channel head coil with Siemens FatSat, and if you
want isotropic continuous 3x3x3mm coverage, you will need about
37 slices to safely cover the whole brain. This usually requires
a TR no less than 2550ms. If you are satified of this time
course resolution, it is perfect. However, if you require a
TR shorter than 2550ms, you will have to consider one of the
following solutions.
- First of all, we do not recommend using TR shorter than
2500ms. The human brain gray matter has a T1 of 900~1000
ms. In TR=2000ms, 11% of the protons have not yet relaxed.
This will not only reduce your expected SNR by 11%, but also
will potentially increase uncontrollable artifacts caused
by the still tipped over spins. If you use TR>=2500ms, the
leftover will be less than 6%, and post minimum noise into
your data.
- If you are sure that some part of the brain is not
interested, you can use 29 slices for 87mm coverage.
- If your expected activation area is much greater than
3x3x3mm, you can consider using 3.4x3.4x3.4mm resolution,
and have 29 slices to cover 98.6mm. This is close to whole
brain coverage.
- Also, you can consider to insert about 10% gap in between
slices to obtain some more coverage without significantly
reduce your space resolution.
- If your subject and your protocol are tolerable of
using the much tighter 8-channel head coil, it can be set
up using GRAPPA acceleration, and enable doing 37 slices
in TR=2000ms. Certainly this will also take the toll of SNR.
[TOP]
Q. The eye-tracker is not functioning properly.
What's the problem?
The hardware of the eye-tracker is a telescope with illumination
and an infrared seneitive CCD digital video camera. A tampered
optical path and/or an electronic device failure will cause it
stops functioning. We actually experienced both in the past.
The eye-tracker illuminator is a halogen light bulb. It produces
a wide spectra covering visible light and infrared light. There is
a filter that blockes most of visible light and convert the light
source into an infrared one. Then a convex focus the light to
a parallel beam, and a fixed 45 degree mirror [M1] reflects it down into
the main optical path onto a turnable 45 degree placed glass [M2].
This glass reflects the illumination beam toward another 2-D adjustable
mirror [M3], which reflect the beam into the magnet bore on the
eye-tracker mirror [M4] that is made able to be mounted on the
standard Siemens birdcage head coil. The reflection from the
monitored eye goes back through the same optical path (reversed
order, M4-M3-M2) onto the half reflection mirror M2. The passed
through protion of image of the eye is focused by the long focus
lens onto the CCD digital video camera, which takes the real time
video and transfer it through a pair of electronic-optical converters
(to reduce the RF noise) to the eye-tracker tracking electronics
and the two monitors (the smaller one [S1] is on the eye tracker optics
and is inside the scanner room, the larger one [S2] is in the control
room).
Self diagnosis: First of all, please check if the light source
is turned on.
If any of the above-mentioned optical device is misplaced,
misadjusted, or dust-covered, the eye-tracking is guaranteed
fail or unclear.
To check this, please remove the filter to allow the visible
light. The light spot should fall on the eye-tracker mirror (M4),
if not, the optical path is tampered.
If this is the case, we recommend you to call
the BITC
hardware person as soon as possible. He will help you to
re-adjust the optical path.
If the light spot falls on the eye-tracker mirror (M4), but
you still cannot see the image, either M3 was tampered or the
focus of the telescope is tampered. Also please call
the BITC
hardware person for an instant fix.
If you can see the image however it is misplaced, blurred,
tilted, or low in contrast, it usually means that the system
is slightly misaligned, off-focused, or dirty. Please ask
your experiment coordinator to adjust it
for you.
If the eye-tracking video shows up on the inside screen (S1)
but not on the outside screen (S2), one of the optical-electronic
converters might be malfunctioning. Please call
the BITC
hardware person immediately. He will fix this for you
in minutes.
The inside screen (S1) is a RF source. So please remember
shut it off before you leave the scanner room for scanning.
Otherwise severe artifact is guaranteed to appear in your
MRI images.
[TOP]
Q. The eye-tracker is not stable.
What's the problem?
Currently the eye-tracker is used associating the Siemens CP
Head Coil. Since the eye-tracking is usually combined with
visual stimulation, the optical path design has to satisfy
both the need of eye monitoring and the screen viewing.
However, the current optical path design for the dual-function
request is a two-mirror design. A mirror inside the CP head
coil is for viewing and a mirror outside the CP head coil is
for eye tracking.
To avoid overlapping of the two optical path, right now we
have to locate the view mirrow toward the nose to allow a 90
degree eye tracking beam inlet.
With this set up, the subject has to look down for viewing
thus the eyelashes get into the way of the pupil and partially
blocks the optical path of the eye-tracking beam. Under this
circumstance, the pupil size and shape are very interrupted
by the eyelashes, and cause jumping noise and failure of
eye-tracking.
Currently good eyetracking can only be achieved on some
subjects with very careful eye-tracker adjustment.
We are processing getting a single mirror set up, which will
bring in the eye tracking beam side way and reduce the
interference of eyelashes. When this is implemented, it is
expected a much more easier eye-tracker set up and more
applicable population.
[TOP]
Q. How may I project my stimulation
on to the screen?
The system is configured to use the white Gateway2000 computer located
in the right end of the bench in the control room. You can either copy
your stimulation into that computer or use your laptop computer for
your stimulation. There is a grey VGA distribution box on the lower
shelf at the right hand of the scanner console. A blue plug is the
input, which is supposed to be hooked on the visual stimulation source.
There are three output on the box. One is permanent VGA port that
goes to the projector. Another free VGA port can be hooked on the
GATEWAY2000 monitor as local display. A fixed video ouuput is hooked
on a 9" BW TV monitor as secondary local display, in case the
play back quality is important to your project and the GATEWAY2000
monitor has to be disconnected for it interfers with the projector
and reduces the play back quality.
[TOP]
Q. My stimulation computer is properly
hooked up, but there is still no display on the screes.
- Please ask your experiment coordinator
to check if the projector is turned on. The projector is located in
the service room.
- If not the above mentioned case, your experiment coordinator will
is supposed to check the following items:
- if the projector lamp is not burnt
- if the projector is set on the correct input channel
- if the optical path is unblocked and properly set
- if all cables are properly wired
and this should cure this issue.
You are recommended to tell your experiment coordinator that you will
need the projector as soon as, or prior to your arrival.
- If this still does not work, and the projector produces
a white or a blue screen, please check the video set up
of your presentation computer/laptop. The technology is
advancing rapidly. Now most of the laptop is supporting
more than 1280x1024 resolution. However, this is the maximum
the 3-years old projector can take. If your laptop is set
at 1400x1152 or 1600x1200, it is guaranteed that you won't
have it displayed correctly on the projector.
[TOP]
Q. The projected image looks blurred,
distorted, shaded, or too large to fit in the screen. Can it be
improved?
- Blurring : the focus of the projector has been shuffled, or the
projector lens and/or the mirror are dirty.
- Misplaced or distortied : the projector and/or the mirror have
been moved.
- Shaded : the projector is misplaced and the projection beam
hits on the wave-guide wall.
- Too large to fit in the screen : we are sorry that with the
present projector, even at the best optimization, the lower two
corners of the projected image still fall off the screen. But
this should not significantly influence your project. However,
if the projected image looks enormously bigger than the screen,
it means that the lens of the projector has been tampered.
The above information is for your reference. Your
experiment coordinator is responsible to correct these and
provide you projection with the best available quality. We do
not recommend users to correct the above issues by themselves
for it involves sensitive fragile optical devices which may be
easily damaged.
[TOP]
Q. The projected image looks unstable, flicker,
and/or not as sharp as what appears on my computer screen. Can it be
improved?
Just like any LCD monitors, the projector is a discrete pixel display device.
Its physical resolution is marked 1024x768, which is lower than the physical
resolution of most up-to-date laptops. When you feed signal with higher
resolution to the projector, it actually aumatically reduces it to 1024x768.
This will merge edge pixels and may cause instablity to the location of the
edge, and show as flicker on sharp edges.
Also, some not-high-ended display cards output interlaced signal at high
resolution as the trade of its limited processing speed and memory size.
But it may not always tell you about this. This is by default corrected
at the motitor side, and monitor dependent. So, even if you have tuned
your local motior against zigzag, the projector's parameter may not match,
and a vertically zigzag edged image will show up. This effect is enhanced
by the larger pixel size of the projection.
If you use the Gateway2000 computer to present your stimulation, as what
we tested, the best result is obtained at 800x600
resolution and 75Hz refresh rate. Please always design and
test your presentation under these parameters.
If you prefer to use your laptop to do the presentation, you are recommended
to design is at no more than 1024x768 display
resolution and 72 or 75Hz refresh rate.
[TOP]
Q. My subject complains that the projection screen is
not at the right distance. Or I want the screen to be closer to the subject.
What can I do?
The screen is on a skid that can be shifted through the scanner tunnel.
To make it immobile to the tunnel wall, we purposely made it a
relatively tight fit. However, there is a rubber barrier on the
farther end of the tunnel, which prevented the screen skid to be
shifted deep into the tunnel. This place is about 3 feet to the center
of the scanner, where the head of the suject reaches. This is
indeed farther than the most comfortable reading distance, 10-15
inches. However, two reasons make this place the optimized solution
for the screen besides the easy-removal feature.
- The eye-tracker needs the gap above the screen to work properply.
If you shift the screen too close to the head coil, you may have
difficulty to tune the eye-tracker.
- It has already reached the zoom-in limit of the present projector
to display a matching sized presentation at the current screen
location. If the screen is set deeper in the scanner, more
edges will fall off the screen.
In case you do need a closer screen, your experiment coordinator
can assist you to make the change. However, you will have to
be prepared that the edges of the presentation will be cut. Please
test your presentation at your optimized screen distance prior to
your experiment, for the shift usually takes at least 15 minutes.
[TOP]
Q. My stimulation is not centered on
the screen though I have carefully centered the projection
of my computer display. What's the matter?
The 3 years old projector has been a bit obsolate. It is not
perfectly compatible with the most resent laptop computers which
feature 1280x1024 screen resolution as the native resoultion
of their LCD displays. The projector's native reosolution
is 1024x768, which is 4:3 ratio. When an input is set at different
ratio, for example, 1280:1024 = 5:4, and 1280:768 = 5:3,
the projector will left align the display and causes either
pattern shift and/or partially image missing.
To avoid this, you have to make your presentation at exactly
4:3 ratio. The compatible display models are
- 800x600x24
- 800x600x32
- 1024x768x24
- 1024x768x32
- 1152x864x24
- 1152x864x32
- 1280x960x24
- 1280*960x32
[TOP]
Q. My visual stimulation relies on
the brightness and the contrast. How may I calibrate the
projected presentation to match the lab result?
We currently do not have a photometer to do accurate calibration
for you. However, there is a way to briefly objectively calibrate
the screen brightness with a fine digital camera.
Setting your reference screen to a single tone brightness,
measure its aperture size and shutter speed by zooming the
digital camera so that the FOV is the full screen. Then
display the same screen on the projector, do the same measurement
using the same digital camera. Be ware that the camera must
be hold outside the red line in the scanner room. Misuse will
lead to damage of the camera and the magnet. Adjusting
the screen brightness so that measured aperture and speed
match the lab value.
Repeat this for different tone/color/brightness to cover your
desired dynamic range. Then you will have the data for a numerical
calibration.
Since the aperture and speed measure is discrete, the measure
is not scientifically accurate. However, to our experience,
it is mentally accurate enough for brightness related visual
stimulations.
[TOP]
Q. I need to work behind the scanner. The mirror is
in my way. May I remove it?
Yes. But you should ask your experiment coordinator
to do this for you.
The mirror is a fragile glass object. Caution must be take when
handling it. Also, though we had done our best to replace magnetic
part off the tripod, there are still several small internal magnetic
parts remain in the lower part of it. They are far away enough to the
scanner and won't bring in any visible artifacts as what we have tested.
However, we dare not to test if they are positively capable to cause
the tripod be dragged in the scanner. Please NEVER
lift the tripod. In case you have to move it, ALWAYS
push it slowly on the floor.
For the convenience of replacing the tripod, we marked and numbered the
floor of the leg numbers and feet prints. Please always slide the tripod
back to the marked location for the convenience of other users.
[TOP]
Q. Is my stuff MRI compatible?
There are four increamental MRI compatibility levels.
- High magnetic field compatibility
This is fundamental and applies to everything you are going
to bring in the scanner room. Anything that contains significant
magnetic parts is not high magnetic field compatible. They
are surely fatal hazard for they are potentially expected
to be sucked in the scanner bore and place fatal hazard
to anything inside and may destroy the scanner also.
ALWAYS inspect or ask your experiment
coordinator to inspect anything new that will be bring in
the scanner room for magnetic parts.
Keep an eye on iron screws, which hide in nearly everything.
- Gradient/RF magnetic field compatibility
This applies to everything that is to be bring in the magnet
bore. Anything that contains significant conductors, especially
conductor loops, are not gradient/RF magnetic field compatible.
The repid changed electro-magnetic field generated by the
gradient and RF coils is supposed to excite tremendous Eddy
current in conductor parts, especially in conductor loops.
The magnetic field of this current will react with the strong
main magnetic field and cause those things to move unexpectedly,
and be a hazrd of injury. Also, those stuffs may be warmed up
and cause burn to the subject and/or clothes that contact with
it. And, if any sharp edge/angle exists on such conductors,
it can potentially cause electronic shock.
ALWAYS inspect or ask your experiment
coordinator to inspect anything new that will be bring in
the scanner bore for metal parts.
Keep an eye on necklaces, bracelets, wrist watches, and always ask
the subject about metal implants.
- Imaging compatibility
Even a thing is high magnetic field and gradient/RF compatible,
it may still be not imaging compatible. All things that can
induce not neglectable imaging artifacts are categorized
not imaging compatible. You cannot expect to obtain a high
quality MRI image with the existence/operating of such thing.
However, some of them may only influence particular type of
sequences. So it is recommended to test every sequences
you will need.
If you are going to bring a new thing
into the scanner room, after checked their magnetic field
and gradient/RF compatibility, it is recommended to do a
phantom scan before your research, to check the imaging
compatibility of this thing.
The usual non-imaging compatible stuffs are, electronics
that generate RF radiation, cables that can carry RF into
the scanner room like an antenna, and small metal pieces
that causes local image distortion (like hair pins)
- Inversed functional compatibility
Something, especially electronics, may not dramatically
react with either magnetic field, gradient, and RF, and
won't be seen as artifact in images. However, they will
just not work properly, or just be damaged with an MRI
scan. Those things are functionally not compatible with
MRI.
It is generally not recommended of using electronics
in the magnet bore. If it is not avoidable to your project,
it is your risk of doing so. You may expect instrument
damaging, fause activation, noise in data and other
unexpected reactions. It is recommended for you to
ask the vendors of your instrument about its MRI compatibility.
[TOP]
Q. I need to bring a device/instrument/cable
into the scanner room. How may I do this?
Fisrt of all, you should ask your experiment coordinator
to inspect if it contain magnetic parts. If not, it should be put in the
scanner room and switch to normal operation mode and perform a phantom
scan with your desired sequences, to check if it is a positive RF noise
source, or an artifact introducer, or a RF energy collector. In most
case AC/DC converters, which exists in most electronics, are strong
magnetic. This is prohibited in the scanner room. And most digital
electronics are positive RF noise source. Objects cantain large area or loop
conductors are positive RF energy collector and may cause fire hazard
or serious body injury to the subject. You are suggested to bring in
only factory certified MRI compartible devices into the scanner room.
In case this is not available, extra caution and extensive tests must be
accomplished.
The following is a list of common MRI hazard objects:
- non-MRI compatible oxygen bottle or other gas bottle -- they are
bulk iron that nobody can hold against the magnetic field, may cause
total distruction of MRI scanner and fatal to people arround.
- non-MRI compatible patient table and wheel chair -- ditto.
- AC/DC converters -- most of them have a magnetic core, can cause significant
property damage and serious body injury, and fatal to the subject in
the scanner.
- Anything with speakers -- only piezoelectric speakers are not magnetic. Can
cause serious body injury and distruction of your instrument.
- Screws and bolts that fix the box of your device -- This is a very easily
ommited item. Can cause serious body injury and distruction of your instrument.
- Tools -- only certain type of stainless steel tools are compartible
with MRI. We recommend you to use the tools in our MRI tool box.
Your experiment coordinator can help you
to find them.
- Aluminum box or aluminum/copper framed structure -- they are safe outside
the scanner tunnel. However, they can collect significant RF energy
and cuase fire and burn hazard.
- Any cables that are not properly fed in the scanner room may act as an
antenna and introduce noise to the MRI image. Cables that go into
the scanner tunnel can positively collect Eddie current and cause permanent
damage and/or misfunction of your devices.
If it is tested MRI compatible, you are allowed to set up it always in
the certified way. You must ask Your experiment coordinator
for approval if any changes, especially new parts, are to be made.
If it is not MRI compatible, but can be placed outside the scanner room,
the BITC hardware person
can help your to find a solution to wire your signal into the scanner room. Currently
we have 9-pin (serial adaptor), 15-pin high density (display adaptor),
15-pin low density (game adaptor), and 25-pin (parallel adaptor) D-Sub ports,
coaxial, and single pin ports available. Custom ports are practical but will
take time to be installed.
If you want cables into the scanner tunnel, the cable is limited to transfer
only low frequency signal, otherwise it will be significant RF noise source and
is guaranteed to mess your images up. Meanwhile, the cable has to be equipped
with one or two RF attenuators (sort of band blocking filter or low-pass filter),
to protect both the subject and your instrument against RF surge damages.
The BITC hardware person
can build such cables for you.
Also, in limited case, we can offer replacing unsignificant parts in urgent case,
like screws and bolts of your device. However, we are not responsible if this
will void the warrant of your device. We highly recommend you to obtain MRI
compatible modification from the divice vendors.
[TOP]
Q. I have cables into the scanner tunnel. However,
they show random unexpected activities. What is that?
Even though the cables are not in the RF transmitter region, the fast gradient
slewing for certain sequences is responsible for the faradic current in your
cables. As what our test, this current is strong enough to light up LEDs. This
will surely tamper most of the low voltage signals.
We found an easy solution to this issue, to tie some knots on your cable, which
perform as a series of inductors, to suppress and cut off the faradic current.
So, if you see knots on cables provided by BITC, do not remove them without
consulting Your experiment coordinator. They may
be put there on purpose. If you have trouble to do this right on your cables,
the BITC hardware person
can help.
[TOP]
Q. The audio system heard with spark like noise. What is that?
The current audio system of the 3T MRI scanner is an Avotec
SS-3100 Silent Scan system. It is designed as a satisfactory
solution for investigator - subject intercommunication while
no sequence is running with perfect MRI compatibility and
average hearing protection against gradient noise. However,
there are critical flaws that hinder it from being an eligible
audio stimulation platform. We have thoroughly investigated
its limitation and are researching for solutions. The following
is a list representing the current process status.
- Limited maximum output power
The Avotec system limited its output at 120dBA maximum.
This is loud enough and safe to hearing for normal
investigator - subject communication. However, we
were inquired for stronger audio output for particular
projects which need to feed an audio shock to the subject.
This cannot be fulfilled without a major upgrading of
the Avotec audio system.
The power amplifier of the Avotec transducer is inside
the transducer box, which is located on the MRI scanner.
This design voided any possibility of adding on additional
power amplifier to the transducer device.
We are discussing about a custom designed transducer in
place of the Avotec one. However, up-to-date this has
not been on our schedule. We apologize for the inconvenience,
and welcome your sponsoring to boost this proposal. The
estimated cost of this is about $500-$800.
- Preamplifier early saturation
There is a mixer/preamplifier/liminator in the Avotec
console box. It amplifies weak input signal and chop
off strong input signal to about 2Vpp, as the input of
the transducer amplifier. When the LED display on the
console front panel is above 7 (of 10 as full), the
output will suffer chopping off, and renders a distorted
voice to the transducer. This is why the investigators
who required a loud sound stimulation play back
complained sound distortion.
This is not a user configurable feature of the Avotec
system. Probably this setup is for the protection of
the more expensive transducer.
The only thing that can work around this issue is to
have a custom designed transducer built in place of the
Avotec transducer, as listed in issue 1. In this way,
we can lock the maximum output of the console below
7 and still get loud enough play back.
Just like mentioned above. This plan is still staying
on the paper. We hope strong enough user demand and
sponsor will boost the accomplishment of this.
- Left and right channel cross talk
When you purposely mute one channel, either left or right,
you will still be able to hear the play back from the
muted channel, which is weaker but the same content with
the other channel. This renders the research design that
need single ear stimulation impossible.
My tests show that this is the problem of the cable. This
cable is shielded against RF noise in the air. However,
the shielding in between wires are weak or absent. This
should be blamed for the cross talk issue.
The only solution of this is to have the cable totally
replaced, with every channel separately shielded. This
is supposed a $100-200 cost, for really high quality
cables and proper plugs.
Currently there is not particular researches that need
this feature. We will consider fixing it when there are
strong demand.
- Head set mounting instability and unbalanced left and right channel
The Avotec Full Coverage Headset is frequently complained
slipping off optimized position and greatly weaken the voice.
And this is the cause of unbalanced feeling of two channels,
as what I have known.
I have made a full coverage head set out of the 3M 1440
hearing protection ear muff. After we try it in our
projects, we will release it for public. Everybody is
welcome to test this in your projects.
- Poor equalizer quality
The equalizer provided by Avotec is an analog equalizer.
It is either broken or has a terribly designed built-in
poor power supply, which pump in the sound lines a more
than tolerable 60Hz AC noise. I have sent Avotec an
inquiry about replacing or return this unit.
If Avotec cannot help solving this issue, we will need
an alternative high end digital equalizer, which is
supposed about $1000 worth (not yet quoted). This
upgrading is under considering and demands from users
are welcome.
- Sound playback quality and intensity changes day by day
This issue had been identified as the noise from the three
computers below the Avotec equalizer and console. The
audio cables from your audio output device (Laptop) to
Avotec were unshielded analog audio cables, which picked
up the RF radiation from the computers and mixed them into
your presentation, which degraded the sound quality, reduced
the voice to noise ratio, and was sensitive to relative
location of your laptops and the cables.
We remodeled the 3T control room and relocated the Avotec
equalizer on top shelf, and replaced all input audio cables
to high grade digital double shielding audio cables. This
cleared this issue.
Customers claim that there is still a low tone 60Hz AC
noise exists. This is identified from the power supply
of your computer. If you have your stimulation laptop
powered by battery, this will disappear. We cannot help
of this.
[TOP]
Q. How may I record the subject response?
This is a recent implemented function. A bypass from the AVOTEC
speaker was brought out in a standard computer microphone jack.
A cable is ready to be plugged into the microphone jack as
voice input. The knob on the AVOTEC console for adjusting the
output volume of the speaker is also for the input power of
your computer microphone jack. It is your responsibility to
buy the license of a sound recording software, which we do
not have free downloading or right of distribution. Also,
you can use the old console computer to do sound recording,
where a recording software is ready. Up tp date we do not
have a software to filter out the scanner noise from the recorded
sound track. However, with the headset locally made, you can
at least figure out and understand the human voice by ear.
[TOP]
Q. The subject felt cold in the magnet bore. Is this normal?
Yes. This is normal. The room temperature of the MRI scanner room
is set to 66-68 F (19-20 C). This is a bit lower than the comfortable
temperature. We have blanket available to help subjects feeling better.
Please ask your experiment coordinator for it.
[TOP]
Q. The subject felt warm in the magnet bore. Is this normal?
No. This means that some parts of the magnet is radiating
extra heat. You have to report this to your
experiment coordinator to inspect the scanner. He will
decide if you can go ahead of your experiment or you will have
to cancel. We understand the importance of your research. But
safety is always the topmost concern.
[TOP]
Q. The subject complained uncomfortable
in the middle of a run. What could I do?
We understand the importance of your research and the worth of
your time. However, it is always the highest priority of the
health of the subject. You have to yield his request in this
case. However, we recommend you never omit bringing the following
issue to your subject besides the normal safety survey questions.
- You are expected to stay still in the scanner for 1 hour.
Do you want to use the bathroom now?
- You are expected to lay on your back and stay still in the
scanner for 1 hour. Could you please loose your hair?
- The temperature of the scanner room is low. Do you need
a blanket over your body?
And after all, please never forget giving the subject the squeeze-ball
so that he will have a way to let you know in case he does have
trouble staying there.
[TOP]
Q. The MRI console said that local database full. What could I do?
This means the hard driver runs low on disk space. Please ask
your experiment coordinator to clean it up
for you. We usually routinely service the OS. However some
applications bring in large amount of data in one run and may
cause this issue to the users thereafter. Sorry for the inconvenience.
[TOP]
Q. The MRI console's response to my command is too slow
to be normal. Is anything wrong here?
The console has been noticed under heavy threaten of spy-wares and virus
for many times. The OS of the console computer is not a general purpose
OS. It was modified by Siemens for better real time performance, and cannot
do regular windows updates and real time virus and spy-ware filting. It is
very vulnerable to virus and spy-ware. Meanwhile, Microsoft Internet Explorer
is very favorable to spy-wares and trojans in the shape of IE plug-ins. Your
normal web surfing often induce in those spy-wares and trojans from looked
harmless and always ignored advertisments on common websites. You may not
even notice there existence on your computers if you are equiped most recent
windows patches and up-to-date virus and spy-ware filters. However, the console
will be infected and plenty resource will be allocated to log your keyboard/mouse
activities, and slow down its response. In the most serious case we have
experienced, the IE was terribly modified and some of the the console functions
are blocked. It tooks us thousands of dollars worth of labor to nail down the
problem for we cannot do popular uninstall/install to fix it.
Meanwhile, for Siemens service requirement and data transfer ability, we cannot
just disconnect it from the internet.
For this reason, we highly recommend our users never use the console computer
to surf the web. We understand that it is boring in the middle of a long scan.
You are welcome to use the two user terminals (One Dell Dimension desktop, black,
one Gateway2000 desktop) to enjoy the web. If possible, we may concern providing
user laptop connectivity in the future.
This issue always takes at least hours to fix. We are sorry that you
will have to live with this inconvenience for this run. However, please
send a memo to the BITC hardware person.
He will fix it when available.
[TOP]
Q. May I browse Internet where doing experiment?
Yes. However, for security reason, both the scanner console and the
satellite workstation is denied of internet access. If either the
computers located at the right side of the console is not
engaged in presentations or data acquisition, you can use them to
surf the web. If you want to hook you laptop on the internet,
there may be one port available. However, since the hospital
network does not provide DHCP, it is your responsibility to set
up your TCPIP right for internet connection.
We cannot provide wireless hotspot there for it tends to reduce
the image quality.
[TOP]
Q. Where is my data?
The experiment coordinator will pipe all your
data to BITCArchive, which is the BITC computer server, after
your experiment. Your data is supposed to stay there infinitely.
If you are an existing user, you should have an account on
our server. And you can either ssh (secure shell) or sftp
(secure ftp) to access it. If you are a new user, please ask
Steve LaConte or Lei Zhou to open
one and set the path for you.
We also offer free CD-R data back up when your data is still
on the scanner console or the satellite workstation. Please
ask your experiment coordinator for this
option.
Limited by the hard drive capacity of the console, we usually
only keep data 1 month of shorter on it. So please check the
availablity of your data within one month after your experiment.
We cannot take the data loss responsibility if you do not
check for it within one month.
For the BITCArchive, we principly never delete any data. However,
very old data (2 years or older) will be tape archived and
no longer instantly available. Please contact
Steve LaConte if you do need very old data and cannot find
it in the BITCArchive.
[TOP]
Q. How may I put my data back to the
console or the satellite workstation?
Since the limitation of the local hard drive of the scanner
console, your data are supposed to be shipped to BITC_archive
once your scheduled work is done, and removed from the console
after 1 month. An automatic data delivering service runs
on the BITC archive, and ships your data into your BITC data
directory.
For two reasons, the shipped data are no longer left in the
DICOM server of BITC_archive. First, to conserve disk space
by not double saving the data. Second, to avoid the ability
of the DICOM server being saturated by the ultimate increasing
data amount.
To enable retrieving data from BITC_archive, the data must
be kept under the DICOM server in original DICOM format, but
not the renamed filed format in your directory. Once the
total data amount under the DICOM server exceed a certain limit,
the searching of old data may take infinite. Thus we disabled
this option.
The only working way to put the data back now is to have your
data burnt on a CD at the console. Then at any time if you
need it back, you can reload it.
So, if you are planning to take the advantage of the embedded
data analyzing software on the console or the satellite
workstation, please ask your experiment
coordinator to burn a CD for you right after your
experiment.
[TOP]
Q. Something does not work normally.
What could I do?
Most important, never try to solve it by yourself. It may cause
injury and more property damage. Stop every activity, inform the
experiment coordinator. He will inspect
and/or contact proper personnels to investigate it.
Usually, if it is a scanner fault, Siemens service will be
contacted. Otherwise, the BITC hardware person will be the
first one to perform diagnosis, before the system vendor is
involved.
There are some scanner cases that we can solve locally as listed:
- Imager receives no data. Fix: restore most recent
version of scanner system back up.
- Cooling system reports a temperature over threshold.
Fix: clean related filters.
- Anything related with a bad cable.
[TOP]
Q. I got things trapped on the magnet or got somebody injured. What could I
do?
Most important, never try to solve it by yourself. It may cause
more injury and property damage. Stop every activity, evaculate
all movable person from the scanner room, inform the
experiment coordinator. He will perform
aftermath procedure and assist emergency department in necessary.
[TOP]
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