The head-only 3.0 Tesla Siemens Allegra unit previously located in the ALBMC has been moved to the 6th floor of the Ronald Reagan Medical Center. Questions relevant the Allegra scanning are addressed in a separate section of this FAQ.
Both whole body scanners have a wide range of different types of structural and functional MRI pulse sequences including 3D volume imaging (T1-weighted), T1-weighted and T2-weighted multislice imaging, BOLD fMRI, contrast bolus passage perfusion imaging, diffusion imaging (DWI, ADC and DTI), angiography (MRA), single voxel proton spectroscopy (MRS) and single slice spectroscopic imaging (CSI). These pulse sequences can be applied to the head, neck and spine.
Multi-nuclear spectroscopy (i.e., spectroscopy of nuclei other than protons) is not supported.
The Sonata (1.5 T) unit has the following receive-only coils:
The Trio (3.0 T) unit has the following coils, which are receive-only except where otherwise specified:
The systems include ECG pulse and respiratory monitoring capabilities for purposes of triggering gated scans. Unfortunately, at present, the system does not provide the capability to archive such data for purposes of correlating the signals with fMRI time series. Since the system can display the physiologic data continuously on the screen throughout the scan, the best option at present might be to rig a system to record the visual data from the screen.
For the Trio, the inner diameter of the bore, including shim coils, gradient coils and the RF body coil is 60 cm. Without these items, it is 90 cm.
Although the software supports printing to film, we do not have the hardward needed for filming. Your best option is to burn the data to CD for the radiologist. If the radiologist needs film and has a Siemens system, he or she will be able to upload the CD images and have them filmed. However, most clinical reads at UCLA are now based on electronic images, so printing to film will probably not be necessary.
Compressed air and vacuum are currently available. Connections are in place for oxygen, but oxygen is not currently available.
Dr. Jeffry Alger has an FDA approved power injector which is installed in the 1.5 T Sonata scanner room. An FDA approved Spectris MR injector is installed in the Trio scan room. You should contact Dr. Alger to determine whether the power injector can be used for any studies that you are contemplating that would require contrast administration. Investigators requiring contrast administration should be aware that:
Yes, but please note that the scanner beds are not detachable. Consequently, you must transfer non-ambulatory subjects using an MRI compatible wheelchair or gurney, both of which are available and stored in the scanner rooms. Standard wheelchairs and transport beds should NEVER be brought into the scanner rooms. You must become familiar with safe use of the MR compatible wheelchair and gurney before doing studies involving such subjects.
There are no additional coil acquisitions currently planned, but the Trio suite was specifically constructed to allow for future upgrades with ample equipment room space for installation of additional electronics cabinets.
The Sonata penetration panel includes:
The Trio penetration panel includes:
The Trio has software version VB17A
The Sonata has software version VA35A
It is fairly straightforward to get k-space data for most sequences. However, fMRI data is an exception in the sense that a somewhat complicated procedure must be followed to copy k-space data off of the reconstruction system, and the copy must be completed prior to acquisition of the next sequence.
A complete listing of installed software packages can be found here
The scanners have a built-in quality control procedure that is applied quarterly by Siemens personnel to handle many QC issues. The standard phantoms that come with the scanners are all fluid filled phantoms and are not designed to quantify spatial distortions. Standard daily QC protocols are run on phantoms for the Siemens scanners.
Because the ALBMC is formally separate from the UCLA Medical Center and since we will not perform routine MRIs for clinical purposes, there is no requirement for ACR certification.
Formal ACR certification requires many components that are irrelevant to operations in the ALBMC. For example, it is necessary to present a knee scan as part of the process.
Please see the questions related to safety training and access to the scanners for training and protocol development.
No studies will be scheduled without all of the following:
If you plan to transition an IRB approved protocol from the Allegra to the Trio, you should inform the IRB for administrative purposes and also modify the informed consent form if the scanner was specified in the previously approved consent materials. In particular, if you have made reference to the MR scanner as an "Allegra" scanner or as a "head only" unit or similar language, this needs to be modified to reflect the fact that you will be scanning on a Trio whole body unit. In the unlikely event that you have included photographs of the equipment or physical dimensions, those would also need to be modified, and we can work with you to track down the corresponding information.
You should also take this opportunity to review your consent forms and protocols for any other statements that might have been rendered inaccurate as a result of the scanner upgrade.
Review your consent forms and submitted protocol carefully. Any inaccurate information should be modified by an IRB amendment before submitting the protocol for formal review and approval by ALBMC staff.
All scheduling is handled through the ALBMC database. You can request a database account here. Cancellations made after 5 PM of the day before the study will be charged 20% of the cost of the study. Studies must be cancelled BEFORE their scheduled start time to avoid being charged full price for the study. Cancellations are not accepted once the scheduled start time has arrived.
You and your staff will need to complete a formal ALBMC safety certification process. This process consists of several parts:
Please contact Trent Thixton to initiate this training process.
Yes, unless you are a Radiology faculty member who works in MR regularly.
If you are ALBMC safety certified and have an ALBMC and IRB approved protocol, you can make arrangements with on of our technologists for additional training.
Scheduling is handled through the ALBMC database.
Passcode access to the scanners is currently limited to individuals who have been fully safety certified and who have active MR protocols.
The scanners come preconfigured with a wide range of clinically motivated scan protocols including structural scans, fMRI sequences, diffusion sequences and spectroscopy. Although catalogued by specific body parts, most of the preconfigured sequences are applicable to any scan region. Due to their optimization for clinical applications, these protocols are not necessarily optimized for research purposes, and you may wish to consult with more experienced colleagues regarding specific research protocols. It is fairly easy to build new protocols using the scanner software.
ICBM protocols are available on the Sonata and the techologists are familiar with them. The ICBM project at UCLA did not use the Trio scanner, so ICBM specific protocols are not currently available.
ALBMC faculty and staff with the most experience creating protocols on the Siemens system currently are Jeff Alger, Roger Woods, Trent Thixton and Elizabeth Pierce. In addition, if you have colleagues who have Siemens protocols, it is often very easy to reconstitute a protocol from a single DICOM image from their system.
Siemens will only allow people who have attended their special programming course to do pulse sequence programming.
No. The stimulation protocol information is used to create t-test images as part of automatic data processing. This assumes a simple on-off protocol. You can use this feature if you want, but its validity should have no impact on the raw data that you collect. When appropriate, you may find t-test image helpful in providing an early look at your data (e.g., in deciding whether a pre-surgical fMRI study is of good quality).
Yes. Stimulation equipment is available on the Sonata.
Most fMRI processing software that reads native DICOM data is now able to handle Siemens mosaic data. The scanner software does include an option for reversing this mosaicing process. However, this will create an enormous number of files since each slice is saved as a separate file. The LONI Debabeler is able to convert mosaiced images into regular 3D Analyze files. You may also find software at http://airto.bmap.ucla.edu/BMCweb/HowTo/SpecialFormats.html helpful for unmosaicing Analyze format images. The publicly available xmedcon program will also undo mosaics.
This may no longer be an issue... We have brought this problem to Siemen's attention and hope to have a resolution to this problem soon. The requested TR is used when computing the predicted scan time, but the actual scan time reflects the use of a rounded off value. The image headers reflect the requested TR, not the actual TR.
The number of preparation scans is set such that the total preparation time is greater than three seconds. This table gives some examples:
| TR | Number of preparation scans | Explanation |
| 3001 to infinity | One preparation scan | 1*3001>3000 |
| 3000 | Two preparation scans | 2*3000>3000 but 1*3000=3000 is not >3000 |
| 2500 | Two preparation scans | 2*2500>3000 |
| 2000 | Two preparation scans | 2*2000>3000 |
| 1501 | Two preparation scans | 2*1501>3000 |
| 1500 | Three preparation scans | 3*1500>3000 but 2*1500=3000 is not >3000 |
| 1001 | Three preparation scans | 3*1001>3000 |
| 1000 | Four preparation scans | 4*1000>3000 but 3*1000=3000 is not >3000 |
| 751 | Four preparation scans | 4*751>3000 |
| 750 | Five preparation scans | 5*750>3000 but 4*750=3000 is not >3000 |
| 601 | Five preparation scans | 5*601>3000 |
| 600 | Six preparation scans | 6*600>3000 but 5*600=3000 is not >3000 |
| 501 | Six preparation scans | 6*501>3000 |
| 500 | Seven preparation scans | 7*500>3000 but 6*500=3000 is not >3000 |
All electrical equipment needs to be reviewed to assure that it is implemented in a way that does not introduce electrical noise into the scanner environment. All objects to be brought into the scanner room must first be screened to assure that the are MR safe. A powerful handheld magnet is available for such screening. All such devices must be reviewed with an ALBMC technologist and approved before use by Roger Woods or Jeff Alger.
The Sonata allows user defined DTI directions and theoretically can support an arbitrary number of directions, but memory issues practically limit whole brain scanning to 30 directions. The Trio includes protocols for up to 256 directions and has sufficient memory to support 256.
You will have two options for data transfer:
To maintain necessary data confidentiality, DICOM transfers to DICOM servers other than the designated ALBCM server will not be permitted. If you are involved in a project that requires data to be submitted to a specific DICOM receiver, we can work with you to set up a secondary DICOM transmission from the ALBMC server to the receiver.
Spectroscopy is not saved in DICOM format and any DICOM file transfers that include spectroscopy data will terminate with an error when the spectroscopy transfer is initiated. You must transfer spectroscopy data to a CD. Make sure that you do not include spectroscopy data among data that you are attempting to archive using DICOM transmission to the ALBMC server.
The Siemens MR scanners use DICOM as their native file format and this format must be used for CD's burned from the console. It will also be used for files transmitted electronically. Those accustomed to Analyze, EPI, GE MR or MINC files may not find this an easy transition. For example, each two-dimensional image is stored as a separate file, and none of the file's extrinsic file system attributes (name, creation date, etc) is sufficient to determine the ordering or selection of slices to regenerate a volume or to construct an fMRI time series. A method for converting your files to Analyze format is provided here. Many data analysis packages are now able to handle DICOM format data.
Several computers are available in the user's computer room on the first floor of the ALBMC. In addition, a desktop computer is available in the Trio scanner room. All of these computers are equivalently configured, with home directories maintained separately on a server so that a user can log into their home directories from any of the machines. Four floating Matlab licenses are available for these machines. Copies of AFNI, AIR, FSL, ImageJ, MultiTracer, ScanStat, SPM and several other software packages are maintained centrally on the server for use on these machines. A listing of software is provided here. The machines also have the capacity to burn CD's so that data can be downloaded for analysis elsewhere. Anyone with scanning privileges is eligible to get an account on these machines which, like the scanners and server, are the property of the ALBMC.
Yes. Before being authorized to scan independently, you must demonstrate practical proficiency for MR safety measures, including knowledge of the various risks and safety procedures. Failure to adhere to the policies will lead to revocation of scan privileges, even if no adverse event results from this failure.
Precautions and screening measures must be employed to assure that subjects with pacemakers, implanted metal, etc. are not injured. IF YOU ARE UNCERTAIN, DO NOT BRING THE SUBJECT INTO THE SCAN ROOM. ALBMC faculty will assist you in determining whether specified implanted objects are compatible with safe scanning. Any subject who does not pass the standard safety screening procedure cannot be scanned unless specifically authorized by designated ALBMC faculty. Non-faculty staff members are not authorized to provide such authorization.
Even small metal objects can become deadly projectiles in the scan room. Objects should never be brought into the scan room if you are uncertain as to whether they are ferromagnetic. Objects known to be ferromagnetic should never be brought into the scan room except as in accordance with specific guidelines approved in advance for that particular object by Jeff Alger or Roger Woods.
The scanners as currently configured will not allow a scan to run if it will exceed FDA specified limits for energy deposition or gradient induced nerve stimulation in the body. You must correctly specify the subject's age, weight and sex at the onset of scanning since these factors may be included in the computations. The scanners have two operational modes with respect to energy deposition, both modes comply with FDA guidelines.
All subjects should be provided with earplugs and/or headphones to protect them from the acoustic noise associated with scanning.
The scanners are capable of producing nerve stimulation with some protocols. The software will automatically post a warning to the scanner operator when nerve stimulation is deemed possible. Assuring that subjects' arms and legs are uncrossed with reduce the likelihood of nerve stimulation.
Issues related to pregnacy are addressed under a separate question.
The patient beds on the new scanners are not detachable. Consequently, it is not possible to simply wheel a subject experiencing a medical emergency out of the scanner on the scanner bed. An MR compatible gurney is stored in the Trio 3T scanner room. If your study involves subjects at increased risk of a medical emergency, you need to develop a formal plan for handling medical emergencies BEFORE scheduling any such subjects for an MRI study. This plan must be formally reviewed and approved by the ALBMC director. At an absolute minimum, it will be necessary to assure that adequate personnel are available to safely remove an unconscious and/or uncooperative subject from the scan room at any time during the study using MR compatible means. Please see the ALBMC MR Safety Manual for additional details.
Women who are known by the investigators to be pregnant may not participate as subjects in MRI scanning, except:
Laboratory testing to exclude unsuspected pregnancy is not required as part of MR laboratory policy. Compliance with any protocol-specific policies established during IRB review of the project is required.
The ALBMC policy regarding scanning of women known to be pregnant is based on the following document:
In this document, which is a report of the American College of Radiology Blue Ribbon Panel on MR Safety, it is recommended that pregnant patients be allowed to undergo MR scanning providing that the risk-benefit ratio warrants the study. This includes documentation that:
Special consenting procedures, not recommended for routine clinical studies, are recommended for clinical studies of pregnant women to document that the patient understands the risk-benefit considerations.
Items 2 and 3 above clearly imply that it is the opinion of the Panel that MR procedures of pregnant patients should be deferred until after the pregnancy has ended unless it is in the best medical interest of the patient or fetus not to wait. Although many subjects who undergo research studies in the ALBMC are not patients, there is no rational basis for applying different standards to pregnant research subjects than are routinely applied to pregnant patients. When provision of medical care is not part of the research project, there cannot be an argument that participation in a research associated MR study is in the best medical interest of the subject or fetus. Furthermore, unless the research study specifically involves pregnancy, there is no detriment to the goals of the research study expected from excluding women known to be pregnant. Research studies specifically involving pregnancy are excluded from the general ALBMC policy. Scanning of pregnant women in connection with other studies can be considered on a case-by-case basis. Explicit IRB approval to study pregnant subjects will be a necessary condition for approval of any such exceptions to the general policy.
The document referenced above does not recommend routine screening of women of childbearing potential to prove that they are not pregnant prior to MR scanning for clinical purposes. Consequently, no such screening is required as part of ALBMC policy for research studies. ALBMC policy regarding pregnancy is subject to revision as new information and recommendations become available.
In view of HIPAA requirements and the general interest in studying patient populations and sensitive subjects, our data transfer and achiving systems are designed to incorporate all appropriate security measures. As a user of the facility, there are three important steps that you must take to help us assure that your subject's privacy is protected:
All data is automatically transferred electronically to the ALBMC server in a directory where it is only accessible to the server adminstrators and to your group.
If your project is covered by a Confidentiality Certificate, you may transfer data electronically to the ALBMC server. However, you must make sure that the Confidentiality Certificate covers the server, and you must notify ALBMC staff of the special status of the data and provide a copy of the Confidentiality Certificate so that we can produce it in response to subpoenas or queries by law enforcement. It is the PI's responsibility to assure that proper notification has been given--written notification and a request for verification by ALBMC staff is recommended.
Data may be retained indefinitely at the discretion of ALBMC staff until the PI or someone who has assumed the PI's responsibility for the data requests in writing that ALBMC staff delete the data. Written requests to delete the data may require up to 60 days to fulfill on the server, though efforts will be made to accommodate requests for expedited deletion when appropriate. For archived data, a period of up to one year may be required to delete the archived version in response to a written request. Expedited deletion will not be possible for archived data.
Keys to the front (and back) doors are issued by Leona Mattoni to researchers with approved protoccols that require access to the building.
Access codes to the scanners are issued by Leona Mattoni to researchers with approved protocols that require access to the scan rooms. Access will be granted to the Trio, the Sonata, or both, as appropriate for conduct of approved protocols. Please do not share your codes with anyone; if members of your staff need access they will be granted their own codes. Codes discovered to be used by someone other than the person to whom they were issued are subject to immediate revocation.
The phones next to the front and back doors have pre-programmed numbers for the 1.5 T and 3.0 T scan rooms. By dialing the appropriate two digit code, your subjects can call you in the scan room to let you know that you are at the door. You can buzz them in by pressing '9'. Please do not buzz in people you do not know as this defeats the purpose of the security measures.
Lockable cubbies are available in both the Trio and Sonata controls rooms where you and your subjects can separately lock away your valuables. Please make sure that you and your subjects leave the keys after removing your valuables.
Trent Thixton is available Mondays, Tuesday, Thursdays and Fridays (10 hours/day), primarily to assist with Sonata studies. Elizabeth Pierce provides similar support for the Trio on an 8 hour workday schedule Monday through Friday. Mary Walker may be available if Trent or Elizabeth are not. The presence of a technologist will not obviate the need for a member of your research team to be present for MRI studies to handle consenting, set up and running of stimulation paradigms and handling of any unanticipated subject related problems.
All inpatients must be accompanied by a nurse or physician qualified to handle any medical problems throughout the time they are in the ALBMC. The only exception to this policy is patients who are admitted to the CRC whose condition would not justify hospitalization in a non-research setting.
Outpatients with conditions that might require acute medical management (e.g., incompletely controlled epilepsy) must be accompanied by a physician qualified to handle the medical problem. The physician must remain in the building as long as the patient is in the scan room. A crash cart is available in the building, and physicians accompanying patients should be certain that they are familiar with the crash cart's location. The crash cart is metal and should NEVER be brought into the scan room.
Please note that the scanner beds are not detachable. Before scheduling a study of a patient with increased risk of a life threatening event that might also impair their ability to ambulate, you must discuss contingency plans with ALBMC staff for getting such a patient out of the scanner in the event of an emergency.
Contact a Brain Mapping staff or faculty member. Details regarding who to contact will be posted in the scanner control rooms. Other users are not authorized to make service calls to Siemens under any circumstances. Our maintenance contract covers Sonata service from 9 to 5 on Mondays through Fridays, excluding holidays. The Trio service contract covers service from 9 AM to 9 PM on weekdays, excluding holidays. We are charged extra for service provided outside these time frames. Unauthorized calls to Siemens service may result in loss of scanning privileges and/or billing to cover associated charges by Siemens. A list of appropriate Brain Mapping faculty or staff to contact is kept in the printed copy of the MR safety manual in both scanner control rooms.
Contact a Brain Mapping Faculty member. Do not call Siemens service or you will be held accountable for resulting charges. Our service contract does not cover after-hours service, so it is likely that the scanner will remain down until regularly scheduled service hours.
Applications for new projects are handled through the ALBMC database. A detailed checklist was provided above.
When you submit a project in the ALBMC database, you can indicate that ALBMC support will be required to complete the project. You should also indicate in the project description that it is a pilot study and describe your plans for pursuing subsequent funding. If the project is subsequently approved from a scientific standpoint, you may then submit an email request for financial support. Please note that scientific approval of such projects in the database does not constitute a commitment by the ALBMC to provide financial support. Funds available to support such projects vary from year to year. The selection of projects for funding depends on fund availability, the scientific quality of the project. Preference is also given to individuals in early stages of a committed academic career.
No. Technical development is treated no differenty from any other kind of scanning and is charged at the same rate. If pre-production scan time is needed for testing of protocols, etc., this is a justifiable expense that should be incorporated into your grant budget. You may apply for pilot funds for a project that involves technical development as described above, but pilot studies are not "free" or "discounted" scans, but rather scans that are charged at the usual scanning rate to funding sources that are administered by the ALBMC.
Ownership of the Allegra is expected to be transferred to the hospital at a yet to be determined time in the upcoming months. Commitments to allow continuation of ongong Allegra projects were made to the ALBMC prior to relocating the Allegra to the hospital and will remain an absolute condition for transfer of ownership. Users with Allegra projects that are approved and active in the ALBMC database will be contacted during April, 2008 to determine how long they will be able to continue Allegra scanning. Projects that can switch immediately to the Trio without scientific compromise will be asked to do so. We anticipate two categories of projects that will need to continue on the Allegra for scientific reasons: 1) longitudinal studies where subjects previously scanned on the Allegra need to be rescanned; and 2) cross-sectional studies where introduction of a new scanner as a variable would lead to unacceptable loss of statistical power. Arrangements will be made for these two types of studies to continue scanning on the Allegra until the project end date as designated in the ALBMC database when the project was approved. Consideration will be given to compelling arguments for extensions of up to one year beyond the originally proposed end date, but such extensions will need to be justified and approved during April, 2008.
The ALBMC is no longer accepting project proposals that utlize the Allegra 3T scanner. Unless you have an appropriate reason for doing otherwise, you should submit it instead as a Trio 3T project. The ALBMC plans to transfer ownership of the Allegra to the hospital at a yet to be determined time in the future. Once ownership has changed, new Allegra projects can be submitted through mechanisms that will be determined by the committee reponsible for the Allegra. Given the location of the Allegra adjacent to the intensive care unit of an acute care hospital, studies involving inpatients will be most appropriate and will undoubtedly receive priority.
A number of concerns have been posed:
All of these issues are under active discussion as of March 30, 2008 and will be addressed in a way that assures that ongoing ALBMC studies can be completed. Any rumors that you may have heard merely reflect the fact that the details have not yet been sorted out. Please let us know if there are other concerns not addressed on the above list.
Updated September 25, 2013