Announcements 2012
December 17, 2012 - CFMRI 2012 Holiday Schedule
To serve the needs of the research community the Center for Functional MRI will remain open during the official UCSD winter holiday closure between Saturday, December 22, 2012 and Tuesday, January 1, 2013. During this period the CFMRI building will be accessible only by proximity card and a minimal number of staff will be available. Operators planning to scan during the holiday closure should make prior arrangements for building access and staff support as needed.
In case of emergency, please follow the emergency procedures posted on the wall of each control room. All other non-emergency problems should be reported through the online problem report system. While on-campus parking in non-reserved spaces is free during the holiday closure, please note that the CFMRI reserved parking spaces will still require a CFMRI parking permit. There are supplies of the parking permits at the front office window and in each control room.
We wish everyone a happy holiday season.
December 7, 2012 - 7T - Scanner Upgrades and Pilot Hours Policy Change
We are pleased to announce that our 7T MRI Scanner system is now well up to speed and operating reliably. A number of major upgrades have been made to the system and a broader range of protocols is available. These additional protocols include anatomical, diffusion tensor, cardiac and perfusion (ASL) imaging paired with post-processing pipelines to facilitate data analysis and interpretation. To help investigators take advantage of these new services we also offer an operator training program. You can check out details of the new protocols and the operator training program athttp://fmri.ucsd.edu/Howto/7T/index.html.
Now that the 7T Scanner is fully operational we are also updating our 7T Pilot Hours Policy to bring it into line with our Pilot Hours Policy for the 3T Scanners. The new 7T Pilot Hours Policy will be effective from January 1, 2013 and will be based on one pilot hour for every four paid hours of scan time, consistent with the 3T Pilot Hour Policy. Any pilot hours in your account prior to January 1, 2013 will remain unchanged. Details of the new policy are contained in the updated Policies and Procedures for Using the 7T Scanner http://fmri.ucsd.edu/pdf/7TPolicies_rev_073123.pdf
November 7, 2012 - 3T - West Scanner 22x Upgrade Completed
We are pleased to announce that the 3T West scanner 22x software upgrade was a success. We reloaded all the protocols back to the scanner and completed testing on all standard sequences. Here are a few items that you may need to pay attention to, should they apply to your protocols:
1. Echo spacing (ESP) change in EPI sequence. We have provided information and instructions regarding the ESP change in the previous announcement. You can check out all previous announcements on our website (fmri.ucsd.edu) under Announcements.
2. For PROMO users, the standard PROMO scans run fine . However we have seen cases in which small deviations in parameters make PROMO fail. If you have a customized PROMO protocol and experience problems running it in 22x software, please update your PROMO scan with the one provided by GE which is located under fmri3tw->Adult ->Other-> PROMO.
3. For all ASL users, we do not expect any problems with standard ASL applications supplied by CFMRI. If you have non-standard applications or have any questions, please feel free to contact David Shin (ddshin@ucsd.edu).
Should you encounter any problems on the newly upgraded 3T West scanner, please do not hesitate to contact Kun Lu (kunlu@ucsd.edu). We appreciate your understanding and support.
CFMRI
October 29, 2012 - 3T - West software update
We are scheduled to update the 3T West scanner software on November 6th (Tuesday) to the latest GE revision 22M4 from the current rev 20.1. Our 3T East scanner is already at 22M4. Rev 22M4 provides important updates on Service methods and some improvements in scanner performance and work flow. Most of the updates are not directly related to MRI operation and there are minimal changes at the scanner console.
To prepare for the software update and minimize the potential impact to the existing protocols on 3T West, we recommend all current users on 3T West follow these steps:
1. Back up your current 3T West protocols on a USB drive.
2. Review the attached information at the end of this announcement on echo spacing change for EPI in 22M4.
3. The software update will not affect the standard ASL applications supported by CFMRI and the standard PROMO and pepolar applications supported by MMIL. However if you are using customized versions of these applications or have any questions, please contact David Shin (ddshin@ucsd.edu for ASL) and Joshua Kuperman (jkuperman@ucsd.edu for PROMO and pepolar).
4. Groups who are part of a multi-site study should notify the study coordinators of this software update.
5. For any other questions or concerns, please contact Kun Lu (kunlu@ucsd.edu).
We appreciate your patience and understanding as we strive to make the most current equipment and resources available to the fMRI community.
Improvement in EPI Echo Spacing (ESP) in GE software rev 22M4.
ESP in EPI pulse sequence dictates how fast EPI images are acquired. A shorter ESP means faster data acquisition, which translates to reduced geometric distortion and more spatial coverage/resolution in a given TR. In GE software rev 22M4, ESP is reduced compared to the older revs, e.g. for an FOV of 22cm with ramp sampling, ESP is 416us in 22M4 vs. 472us in the previous revision. We strongly recommend taking advantage of this improvement in the 22M4 software.
However, if you are continuing an on-going project and wish to retain the old ESP, we have created a modified protocol “fmri_ucsd”. The protocol is set up to use the old ESP by default, but allows manually switching between the old and new ESP by setting the User CV8 (legacy mode). For example, the CV is set to 1 by default to use the old ESP. If you change User CV8 to 0, the new and shorter ESP will be used. The protocol also provides other convenient features such as turning on and off Fermi filters or GE built-in physiological signal recording through relevant user CVs. The protocol can be found under Adult-> Head->fMRI_Basic-> fmri_ucsd.
If you need help in updating the EPI sequence or have any questions, please feel free to contact Kun Lu (kunlu@ucsd.edu).
August 14, 2012 - Osler Lane Construction
Osler lane will be closed to all traffic on Monday, August 20th from 4:00 a.m.- 9:00 a.m. so the CFMRI Reserved Parking spaces will not be available at that time. Beginning August 20th Osler Lane will be reduced to a one-lane road for approx. 4 weeks but this should not impact parking in the CFMRI reserved spaces.
August 6, 2012 - New Website Launch
CFMRI is excited to announce the launch of our newly designed website which you can check out at http://fmri.ucsd.edu/
The new website is divided into four main sections:
• About Us – lots of information on the Center, Our Mission, Faculty, Facilities and Scanners
• Research – information on fMRI, Research Projects at the Center, Pilot Funding, etc.
• Education - Safety Training, Courses, Seminars
• For Researchers – all the information researchers need to get started and use the scanners
From time to time in the For Researchers - Highlights section on our home page we will feature developments at the Center, such as new equipment, protocols or research tools. At present we are highlighting the 7T small animal MRI scanner which is now fully operational. Check out the new 7T Image Gallery and the 7T Pulse Sequences and Protocols that have been developed for use on the scanner.
We hope that you enjoy discovering the new website and that you find it easy to navigate and pleasant to use.
As the website is a work in progress we would appreciate your feedback, especially if you experience any problems or if you have any suggestions.
Please use the Feedback form on the new website or send an email to cfmri@ucsd.edu.
August 6, 2012 - Construction Alert Lot P604-CFMRI Parking
Please see the Construction Alert Notice in relation to Parking Lot P604 across from the CFMRI Building.
The CFMRI has three reserved parking spaces near the CFMRI building and a backup "A" parking permit to ensure adequate parking for all research participants.
However, as a result of this construction and the elimination of parking spaces in Lot P604 it is likely that the reserved spaces may be used illegally by other drivers desperate for a parking space in the area.
For this reason we will be monitoring use of the spaces very closely to ensure that they remain available for research participants on an equitable basis.
Vehicles parked in the CFMRI reserved spaces without a valid parking permit will be reported to the Parking Office (resulting in a parking citation or towing) so it is extremely important that your research participant has a valid dated parking permit displayed on the dashboard of their vehicle. When reserving parking online please always enter a contact number and name for the operator.
Please read the CFMRI Parking Policy and ensure that all users in your group are familiar with it. http://fmri.ucsd.edu/pdf/CFMRIParkingPolicy0711.pdf
Also please remember that reserved spaces and "A" permits are for use by research participants only. Operators and PIs may not use these spaces.
We are aware that parking at UCSD can be challenging so we really appreciate your help in adhering to the CFMRI Parking Policy.
If you have any questions or concerns, please contact Mary O'Malley at (858) 822 0513 or momalley@ucsd.edu
August 6, 2012 - New Carpet Installation at CFMRI in early April
We will be installing new carpet in the offices, conference room and main corridor at the CFMRI on Thurs/Fri/Sat, April 5/6/7 and Thurs/Fri, April 12/13. There will be no access to the conference room on April 5th and 6th.
The work involves moving furniture and belongings from all offices, removing the old carpet, installing the new carpet and moving furniture and belongings back into offices.
This work does not involve the 3T and 7T scanner suites, the mock scanner or the exam rooms. The installation has also been planned to minimize traffic interruptions in the main corridor and impact to MRI scans. We will alert individual scan teams nearer the dates if any inconvenience is likely to arise on particular days.
Thank you for your patience while we improve the appearance of the Center.
March 21, 2012 - 3T - CFMRI Invivo Patient Monitoring System Reaching End-of-Life
Our Invivo 3150M patient monitoring systems (typically referred to as the physio cart) in both the 3T West and 3T East magnet rooms are near the products' end of life. We received notification from the manufacturer that they will stop servicing these units in 2013. In some instances, users also noticed noisy MRI images that could be associated with the use of the Invivo units when they were placed close to the magnet.
Our plan is to decommission these Invivo units soon because the GE 3T scanners already have built-in functions for monitoring and recording pulse rate, respiration and ECG. These built-in functions are robust and easy to use. We have full information on our website http://fmri.ucsd.edu/Howto/physio.shtml describing how to set up the built-in physiological monitoring and how to perform physiological noise removal using the recorded physiological data. The GE scanner, however, is not capable of monitoring end-tidal CO2. We are looking for an MRI-compatible device on the market for measuring end-tidal CO2. If you know of any product to recommend, or if you have special requests for the CO2 monitoring, please kindly let us know.
The following are our recommendations for researchers who are currently using the Invivo system for physiological monitoring.
1. If you do not measure end-tidal CO2, we recommend switching to the GE built-in physiological monitoring system. Information on the built-in system is on our website http://fmri.ucsd.edu/Howto/physio.shtml. You can also request hands-on training by contacting Kun Lu at kunlu@ucsd.edu.
2. If you need or prefer to stay with the Invivo system to finish on-going studies, please place the cart outside the 10 Gauss line (marked on the magnet room floor) and avoid any loops and kinks in all cables. This should minimize the occurrence of noisy images. One group on 3T West scanner also stated that it may help reduce noise by placing the cart on the east side of the table than on the west side of the table. However, we do not yet have sufficient data to confirm this observation.
We appreciate your understanding and cooperation.
January 31, 2012 - 3T - Improvements to ASL Post Processing Options
We are also happy to announce two additional features on the CBFDAP.
1. Automated ventricle annotation step
2. Support for reprocessing of existing data with different input options
For a further explanation, see the links.
If you have any questions regarding these changes, particularly those related to scanning under new protocols, please contact David Shin at ddshin@ucsd.edu.
January 31, 2012 - 3T - Improvements to ASL Protocols
First, some changes were made to improve the ASL protocols on 3TE and 3TW listed below.
1. Brain_Perfusion_FAIR_4S
2. Brain_Perfusion_FAIR_SS
3. Brain_Perfusion_8pPCASL
4. Brain_Perfusion_OptPCASL
All protocols listed above no longer require a separate CSF scan. For instructions on how to acquire a CSF image as part of the ASL scan and on processing the new data on the CBFBIRN Database and Analysis Pipeline (CBFDAP), please refer to the following link:
https://cbfbirn.ucsd.edu/site/db_sim_asl_csf.action
Another improvement is that users no longer need to manually set research CVs for protocols 3 and 4. Simply prescribe and proceed to scan! Please note that you will still need to acquire a time of flight scan to define the tagging plane. Existing protocols and post processing options can be used just as they were before. However, we encourage you to adopt the improved versions for minimizing user error and convenience.
January 18, 2012 - 3T - NoMoCo Pillow Set available for testing at CFMRI
NoMoCo has left a new vinyl coated pillow set at the Center for users to try out and provide some feedback. More information on the pillow set can be obtained at http://www.nomocopillow.com
If you are interested in trying out the kit, please contact Mary O'Malley at momalley@ucsd.edu
January 2, 2012 - 3T - Winter 2012 Courses
BIOENG 278 / RAD 278 - Winter 2012
Course title: Magnetic Resonance Imaging Lab
Instructor: Eric Wong, Ph.D. M.D., mailto:ecwong.ucsd.edu
Course Time/Location:
Lectures M 1-2 at the CFMRI Conference Room
Labs WF 2-4 at the CFMRI 3TWest scanner
Website: Course Website
Prerequisites: Basic knowledge of linear systems and consent of instructor.
Brief Description:
This lab course provides hand-on experience with MR physics, data acquisition, image formation, and data analysis, using a human MRI scanner. It will focus on the basic principles of MRI, including scanner hardware, spin echoes, gradient echoes, frequency encoding, phase encoding, and RF pulses. Thi! s will be accomplished through 1 hour of formal instruction and 4 hours of scanner time per week. The last 3-4 weeks will be devoted to student projects, and grading will be based on lab reports. NOTE: BENG 280A is listed as a prerequisite for this course, however, because BENG 280A was not offered this fall, the prerequisite is waived for this year, and this course will be more introductory in nature, focusing more on basic concepts than advanced topics.
SOMI-276 C - Winter 2012
Course title: Advanced Topics in fMRI
Organizing Instructor: Rick Buxton, mailto:rbuxton.ucsd.edu
Lecturers: Greg Brown, Rick Buxton, Anna Devor, Frank Haist, Eric Halgren, Tom Liu, Becky Theilmann
Course Time/Location:
Tues/Thurs 2-3:30, fMRI Conference Room, starting Jan. 10
Website: Course Website
Prerequisites: A basic understanding of fMRI, equivalent to SOMI-276A
Brief Description:
This course combines lecture! s and discussion of current papers describing the latest devel! opments in fMRI. This year's topics include: quantitative fMRI (Buxton), mapping networks with resting state correlations (Haist and Liu), combining MR spectroscopy with fMRI (Theilmann), basics of EEG and MEG signals and their combination with fMRI in a multi-modal approach (Halgren), applications of fMRI to test computational neurocognitive models (Brown), and the coupling of blood flow and neural activity (Devor). Presentation of papers is by students taking the course for credit, but other fMRI investigators are encouraged to attend and participate in the discussions.