Announcements 2009
December 29, 2009 - 3teast software update and possible impact on existing protocols
We are planning to update 3teast scanner software to the latest HDx version 15M4 in a few weeks. The 15M4 provides some functional enhancements and additional clinical applications. Moreover, it contains a timing fix which will benefit studies requiring milliseconds accuracy. This update will not impact protocols that uses only GE product sequences or the sequences provided by fMRI center, i.e., ASL, CBF and field maps. However, protocols that use other sequences (including the RIL ones) may be affected by this software update. If you know or suspect that your protocol will be affected, please contact your fMRI lead or Kun Lu (kunlu@ucsd.edu) at fMRI center a.s.a.p so that a solution can be worked out before the software update.
December 29, 2009 - Center recommended anatomical (T1) protocol with great gray-white tissue contrast
We have annouced the availability of an optimized high resolution anatomical (T1) protocol in 2008 which was developed by Dr. James Brewer's group, and would like to remind everyone again of this protocol. It uses GE IR-FSPGR pulse sequence with optimized parameters (inversion time = 600msec, flip angle = 8) to provide great T1 brain tissue contrast comparable to that of the MPRAGE on Siemens platforms.
The protocol has been shown to work well with segmentation tools such as FSL and FreeSurfer. You can find the new protocol on the scanner console under site->head->fmri_Basic->FSPGR_SAG_TI600, or contact Kun (kunlu@ucsd.edu) for assistance. We will continue to support the old FSPGR_SAG_TI400 protocol which was recommended before this optimized protocol became available.
December 17, 2009 - Do NOT transfer protocols between 3twest and 3teast at this time.
We have just updated the 3twest software to the latest HDx version 15M4
(see the next item for the reason). The 3teast is still running an older
version 14M5. Because of the version difference, protocols from the
two scanners are no longer compatible. We will update the 3teast
software to 15M4 too in a few weeks and the date will be announced.
Until then, please do not transfer protocols from one scanner to the
other, or upload previously saved old protocols to 3twest. If you need
certain protocols on the scanner, we will be happy to assist you in
manually creating them.
December 17, 2009 - 3twest software is updated to the latest HDx version 15M4.
The 15M4 contains a timing fix which will improve the performance of
some studies that require millisecond accuracy. It also provides a few
functional enhancements and additional clinical applications. The
update should have no impact on fMRI data and existing protocols.
Operators may notice a few minor differences in the graphical interface.
But they are self-explanatory and no changes are needed in operating the
scanner.
December 17, 2009 - Prepare for the 3twest MR750 upgrade.
We have already announced that the MR750 upgrade of 3twest will start on
Dec 28th 2009. In preparation for the upgrade, We remind all PIs on
3twest to write down important parameters of any protocols that you want
to save. Additionally, please remove any equipment stored in 3twest
suite that belongs to your group. You may have noticed that we have
already started relocating non-critical equipments and storage in that
area. As the upgrade goes underway in the next few weeks, there will be
more constructions and traffic around the 3Ts which may affect the
3teast operations occasionally. We apologize in advance should you
encounter any inconvenience due to the upgrade and urge everyone to be
extra cautious of the surroundings during the upgrade period. As
always, please feel free to notify us if you have any questions or
concerns.
December 17, 2009 - CFMRI will be open during the 2009 winter holidays.
In order to serve the needs of the research community, the Center for
Functional MRI will remain open during the official University winter
holiday closure from 12/19/2009 to 01/03/2010. The 3teast scanner will
be fully available during this time, and the 3twest will be available
before Dec 28th 2009. Operators requiring CFMRI staff assistance should
make prior arrangements with individual staff members as support during
the holidays is limited. 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 scheduling
system. We wish everyone a happy holiday season.
December 10, 2009 - Upcoming Winter Related Courses 2010
UCSD Extension ECE-40262. Principles of Biomedical Imaging
Time: Wednesdays 6-9 PM, 01/20/10 - 03/17/10 (9 meetings)
Location: Room MV25, UCSD Extension Mission Valley Ctr, 404 Camino Del Rio S., Ste. 102, San Diego, CA
Contact: Anna Leigh Rack-Gomer - arackgom@ucsd.edu
Course Description: Discover the principles of biomedical imaging pertaining to radiography, computed tomography, ultrasound and magnetic resonance imaging. Students will gain an understanding of the instrumentation, physics, image reconstruction methods, image quality issues and applications of each imaging modality. Emphasis will be placed on the signal processing aspects of biomedical imaging and the following topics in signals and systems theory will be covered: convolution, Fourier transforms, sampling, noise, filtering and image reconstruction. This course will benefit healthcare providers and biomedical researchers currently employing imaging methods, and anyone interested in the field of biomedical imaging or applied signal processing.
Course URL:
http://extension.ucsd.edu/studyarea/index.cfm?vAction=singleCourse&vCourse=ECE-40262SOMI-276-C Winter 2010
Course title: Advanced Topics in Functional MRI
Organizer: Richard Buxton, rbuxton@ucsd.edu
Instructors: Richard Buxton, Eric Halgren, Anna Devor, Rebecca Theilmann, Frank Haist, Thomas Liu, Giedrius Buracas Course Time/Location:
Tues/Thurs 2-3:30, Center for Functional MRI Conference Room First meeting:
January 5
Prerequisite: SOMI-276-A, or equivalent introduction to fMRI
Course Description: The course combines lectures and discussion of current papers within two general themes: 1) Understanding the physiological origins of the different signals measured with functional neuroimaging techniques, including current ideas about the connections between neural activity, blood flow, energy metabolism, the BOLD response and EEG/MEG signals; and 2) Identifying networks and patterns of activation, including white matter fiber tracts, resting state correlations and the default network, and novel brain reading methods. The course is graded pass/fail, based on student participation in discussing current papers. We encourage anyone interested to attend and contribute to the lively discussions.SOMI-276-B Winter 2010
Course title: Functional MRI in Cognitive Neuroscience Research: Design and Analysis
Organizer: Amanda Bischoff-Grethe, agrethe@ucsd.edu
Instructors: Amanda Bischoff-Grethe, Ph.D., Richard Buxton, Ph.D., David Dubowitz, M.D., Ph.D., Lisa Eyler, Ph.D., Christine Fennema-Notestine, Ph.D., Frank Haist, Ph.D., Tom Liu, Ph.D., Christina Wierenga, Ph.D.
Course Time/Location: Mon/Wed 2:30-4, Center for Functional MRI Conference Room
Prerequisite: SOMI-276-A, COGS-276, BENG-280A, or equivalent introduction to fMRI Course Description: Functional magnetic resonance imaging (FMRI) is an essential tool for the study of brain activity correlates to sensory, perceptual, and cognitive functions. This course aims to provide a solid foundation in FMRI experimental design and analysis sufficient to allow the student to conduct and report high-quality research using FMRI. The course is targeted to students new to FMRI research or those students with some experience in FMRI research that are seeking a deeper understanding of the various options available for analysis of FMRI data. The course will include multiple design and analysis assignments and several open discussion forums to provide practical experience in addition to the lecture format. The course will primarily focus on the use of the AFNI suite of programs for data analysis and visualization. Other software tools will be discussed where practical (e.g., FSL, SPM).BIOENG 278 / RAD 278 - Winter 2010
Course title: Magnetic Resonance Imaging Lab
Instructor: Eric Wong, Ph.D. M.D., ecwong@ucsd.edu
Course Time/Location: Lectures M 10-11
Labs W 2-4 and F 2-4; Center for functional MRI Website for 2008 class:
http://cfmriweb.ucsd.edu/ecwong/BE208W08.html
Prerequisites: BENG 280A or basic knowledge of linear systems and MRI 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 review basic principles of MRI and key applications, including scanner hardware, spin echoes, gradient echoes, echo-planar imaging, MR angiography, fMRI, and perfusion imaging. This will be accomplished through 1 hour of formal instruction and 4 hours of scanner time per week. Each week will cover one topic, and grading will be based on lab reports.
December 4, 2009 - 3Twest upgrade starts on Dec 28, 2009
The 3Twest upgrade schedule has been finalized. The upgrade will commence 8am on December 28th 2009 (last Monday of December), and is expected to be completed by mid to late February 2010. The last day of scanning on 3twest before the upgrade is Dec 27th 2009.
All remaining data on the 3twest console must be transferred before 8am on the 28th or will be lost. For users who store equipment in the 3twest area, please make plans to remove them soon. The Center will back up all protocols on 3twest before the upgrade. However, not all protocols are guaranteed to work on the new MR750 system. So we advise PIs to write down important experimental parameters so that the protocols can be re-created on the new system if needed.
Please feel free to contact us if you have any questions regarding the upgrade. We look forward to a smooth transition to the new MR750.
October 29, 2009 - Updates on the 3twest upgrade plan
We now know that the 3twest upgrade will NOT start in November due to production delays at GE. We expect the earliest start date for the upgrade to be during mid to late December this year. As indicated in previous email updates, we will guarantee a 30-day notice before the 3twest is taken down. Therefore users can schedule time on 3twest up to 30 days ahead until the final upgrade date is announced. Please feel free to contact us if you have any questions.
October 14, 2009 - CFMRI 2009 Winter Holiday Schedule
In order to serve the needs of the research community, the Center for Functional MRI will remain open during the official University winter holiday closure from 12/19/2009 to 01/03/2010. The 3T East scanner will be fully available during this time. Due to the scheduled upgrade of the 3T West scanner, we will be posting updates indicating the availability of the 3T West scanner. Staff support will be limited during the holiday period. Operators requiring CFMRI staff assistance should make prior arrangements with individual staff members. 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 scheduling system. We wish everyone a happy holiday season.
September 28, 2009 - Updates on 3T upgrade plans
The preparation for the MR750 upgrade of the 3T west scanner is currently underway. The upgrade will most likely start in mid-November 2009. We will post the exact date of the upgrade once we know and at least a month in advance. The 3T east scanner upgrade is expected to occur in early 2010, three months after the new 3T west is fully functional. If you have any questions or concerns regarding the proposed time line, please please feel free to contact us.
Sepember 14, 2009 - Upcoming Fall 2009 Related Courses.
Bioengineering 280A. Principles of Biomedical Imaging
Time: Tuesdays/Thursday 9:30-10:50 AM, Powell-Focht Bioengineering
Hall Room 161
Contact: Thomas Liu - ttliu@ucsd.eduFundamentals of Fourier transform and linear systems theory including
convolution, sampling, noise, filtering, image reconstruction, and
visualization with an emphasis on applications to biomedical imaging.
Examples from optical imaging, CT, MRI, ultrasound, and radiographyCourse URL: http://cfmriweb.ucsd.edu/ttliu/BE280A_09.html
SOMI-276A. Functional Magnetic Resonance Imaging in Cognitive
Neuroscience: Foundations
Prerequisite: None
Time: Tuesday and Thursday, 2:00-3:30, CFMRI Conference Room
Contact: David Dubowitz - dubowitz@ucsd.eduFunctional magnetic resonance imaging (FMRI) is an essential tool for
the study of brain activity correlates of sensory, perceptual, and
cognitive functions. This course is the first of a series of 3
courses, and aims to provide an introduction to functional
neuroimaging. Students will gain a grounding in the fundamental
physical principles of magnetic resonance imaging, the underlying
neurochemistry and energetics that make functional neuroimaging
possible, and will learn how functional MRI can provide insights into
neural physiology and cognition function. The course will include
hands-on tutorials with an introduction to using MRI scanners, so
that students will understand how FMRI data are generated and can be
assessed for quality.Course URL: http://learnfmri.ucsd.edu
July 29, 2009 - 3T Upgrade Plans.
As some of you may have heard, the CFMRI is planning a major upgrade of the 3T systems. After extensive research and discussions, we have decided to upgrade our current GE HDX scanners to the new GE Discovery MR750 system. Based upon our testing of the system, we expect that the MR750 system will provide greatly improved performance and stability for a wide range of fMRI studies. We are planning on upgrading the 3T West scanner in the October/November 2009 timeframe. The upgrade of the 3T East scanner is tentatively scheduled for early 2010. As we get closer to the upgrade, we will post information about the exact dates and also provide additional information regarding the details of the transition.
July 29, 2009 - New Administrative Staff Members at the CFMRI.
The CFMRI is pleased to welcome Peggy Totzke and Mary O'Malley to our administrative team. Peggy and Mary bring with them many years of experience working for corporate and non-profit research organizations. Peggy will be taking on many of the duties previously handled by Teresa Hsiao, who retired in late June. Mary will handle the duties previously handled by Linda di Leo, who recently accepted a promotion within UCSD. Please join us in welcoming Peggy and Mary to the UCSD fMRI community.
May 7, 2009 - New reserved parking for research subjects
The Center was able to secure a new reserved parking space for research subjects. The new space is labeled 133D and is right next to the current reserved parking 134D. Both spaces can be booked on-line through the CFMRI website. A CFMRI parking decal is required at all times. A complete policy for using the reserved parking can be found on the CFMRI website.
Please note that, by UCSD policy, the reserved parking and A-permit parking provided by CFMRI are strictly for use by research subjects. The Center may lose the parking privilege if this policy is not adhered to.
May 7, 2009 - Instructions available on CFMRI website for on-line proposal submission
We have added step-by-step instructions on how to submit research proposals on-line on CFMRI website (http://fmri.ucsd.edu/Howto/proposal.shtml). All research proposals for 3T and 7T magnets should be submitted on-line from now on.
April 15, 2009 - Update on subject parking due to SOM constructions.
Due to the recent constructions in School of Medicine, it has been difficult for everyone to find parking spaces across the street from the fMRI Center. This map (http://fmri.ucsd.edu/pdf/fmri-parking-map.pdf) shows all parking lots within waking distance to the Center. Those who reserve A parking permits can park in available A(red), B (green) and S(yellow) spots in any of these parking lots. The reserved parking in front of the fMRI center is not affected by the constructions and available 24/7 for subject use.
We remind all researchers and subjects to arrive at least 15 minutes earlier to allow time for parking. We are actively seeking solutions to alleviate the parking situation and will keep everyone posted.
April 15, 2009 - Researchers: pleases arrive early to greet your subjects.
All researchers please arrive before your subjects do. Wandering subjects cause unnecessary interruptions to the Center's normal operation. In addition to arriving early, please give subjects your contact info (preferably a cell phone number) for them to call when needed. We strongly recommend filling out the Participant Parking Form available on the CFMRI website and asking subjects to carry this form when coming for scans.
March 11, 2009 - Safety update: Don't wear medication patches during MRI.
When you screen subjects for a MRI don't forget to ask them about medicated patches. This is on the screening form (Q20) and on the operator checklist. The patches are quite common (e.g. nicotine patches to stop smoking, contraceptive patches, pain killer patches, anti nausea patches.... etc). They are worn against the skin under the clothing, so they may be overlooked if you don't specifically ask. Even though they appear clear there may be trace amounts of metal in as many as 25% of them which can cause a burn when exposed to the rapidly switching gradients in the MRI.
They don't all carry a warning label (even though some of them are not MRI safe). The recommendation is to remove the patch for the duration of the scan, and then stick it back on again afterwards. Here's a recent news article http://fmri.ucsd.edu/docs/med-patches.html.
Don't forget: If you have any questions or concerns about this or any other safety issues, the safest course of action is to ask for advice.
March 11, 2009 - Research proposal submissions are now on-line.
All new research proposals (3Ts and 7T) should now be submitted on-line through the webschedule program. To apply for a webschedule account, please email Eman Ghobrial (eghobrial@ucsd.edu) with PI information (name, academic title, phone and email). If you need to update the PI and billing information after the on-line submission, please fill out the Proposal Information Update Checklist(available on cfmri website http://cfmriweb.ucsd.edu/forms.html) and email the completed form to CFRMI (cfmri@ucsd.edu).
Please note that IRB/IACUC approval letters have to be emailed to cfmri@ucsd.edu before any proposals can be approved.
March 11, 2009 - The data transfer script 'gecopy' is improved.
We have modified the gecopy script to print out more information on the screen such as subject ID and series descriptions. Its usage remains the same. This modification was motivated by occasional incidents in which operators mistakenly transfered the wrong data. Please review the screen print out carefully before transferring data.
February 2, 2009 - New projectors on 3Twest and 3Teast.
New projectors (Dell 2400MP) have been installed on 3Twest and 3Teast since the start of 2009. In some rare cases, we have found that the display settings of some laptops may need to be re-configured to work with the new projectors. Most users should not have any problems with the new projectors and will not require assistance. However, if you have not already scanned with the new projector and think you may need assistance, you can arrange to have Peter Wong (pywong@ucsd.edu) assist you at the beginning of your next scan session to make sure that your laptop is properly configured.
February 2, 2009 - DTI users: the diffusion directions have been changed since the EXCITE to HDx system upgrade.
It has been brought to our attention that the diffusion directions used by the GE DTI pulse sequence were changed when our 3Ts were upgraded from EXCITE to the HDx platform. 3Twest was upgraded in Jan 2007, and 3Teast was upgraded in Nov 2007. Since most groups doing DTI work work with an experienced technical collaborator to perform their DTI analysis, there is a good chance that your collaborator is already aware of this. However, if you are not sure whether you are using the correct diffusion directions for your DTI data analysis, please check with Kun Lu (kunlu@ucsd.edu).
February 2, 2009 - Do not prop open the front door of the fMRI building.
We have found that some users occasionally prop open the front door of the fMRI building at night and then accidentally leave it open through the night. This poses a great concern to the safety of research equipment and personnel at CFMRI. We again remind everyone that the doors to the entrances of the building and to the scanner rooms should NOT be propped open. Your privilege to access the building will be revoked if you are found responsible for violations. If you suspect malfunctions of any doors of the building, please report them to CFMRI immediately or call campus police after hours.