Announcements 2008

December 10, 2008 - Deleting data and transferring data.

The Center maintains proper disk space on both scanners to ensure their proper functions. However the disks may become more than 50% full occasionally (usually during weekends and long holidays). Under these circumstances, certified operators are allowed to delete old data to free up some disk space. When deleting data, we recommend to start from the oldest data and stop when the disk is < 50% full. It is a good practice to NOT remove the data from the last 2 or 3 days to allow these data to be retrieved should errors have occurred in the data transferring process.

On a related note, we can not emphasize enough the importance of transferring data immediately after the scan for the following reasons: 1). Everyone who has access to the control room can delete data off the scanner, and 2) All data will be removed as necessary by GE during some service and maintenance procedures. We recommend logging into the server and making sure all the data have been properly transferred before leaving the room. The Center CAN NOT guarantee retrieval of any data once you leave the room.

December 10, 2008 - HIPAA compliance when completing screening forms.

We would like to remind all operators to pay attention to HIPAA rules when completing screening forms. The "Pre-entry Screening" form and "Operator's Checklist" (available in the control room and on the website) must be completed by all subjects before every scan and be filed with fMRI Center. These forms do NOT ask for subject specific information, such as name, birth date, address and phone number etc for HIPAA compliance. Should you find screening forms in the control room asking for such information please do not use them and notify us immediately. When you download forms from fMRI Center website, please note that there is a "Recruitment/Advanced Screening" form that looks very similar to the "Pre-entry Screening" form. The "Recruitment/Advanced Screening" form is for use by the principal investigator for subject recruitment purposes only and should not be filed with the fMRI center (in order to avoid HIPAA violations).

December 10, 2008 - New anatomical protocol available with better gray-white tissue contrast.

Thanks to Dr. James Brewer and his group, a new high resolution anatomical protocol is now made available for everyone to use. This new protocol uses GE FSPGR pulse sequence with modified parameters (inversion time = 600msec, flip angle = 8) to provide better T1 brain tissue contrast that is similar to that of the MPRAGE on Siemens platforms. It has been shown that the new protocol works well with segmentation tools such as FSL and FreeSurfer. You can find the new protocol under site->head->fmri_Basic->FSPGR_SAG_TI600, or contact Kun (kunlu@ucsd.edu) for assistance. We will continue to support the old FSPGR protocol until later notice.

November 26, 2008 - Upcoming Winter Courses

Cognitive Science 260 - New course in Winter 2009

Course title:
Introduction to Diffusion Tensor Imaging

Instructor:
Lawrence Frank, Ph.D., lfrank@ucsd.edu

Course Time/Location:
Tues/Thurs 2-3:20pm; Cognitive Science Building Rm. 003

Course Description:
The course will teach the fundamentals of diffusion tensor imaging(DTI).
Participants will gain an understanding of the basic underlying
principles of DTI, as well as theoretical and practical considerations
in research design. Emphasis will be placed on practical application to
problems in neuroscience and bioengineering including tools for
acquisition and analysis of DTI data.

Syllabus

 

BIOENG 278 / RAD 278 - Winter 2009

Course title:
Magnetic Resonance Imaging Lab

Instructor:
Eric Wong, Ph.D. M.D., ecwong@ucsd.edu

Course Time/Location:
Lectures W 10-11
Labs W 2-4 and F 10-12; Center for functional MRI

Website for 2008 class:
http://fmri.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.

 

SOMI-276-C Winter 2009

Course title:
Advanced Topics in functional fMRI

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

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.

November 24, 2008 - Human Neuroscience research proposals can now be submitted on-line.

PIs who currently have projects on the 3TE scanner can login to the webschedule system. Click on the Manage My Proposals button and choose New Proposal. For help click on the Help menu item.

For a new webschedule account please email Eman Ghobrial eghobrial@ucsd.edu to request one.

November 24, 2008 - Computer Resources Policy Document Updated.

Computer Resources Policy Document Updated. We have posted an updated computer resources policy document on our website policies section.

Key changes: a. Reminder to all researchers to move their data from the scanner console onto a server before they leave the scan room.

September 24, 2008 - 7T System available for new projects.

We are pleased to announce that the 7T system is available for new projects. Proposals may now be submitted on-line through the website
at: http://fmri.ucsd.edu/info/7TSubmission.html.

There is also an e-mail list for users interested in updates regarding the 7T. To subscribe to this list, please use the following URL:
https://mailman.ucsd.edu/mailman/listinfo/7tusers-l

September 24, 2008 - Policy Documents Updated.

We have updated several of the policy documents that are available at http://fmri.ucsd.edu/policies.html.

Key changes are as follows:

1) There are now separate documents for the 3T and 7T systems. These documents now include the cancellation policies for each of these systems, which have been simplified to more clearly describe the relation to funded hours. In addition, eligibility requirements for operator status and access to the cancellation policy by non-UCSD institutions are defined more clearly.

2) The Operator and Magnet Room policy documents have been merged into one document.

3) Inconsistencies between documents have been addressed and contact information has been updated as necessary.

August 11, 2008 - Problem report and billing adjustment

The PI and the designated Operator are responsible for reporting any technical problems through the CFMRI Webschedule web page when they occur. Even if you are able to obtain direct help with the problem from someone in the Center, we still ask that you report the problem and how it was fixed. This will benefit everyone and provide us with a better record of how often problems occur. In addition, billing adjustment to reimburse for time lost due to scanner problems is contingent on a report being filed within 72 hours after the problem occurs. Additional details will be provided in an updated policies document that will be posted on the CFMRI website in the next week or two.

August 11, 2008 - Normal Mode vs. First Level Mode

After the Patient ID is entered, the "dB/dt and SAR Limits" window appears. Please make sure to click on the left button ("Accept") to enter the First Level mode. If you inadvertently click on the right button ("Normal Mode"), you will be operating in the Normal Mode and may encounter errors in loading protocols that work fine otherwise. Typical errors include invalid slice thickness, TE, FOV or number of slices. This is because user protocols are usually created under the First Level Mode which allows for shorter TR/TE and thinner slices than the Normal Mode. Therefore it is important to select First Level Mode to ensure a successful scan session.

Below is a brief explanation to help you understand the differences between the different modes: dB/dt and SAR are very important MRI safety limits. dB/dt measures how fast the magnetic gradient field changes. Because changing magnetic fields can induce electrical currents, fast dB/dt is often associated with peripheral nerve stimulation (e.g. muscle twitching). SAR measures the amount of radio frequency deposition per unit mass of the patient. It is typically manifested as heating of the body tissue. There are currently three levels of limits (corresponding to the three Modes) on the 3Ts:

_ Normal Mode: Normal Mode is the most conservative mode, it limits the SAR and dB/dt to a level that all persons, regardless of health status, should be able to tolerate.

_First Level Mode: First Level Mode is the typical selection. In most cases, First Level allows for the shortest TE and TR values resulting in optimum image quality and number of slices per acquisition. Therefore, First Level Mode is almost always recommended, especially for research purposes.

_ Second Level Mode: Second Level is password protected. It requires approval by Center director and university IRB, and is not recommended at this time.

April 8, 2008 - Updated Safety Policies

We have recently updated the Center's safety policies, especially with regards to the scanning of children and other subjects who may require additional attention. Copies of the supplementary safety guidelines are available at one of the following links: http://fmri.ucsd.edu/info/safety.html, http://fmri.ucsd.edu/info/policies.html, and http://fmri.ucsd.edu/event/safetylectures.html.

Please take a moment to read over these policies. Principal Investigators should discuss these policies with their groups and make sure that their groups are in compliance with the updated policies.

April 8, 2008 - Training Session for Pediatric Scanning

Operators and investigators who are involved with pediatric scanning will be asked to attend an additional training session focused on the issues particular to the scanning of children. Notifications for these training sessions will be sent out over the next month.

April 8, 2008 - Emergency Call Lists

Emergency Call Lists are now posted in each of the console rooms. Please take a moment to familiarize yourself with these call lists during your next scan session.

April 8, 2008 - Audits

To help ensure that all researchers are in compliance with the Center's safety policies, staff members from the Center will occasionally audit scan sessions. Unscheduled usage of the scanner poses a safety risk, especially after hours. To address this risk, scanner usage will be regularly audited to verify compliance with the webschedule.

Mar 20, 2008 - Touchpad locks installed on the console room doors

For safety purposes, the Center has installed touchpad locks on both the 3Tw and 3Te console room doors. We will send out security codes by the end of today to PIs who have active projects at the Center (one code per PI). The codes will go into effect on Monday (March 24, 2008). Make sure to contact your PI a.s.a.p. if you need access to the console room. The code must not be shared outside your group. We reserve the right to remove any security code if signs of abuse are indicated. Please contact CFRMI (cfmri@ucsd.edu) for problems related to the touchpad locks.

Mar 20, 2008 - Online problem report: a two way portal

Do you know that the online problem report system actually serves as a two-way portal between fMRI users and the Center? Users can use the system to report problems related to the MRI scanner and peripheral equipment. The Center uses the system to send important updates, such as changes in scanner status or availability of the peripheral equipment. Therefore, it is important to check the online problem report regularly before an upcoming scan session. Pay attention to the entries that have an "open" or "in progress" status. Will they pose a problem for your study? Do you need to reschedule the study or contact the Center for more information? If a problem report has not yet been updated by one of the Center personnel and you are not sure if it will affect your upcoming study, it is recommended that you check with one of the Center's technical staff members for more information before changing your plans.

There are two ways to access the online problem report for scanner updates:

1. After you log into the web scheduler, scroll down to the bottom of screen. You will see a table listing all outstanding problems (if there are any). You can click on a problem entry to obtain more details; or
2. After you log into the web scheduler, click on the problem report menu on the top of the screen, and then click Check Status Log. This will give you a list of not only the currently existing problems, but also a history of all previously reported problems.

Mar 20, 2008 - Maximum of 5 people allowed in the console room

To ensure the safety of personnel and equipment, a maximum of 5 people including the operator(s) are permitted in the console room at a time. In the event of a tour or a class when a group of more than 5 is needed in the console room, please coordinate with CFMRI (cfmri@ucsd.edu) prior to the event. Additionally, at least TWO Center certified operators must be present with the group during the event or whenever there more than 5 people are present in the console room. If you have trouble finding a second certified operator, please indicate to Center Admin Staff when contacting us. Note that even when more than one certified operator is present, one operator should always be designated as the primary operator (and assumes responsibility for safety during the scan session).

Mar 20, 2008 - ppge4 updated to handle ASSET

A new version of ppge4 is now available. The new ppge4 is capable of handling fMRI data acquired with the "ASSET" option and is backward compatible with the old ppge4. There is no change in usage. You can download the new program from the CFMRI website ->How TO-> Advanced Topics -> Field Mapping (http://fmri.ucsd.edu/howtos/fieldmap.shtml)