Center for Functional MRI In the Department of Radiology

Announcements 2007

Dec 18, 2007 - Magnetic Resonance Imaging Lab Course Announcement

BIOENG 208 - Winter 2008
Magnetic Resonance Imaging Lab

Instructor:
Eric Wong. ecwong@ucsd.edu

Website for 2007 class:
http://cfmriweb.ucsd.edu/ecwong/BE208W07.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 cover 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. The last two weeks are reserved for a final project, which can be student initiated.

Dec 17, 2007 - Advanced Topics in fMRI Course Announcement

SOMI 276C (Winter 2008)
Advanced Topics in fMRI

Time: Tues and Thur 2-3:30, starting Jan 8, ending March 13
Location: fMRI Conference room
Contact: Rick Buxton (rbuxton@ucsd.edu)
Other Instructors: Anna Devor, Eric Halgren, Frank Haist, Tom Liu, Giedrius Buracas

Prerequisite: Familiarity with fMRI basics and data analysis (equivalent to 276A and B) Grading: Pass/fail

Each year we plan to offer the Advanced Topics course in the Winter Quarter, with the topics changing each year.

This year we will combine lectures and discussions of recent papers to explore three themes:
1) How can we use CBF measurements to better interpret the BOLD response?
2) How are fMRI responses related to electrophysiology and other measures, and how can these methods be combined?
3) How can we use fMRI to investigate dynamic patterns of activation?

As always, students, fellows and faculty are welcome to join us. Please contact Rick if you are interested in attending, and whether you would like to take the course for credit.

Nov 7, 2007 - Protocol reload on 3Teast
The upgrade of 3Teast to the HDx platform (14x) has been completed.
We are now reloading user protocols to the scanner by request. A list of the old user protocols can be found here: http://cfmriweb.ucsd.edu/download/3teastprotocol_list.txt
Please send Kun Lu (kunlu@ucsd.edu) the EXACT names of the protocols that you would like to reload onto the scanner. Keep in mind that most of the old protocols require modifications to work in the new system.
Nov 7, 2007 - Renaming/reordering DICOM Images
DICOM files generated by the upgraded 3T scanners (HDx, 14x) are not saved in sequential order. For the AFNI to3d program to create an AFNI BRIK with the correct slice order, these dicom files need to be reordered. We have developed a Perl script 'imseq' for this purpose.
The script is now available on all our servers as well as for download. For more information, please visit the CFMRI website and look under HowTo->Data -> Pre-Processing.

Currently 3Twest scanner automatically reorders the dicome files during data transfer using gecopy. Starting from Nov 12th, this feature will be disabled. Users on both 3Twest and 3Teast scanners will need to run the imgseq script offline before procssing the data.
Nov 7, 2007 - Removing data on the scanner
The chance for a system crash on our 3T scanners increases dramatically if the database is more than 50% full. Therefore we appreciate everyone's cooperation in removing data promptly after having securely transferred the data. The following steps are recommended for transferring and removing data off the 3T scanners:
a) Use gecopy to transfer your data to one of our servers
b) Login to the server and make sure the data has been correctly transferred
c) On the scanner console browser, highlight your exam
d) Click 'Remove' on the top menu bar
e) Select 'remove examination' from the drop-down menu
Nov 7, 2007 - User WIKI website
The fMRI users group WIKI is now online. The purpose of the WIKI is to facilitate the sharing of ideas, methods, and expertise amongst the members of the UCSD neuroimaging community. Please follow this URL http://fmriusers.ucsd.edu to visit the WIKI website.
Nov 5, 2007 - Next Safety Lecture Date is Nov 9, 2007
Next Safety Lecture Date:
Nov 9, 2007
Center for fMRI Conference Room
1:30 - 3:00pm
Please e-mail CFRMI (cfmri@ucsd.edu) if you need training.
October 18, 2007 - fMRI Users Group Meeting
Date: Thursday, October 18, 2007
Time: 4:30 pm to 6 pm
Place: Room 2047, Cellular and Molecular Medicine East (CMME)
(Bldg 803 on the UCSD map).

The agenda for the meeting is:
(a) Introductory remarks
(b) An overview of field mapping software by Kun Lu.
(c) Top 5 highlights of FSL software by Adam Aron.
(d) Top 5 highlights of AFNI software by Alan Simmons.
(e) Time for open discussion.
September 19, 2007 - HDx training for the 3TEast users
As previously announced, the 3TEast scanner is scheduled for a system upgrade to the HDx platform at the end of October.
Compared to the current platform, the HDx upgrade introduces a number of performance enhancements as well as changes in the graphical user interface. To facilitate a smooth transition, we are offering training sessions on the 3TWest scanner to help users become familiar with the HDx platform and test out their protocols on the new platform.
HDx protocols tested on the 3TWest scanner can be transferred to the 3TEast scanner once the upgrade is complete. Interested users should contact CFRMI @ cfmri@ucsd.edu to schedule a a training session.
For more information on the new features of the HDx platform and the impact on user protocols, please refer to the notes (http://cfmriweb.ucsd.edu/kunlu/070417usrmtgpub.pdf) from the last fMRi User's Group meeting.
If you have any further questions please contact Kun Lu @ kunlu@ucsd.edu
September 10, 2007 - Update on the Brain Perfusion Protocols on 3twest
Dear fmriusers,

We have just updated the the brain perfusion protocols on 3twest. The updated protocol does not require users to wait 30 seconds before the CSF calibration scan. Instead, the wait time is built-in to the pulse sequence and as a result the CSF calibration scan is now 36 seconds long (v.s. 4 seconds before the update). This change was motivated after numerous occurrence of unusable data due to user forgetting to wait before pressing scan. Therefore it is strongly recommended that everyone who acquires brain perfusion data takes the advantage of this change.

There are two ways to update:

1. Grab the new CSF scan from the center protocol list: Head ->
    Brain_Perfusion_SS (or Brain_Perfusion_4S) -> CSF.

or

2. view edit the CSF series, click on user CV screen, and type -8 in
    the first field: CV0 Number of dummy samples, and save. (-8 as in
    negative eight.)


Additional notes:

1. The updates does not eliminate the need for pressing manual
    prescan and DONE.

2. The update does not affect the data quality.

3. Do nothing if you do not wish to update.

4. All future users will be automatically using the updated protocol.

5. The updated protocol will be available on 3teast after the
    scheduled system upgrade in early November.


For questions, please contact Kun Lu (kunlu@ucsd.edu).

Thank you.
September 10, 2007 - ppge4 for FSL4.0
Dear fmriusers,
The recently available FSL4.0 introduced some changes to the avw tools, and as a result, ppge4 fails when calling these tools. You can now download a new version of ppge4 that is compatible with FSL4.0. More information can be found in How To Page -> Field Mapping.
August 23, 2007 - Fieldmap code (ppge4) is updated and now available for Macs.
ppge4 did not use to work in Macs because ppge4 uses the program dicom2 which was complied only for Linux. Thank for the help of Dr. Brock Kirwan, ppge4 no longer calls dicom2, instead, it uses AFNI build-in command dicom_hdr. Therefore users can now process fieldmaps in Mac OS with AFNI (Mac version) and FSL installed.

This update does not impact Linux users. Linux users may choose to update ppge4 to remove the dependence on dicom2. No difference in usage is expected.

The updated files can be downloaded here:

http://fmri.ucsd.edu/howto/fieldmap.html#2

July 31, 2007 - Upgrade of 3T East Scanner

We will be upgrading the 3T East scanner to the HDX platform (also referred to as 14x) during the week of October 29 thru November 2nd. In addition, we anticipate that our acceptance testing of the system will last until Nov 10.

As many of you know, HDX is GE's latest MRI operating platform and offers a number of performance enhancements, such as real-time parallel imaging. The 3T West scanner was upgraded to HDX earlier this year.

We have tried our best to coordinate the scheduling of this upgrade to facilitate the completion of ongoing studies, and we appreciate your continued cooperation and understanding as we move forward. We will be posting additional information as the upgrade date approaches.
July 31, 2007 - A new version of the field map processing code, ppge4, is now available

Compared to the previous versions (i.e. ppge and ppge3), ppge4 offers more robust performance in dewarping EPI and DTI images acquired on the GE 3T scanners, especially when there are large phase variations in the field map data due to field inhomogeneity and subtle subject movements. Note that ppge4 requires NIFTI neuroimage format. Please visit the How To Page -> Field Mapping for more information on ppge4 download and usage. Because of the improved performance, we strongly recommend that all users switch over to ppge4.

Apr 30, 2007 - New Cancellation Policy -- May 2007
*** new policy goes into effect--revise your June schedule now ***

As you know, the cancellation policy has become a critical issue because
some PI's are scheduling far ahead for many more hours than they plan to
use. As a result the reserved schedule is full, but the schedule of hours
actually used is more sparse, with slots going unused that other
investigators wish they could have used.

Following on the recent Users Meeting and discussions with PI's, we are
implementing a new policy that ties pilot hours closely to cancellations
http://cfmriweb.ucsd.edu/pdf/cancellation_policy_may2007.doc
 Please take a close look at this, because we are making it effective for
the month of June. By the new policy a PI may retain responsibility for up
to 30 days for a time slot they reserve and subsequently cancel. For this
reason, I strongly encourage you to revise your June schedule right away.
That is, if slots you have currently reserved for early June are not
cancelled this week, you may be responsible for them even if you cancel them
later. And even though the new policy starts with the June schedule, if you
can cancel excess reserved slots in May as early as possible it will help
everyone with this transition.

I appreciate the thoughtful comments from several of you--this is a tough
problem and everyone's ideas are helpful. I think the new policy will help
us all, making it easier to get time on the scanner for everyone. And for
those of you who are already scheduling responsibly and using the slots you
reserve, you will do better in pilot hour rewards under the new policy.

Richard B. Buxton, PhD

Apr 17, 2007 - 3TWest Upgrade Info
Where: CFMRI conference room
When: April 17, 2007, 12-1:00 pm
Topic: 3TWest upgrade and cancellation policy

(Link to the PowerPoint file)

Dear colleagues,

Now that the upgrade of the 3T West scanner is complete, we are planning a fMRI users meeting about what this upgrade means to the researchers. The new system offers new possibilities but also some details about how to run the scanner have changed. We will also discuss issues related to the planned upgrade of the 3T East system etc.

The meeting will take place on April 17, at noon in the CFMRI conference room. We look forward to see you at the meeting!

Center for Functional MRI

Feb 26, 2007 - New Scanner Rates Effective March 1, 2007
Due to the rising operating costs in the last few years, the 3T scanner recharge rate will be increased to $525 per hour as of March 1, 2007. The rate for non-University users will be at $761 per hour.

The 7T rate and rates for other services will remain unchanged.