This notice pertains to the data handling of CFMRI MB fMRI/DTI protocols.
As of today, the raw data (P-files, .dat files) will stay in the S3 Bucket for three days before being archived to a CFMRI backup server. Therefore, if you opt to save the raw files, it is important to copy them from the bucket within three days after your scan session.
The reconstructed NIFTI files will be available on the scanner and can be transferred out using the 'cfmricp' command along with the DICOM/physio files.
Note that if you need to copy the NIFTI files from the bucket, the same three-day policy applies.
By now all MB users should have direct access to the S3 Bucket. If not, please contact David Shin (firstname.lastname@example.org) for further assistance.
As part of the Center's OceanX initiative, we are making realtime recon available for CFMRI MB fMRI/DTI protocols on both 3T systems.
Users are no longer required to move large data from the scanner and run offline reconstruction, which incur heavy use of CPU/memory resources and hours of processing time.
At the end of each MB scan, your P-file and associated .dat files will be archived automatically and a reconstruction job will be initiated with powerful compute resources, which will return the reconstructed NIFTI files to the scanner computer (/export/home/007) in minutes (DTI: about 10:00 minutes; fMRI: about 15 to 20 minutes).
One of the major benefits of this new option is the ability to review your data on the scanner. During your session you will have the ability to assess quality and determine if a rescan is required within the same session.
As before, your DICOM and NIFTI files can be transferred out to your account on CFMRI servers (e.g. cfmri, fmriserver, fmrimems, fmri2) using the ‘cfmricp’ command. If desired, your P-files and .dat files will be made available for retrieval from an archived repository for up to 3 months.
Over time, our plan is to build on this capability to offer additional processing solutions to our users.
A couple of side notes:
- When we upgrade our 3T systems to the latest software (DV26)/hardware, we are likely to transition to vendor supplied real-time recon solutions for most multiband protocols.
- If your last run of the session is a MB fMRI, please note that it can take up to 20 minutes before it becomes available for cfmri cp transfer. The CFMRI tech staff is happy to help if your NIFTI files are missing.
Due to unexpected shipment delays from GE, we will be completing a partial upgrade of the 3TW scanner on the week of November 6th.
The partial upgrade will incorporate the latest RF technology that will improve data quality. The software (DV26) and reconstruction engine upgrade will be rescheduled in the near future.
The updated closure of 3TW will take place beginning Monday, November 6th and ending Thursday, November 9th (noon). At noon on Thursday, 3TW will be re-opened for general usage. Please feel free to book these slots in CALPENDO!
If you have any questions or concerns, please do not hesitate to contact us at email@example.com.
We are planning to upgrade the software on 3T West to the latest version supplied by GE (DV26). We expect this upgrade to improve system performance and support next generation imaging protocols and hardware. DV26 will add advanced multiband reconstruction capabilities to 3T West.
The proposed upgrade schedule and closure of 3T West is currently set for Monday, November 6th through Sunday, November 12th. In the coming weeks, we will send further instructions on how users can prepare for the upgrade.
In the meantime, if you have any questions or concerns about the upcoming DV26 software upgrade, please do not hesitate to contact us at firstname.lastname@example.org.
We appreciate your patience and understanding as we strive to make the most current equipment and resources available to the research community.
Since the closure of parking lot 604, there has been a significant increase in illegal parking in our reserved spaces. As a result, it is necessary to modify and strictly enforce our parking policy.
- Parking spaces and A permits may only be booked on Calpendo in conjunction with a 3T or mock scan booking.
- We now have two A permits available for booking on Calpendo.
- In order to ensure it is returned after being used, an A permit requires a deposit (e.g., driver’s license) from the Operator/Research Coordinator.
- All cars parked illegally will be photographed and kept on record here at the Center.
- Illegally parked cars will receive one warning on their windshield.
- Repeat offenders are subject to citation and/or towing at the owner’s expense.
- Cars with CFMRI Permits, but no reservation in Calpendo, are considered illegally parked and subject to citation and/or towing at the owner’s expense.
- If there is a car parked in your subject’s parking spot, please see Juliana in room 1002 as soon as you are aware of the issue. Please do not have your subject park in a different reserved space without speaking with Juliana.
- Parking is for human subjects only. This is UCSD policy.
As a reminder, valet parking is available in the newly opened lot on Osler Lane. It is $5/day with an “A” permit, and $20/day without.
When the fall term begins, we expect parking to become even more difficult for staff. It is imperative that you plan extra time to ensure you can park and be at the Center prior to your human subject’s arrival.
We appreciate everyone’s cooperation to ensure that the reserved parking spaces are available for the human subjects who need them.
The post upgrade interface on the 3T East console includes a few minor changes that you should be aware of.
- When you initially run your protocol, you will need to set the anatomical region of interest before the system will allow the localizer to run. To set this parameter you will need to select the “Anatomical Region…” button on the bottom left corner of the graphical user interface (see image below). For most protocols, you will select Head -> Brain in the dialog box that appears after selecting the “Anatomical Region…” button. Your preferences can be saved into your protocol to ensure that you are only required to enter the anatomical information during the initial acquisition.
- As part of the upgrade, GE installed state-of-the-art RF hardware. On the user interface, an updated parameter field exists labeled “RF Drive Mode”. Please ensure that RF Drive Mode is set to “Quadrature” to prevent protocol inconsistencies across software versions (see image below). Quadrature is the default RF Drive Mode setting in the overwhelming majority of user protocols, post upgrade.
The 3TE scanner upgrade has been completed successfully. In addition to the software upgrade, the scanner is now equipped with the latest RF technology from GE that will improve data quality for the body and muscular skeletal imaging.
If you have questions or issues with your existing 3TE protocols, please contact David Shin or Aaron Jacobson.
We are also making the new data transfer script available (already running on the 3TW scanner) that replaces gecopy, physiocopy, pcopy.pl, making it easier for operators to transfer scan data. Just open a terminal and type 'cfmricp'. It will show a list of scan sessions for the last 48 hours (labeled with a unique number). Operators can enter the session number and the script will automatically grab relevant files (e.g. P-files, DICOMs, physio files) and transfer them to the user defined cfmri account/server. Note that operators can continue to use the original data transfer scripts if desired.
On February 1st, we sent you an email in regards to our system upgrade plan for the 3TE scanner by the end of the first quarter of this year.
We have scheduled the upgrade during the week of 04/24 to 04/28.
If you are a 3TE user, please read the following to prepare for the upgrade:
Backup your current 3T East protocols on a USB drive.
If you have multiple protocols that were saved in the past but may no longer be used, please identify these protocols (backup to your USB drive if needed) and remove them from the protocol list.
If your protocol uses non-stock GE sequences that are not developed by CFMRI, please notify us soon so we can coordinate with you to obtain the updated sequences. Below is a list of projects that are most likely to need to contact us:
If you have any questions or concerns about the upgrade, please do not hesitate to contact us at email@example.com.
We are planning to upgrade software on 3T East to the latest version supplied by GE (DV25). We expect this upgrade to improve system performance and support next generation imaging protocols and hardware. DV25 will add multiband capabilities to 3T East.
The upgrade date is to be determined but we expect to complete the upgrade by the end of the first quarter of this year. In the coming weeks, we will send further instructions on how users can prepare for the upgrade.
In the meantime, if you have any questions or concerns about the upcoming DV25 software upgrades, please do not hesitate to contact us at firstname.lastname@example.org.
We are pleased to inform you that the 3TW scanner has a new data transfer script that replaces gecopy, physiocopy, pcopy.pl, etc, making it easier for operators to transfer scan data to cfmri servers.
It's simple to use. Just open a terminal and type 'cfmricp'. It will show a list of scan sessions for the last 48 hours (labeled with a unique number). Operators can enter the session number and the script will automatically grab relevant files (e.g. P-files, dicom images, multiband calibration files, physio files) and transfer them to the user defined cfmri account/server along with a detailed data summary file.
Note that operators can continue to use the original data transfer scripts if needed.
For questions or problems, please contact David Shin.
To serve the needs of the research community the Center for Functional MRI will remain open during the official UCSD winter holiday closure from Monday, December 26, 2016 through Tuesday, January 3, 2017. 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 Problem Reports system in Calpendo. Further
information on Reporting a Technical Problem can be found at: http://fmri.ucsd.edu/Howto/3T/calpendohowto.html
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 and look forward to working with you in 2017.
We are pleased to announce that the 3TW scanner is now equipped with IDEAL IQ, a pulse sequence and post processing suite that allows quantitative assessment of fat for the body and muscle imaging applications.
If you are interested in using this tool for your study, please consult the CFMRI technical team.
Additional product description can be found from this link.
We are pleased to inform you that the 3TW scanner upgrade has been completed successfully. In addition to the software upgrade, the 3TW scanner is now equipped with a next generation image reconstruction engine. This hardware upgrade will significantly improve data throughput, which will benefit all users.
Multiband users, in particular, will notice dramatic improvement in scan processes as time lags between multiband scans are eliminated. Also note that multiband users will no longer need to use RDS for data transfer. Instead, the image data will be saved directly on the scanner computer. Please schedule a few minutes of informal training with the CFMRI technical team prior to your first multiband scan so we can explain how the new process works.
The DV25 software upgrade for the 3TW scanner has been rescheduled for the week of 10/10 - 10/16. The 3TW scanner will be down starting at noon on the 10th and will be available for general use starting 10/17 after the morning QA.
For any questions or concerns, please contact email@example.com.
Due to an unexpected delay in shipment, we are postponing our DV25 software upgrade which was scheduled during the week of September 5th. We are working closely with GE to confirm the new shipment date. Once finalized, we will notify you of the new upgrade date.
The 3TW scanner is now open for booking for the week (09/06 to 09/11) so please go ahead and use the time for your studies.
CFMRI has upgraded the fORP interface and button boxes (2-button, 4-button) in 3T East and West. Instructions on changing the output of the response devices are on the inside of the door to the cabinet that contains the fORP box and projector. Below is a summary of the directions.
Please contact Aaron Jacobson (firstname.lastname@example.org) if you have questions, or need assistance.
To Change Mode:
- Push the Knob on the front of the fORP box
- You will see “CHANGE MODES?” on the LCD display
- Turn knob to “YES” (push knob to select)
- Turn the knob to “MODE SELECT” (push knob to select)
- Choose desired mode from the list (push knob to select)
- 002 = BYGRT (Corresponds to mode “0” (STANDARD) on the previous button box)
- 003 = 12345 (Corresponds to mode “4” (NUMERIC) on the previous button box)
On May 4th, we sent you an E-update in regards to our software upgrade plan for the 3T scanners (see posting below)
This is another reminder that the 3T West software upgrade is scheduled for September 6th, the day after Labor Day.
If you are a 3T West user, please read and follow the instructions below:
Backup your current 3T West protocols on a USB drive.
We have noticed that many users have multiple protocols that were saved in the past but may no longer be used. To save space and minimize clutter, please identify these protocols (backup to your USB drive if needed) and remove them from the protocol list. Starting August, we will review the list and contact PIs if we suspect redundant and unused protocols under the PI's study.
If your protocol uses non-stock GE sequences that are not developed by CFMRI, please notify us by the end of July so we can coordinate with you to obtain the updated sequences. Below is a list of projects that are most likely to need to contact us:
* Projects in collaboration with the Multimodal Imaging Lab (MMIL) * Projects in collaboration with institution/organization outside UCSD * Multisite longitudinal studies
In addition to the regular headphones, the 3TW is now equipped with the Sensimetrics audio system that supports in-ear headphones suitable for use with the 32-channel Nova coil.
The system uses a pair of earbuds along with disposable tips. We have a few spare tips but generally you will need to bring your own, which can be purchased from here.
If you are interested in using the Sensimetrics system, please refer to the instructions below:
- Locate the earbuds inside a small black leather case in the 3TE Noah's cabinet
- Locate the audio system in the 3TW projector cabinet and turn the power on
- Connect the 3.5mm stereo cable attached to the system to the desired sound source (e.g. laptops, mp3 players, phones, etc.)
- In the magnet room, identify the BNC cables labeled 'SENSI Audio OUT' on the wall (the BNC cables merge into a single grey cable). IMPORTANT: Unwind the grey cable to ensure there is no loop!
- Attach the earbuds to the grey cable
- Provide the earbuds and the disposable tips to the subject
Note: When the Sensimetrics earbuds are in use, you will need to use the GE intercom system (unit on top of the keyboard) to maintain communication with the subject.
After you are done with your study, please make sure to place the earbuds back in Noah's cabinet and power off the main amplifier unit in the projector cabinet.
Due to increased usage, the 32-channel head coils used in 3T East and 3T West have been relocated from the locked cabinet in the console room to the unlocked receiver coil cabinet in the magnet room (on the same shelf as the 8-channel receiver).
CFMRI recently purchased an MR-safe walker for patients/participants with mobility issues. It is located in the 3T West magnet room. The walker can also be used in 3T East when needed. Please return it to its original location in 3T West when it is no longer in use.
If you have any questions or comments, please contact us at email@example.com.
We are planning to upgrade software on both of our 3T scanners to the latest version supplied by GE (DV25). We expect this upgrade to improve system performance and support next generation imaging protocols and hardware.
Based on initial user feedback, we selected the week of September 12th, the week after Labor Day, to upgrade the 3T West scanner. The 3T East scanner will be upgraded later, most likely before the end of the calendar year.
In July, we will send further instructions on how users can prepare for the upgrade.
In the meantime, if you have any questions or concerns about the upcoming DV25 software upgrades, please do not hesitate to contact us at firstname.lastname@example.org.
On Saturday, January 30th, between 7:00 am and 3:00 pm, a new magnet will be installed at the W. M. Keck Building. During that time the CFMRI scan systems (3Ts and 7T), mock scanner and exam rooms will be unavailable.
For your safety, we ask that you do not enter the building during that time.
The CFMRI computer systems, including Calpendo, the CFMRI website, and data servers will be unaffected by the magnet installation.
We appreciate your cooperation and apologize for any inconvenience.