Archive for the ‘Hardware’ Category

2017 Recap and Upcoming at CNI

January 12th, 2018

As we embark on a new year (Happy New Year!), the CNI team would like to take a moment to highlight some of the things that happened last year and to preview some of the things we’re working on for 2018.

Looking back at 2017

Personnel Changes

In May we said farewell to Bob Dougherty, who ventured off to a new life at a startup company here in the Valley. Bob remains close to the CNI and at the risk of being sappy, we’ll just say we miss him very much.

During his tenure at the CNI Bob had developed great working relationships with others on campus. For this reason, we were both confident and excited to welcome two new additions to the CNI team, both of whom were very active in CNI work. The first is Adam Kerr, who is the new Research Director at the CNI. Hopefully many of you have had a chance to meet and talk with Adam. Adam is a Stanford alum (PhD, EE) and a wonderful addition to the CNI staff.

We were also happy that Michael Perry could increase his efforts at the CNI to become our new IT Director. Michael fully supports the extensive compute infrastructure at the CNI, including the NIMS data management system. Michael is a Berkeley product, but he is excellent in many ways that compensate for this one flaw.

Policy updates

The Advisory Board made some adjustments to the scanning policy at the end of 2017. First, there was a change in how after-hours time (10pm – 7am) can be scheduled. Groups must first meet with Laima to address the increased risks of scanning after-hours.

Second, there was a change to how protocol development time can be used. There is now a cap of 10 hours per grant and the protocol development time for seed grants starting in FY18 will no longer be available.

Please take the time to read through all the scanning policies that are available on the Getting Started page of the WIKI.

DV26 upgrade

After weeks of testing, patching, and more testing, we upgraded the scanner software to DV26 on Monday, Nov 12, 2017. This brought along with it some small changes in operational protocol (e.g. SAR limit settings, spectroscopy prescriptions). For more information about the upgrade, please see this post.

EEG Refresh

This past year we sent out our EEG equipment for service. The EEG caps were refurbished and the software was upgraded to the current release. Please contact the CNI staff for information on how to get started if your group is interested in using the EEG equipment in your study.

Penetration Panels

We had two new 10” x 12” penetration panels installed in the scanner wall common to the equipment room. These penetration panels are used to support the introduction of new instrument connections into the scan room and were a critically required expansion as we had already exhausted all of our research penetration panel space.

Looking forward to 2018

Here are just a few things that we are planning for this next year.

New laptops and E-Prime upgrade

We have purchased new Windows and MAC laptops to support stimulus delivery at the CNI. In the upcoming weeks we will retire some of the old laptops. To help make this transition smooth, please migrate your scripts to the new workstations as soon as possible. Please get in touch with the CNI staff if you have concerns or issues transferring your scripts.

In addition to the workstations, we purchased E-Prime 3 upgrade licenses for our laptops. This version of E-Prime will be installed alongside existing versions, so code requiring older versions will continue to function.

Fee structure updates

Starting March 1, 2018 scan time will increase slightly. Fees will be as follows:

Time SlotHourly Rate

Peak: 8:00 AM to 6:00 PM weekdays $425
Off-hours: 6:00 PM to Midnight weekdays. 8:00 AM to Midnight weekends $325
Owl: Midnight to 8:00 AM weekdays. Midnight to 8:00 AM weekends $100
EEG: Anytime usage $50

CNI Innovation Seed Grants

This year we are again in the fortunate position of being able to support innovation. We now welcome applications for funds to purchase scan time at the CNI. Innovative projects that require up to 30 hours of scanner time for data acquisition will be considered. Note that these funds can only be used for scan time at the CNI. The deadline for CNI Innovation grant applications is Wednesday, January 31st, 2018; award announcements will be made in early February. You can apply for an award using the Google Form here.

NIMS transition to Flywheel

In October of last year we started mirroring NIMS on a new data management system, Flywheel. Data collected on or after October 1, 2017 are already in the Flywheel system, in addition to being in NIMS. This has allowed a few groups to begin testing this next generation system. While NIMS will continue to operate as usual for the time-being, we expect to transition to Flywheel during this year, with new data going only to Flywheel by the Summer 2018.

Flywheel is running on Google Cloud, which allows us to expand data storage without purchasing and installing new hardware. We also save costs of system management (e.g., backups, disk replacements, operating system upgrades). The hardware that we purchased in the past, and which is running out of warranty, will be maintained for the time being. But we expect that it will start to fail over the next few years and be replaced by Cloud systems.

The Flywheel system originated from NIMS, but it has a large number of features that make it feel different and also enable certain new capabilities. We believe the data management features include everything in NIMS but extend them significantly. Most importantly the Flywheel system will integrate tightly with scalable Cloud Computing. We anticipate that this system will support reproducible research and data sharing.

Expect to hear a lot from our team about the new Flywheel system during the upcoming weeks. We will offer group and individual training sessions that cover a number of topics, including:

  • Data Migration Efforts
  • DV26 Impact on reconstruction and data capture in Flywheel
  • Flywheel Center Edition training
  • Flywheel Lab Edition computational methods
  • User rights management training and demonstrations

If you or members of your group would like to be part of the pilot program with Flywheel, please contact Michael Perry, who is leading this effort.

See you around the magnet!

- The CNI Team

Planning for hardware upgrades

May 23rd, 2016

The CNI is planning for a significant equipment upgrade, which we expect to be available in about a year. This message describes our plans, which are rather uncertain. Despite this uncertainty, we thought it best to write this note to give you plenty of time to plan.

About a year ago, Siemens released a new scanner (Prisma) that has particularly strong gradients. Many NIH grants are now being written with the specification of matching the Prisma performance. Bob has worked hard at the CNI to implement the sequences and reach the quality of images that are required for these grants. The CNI team have documented the SNR of the data, and we think it is pretty good and should make us eligible for these NIH awards.

GE is responding to the competition. In particular, they have told us that they expect make available a gradient system upgrade within the next year. The stronger gradients will make our scanner competitive with (GE says better than) the Siemens Prisma.

We are funding this upgrade through a GE non-obsolescence service contract that costs about $100k per year for the next three years. The funds for this service contract are coming from user fees (which have barely gone up over the 5 years of operation). We can afford this because of the heavy usage at the CNI and our efforts to keep other costs in check. An additional $200k was needed to bring our system up to the current GE hardware platform, and this funding was provided by the Dean of Research. This upgrade was implemented last year and involved a faster host computer and reconstruction server. Some of you may have noticed this upgrade in the form of reduced delays between multiband scans. (It did not affect the data acquisition systems, so it has no impact on data quality.)

We will keep you informed as we learn about the likely delivery dates for the scanner upgrade.  We expect the new hardware to be available in about a year, and the system will likely be down for about 2 weeks during the installation process. The new gradients can be run at the current system’s lower performance level to maintain compatibility with data collected pre-upgrade. Diffusion sequences and a few others will benefit significantly from the new gradients (not such much for fMRI).

Feel free to post questions about the upgrade here. We will let you know more as we learn more.

Brian and Bob