Category: Data Acquisition

Recent advances in in-vivo spectroscopy methods at CNI

Recent advances in in-vivo spectroscopy methods at CNI Background Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities… Read more Recent advances in in-vivo spectroscopy methods at CNI

Recent advances in in-vivo spectroscopy methods and applications at CNI

Recent advances in In-vivo spectroscopy methods at the CNI Background A growing number of people at the CNI are interested in measuring metabolic changes in the brain using in-vivo spectroscopy (MRS) techniques.  Often, they combine this information with functional MRI measurements. The special interest spectroscopy group at CNI  develops and supports new MRS data acquisition and… Read more Recent advances in in-vivo spectroscopy methods and applications at CNI

UHP Upgrade Update (Continued)

1. Introduction Good news — after a lot of hard work over the weekend by the CNI staff, we are most of the way back to normal operation with our upgrade to GE’s RX28 release.  The significant accomplishments over the weekend include solving the issues with the research SMS sequences as well as the spiral… Read more UHP Upgrade Update (Continued)

Update on Physiological Data Association in Flywheel

Dear CNI Users, In August we wrote to you regarding a problem we found within the CNI Flywheel instance (cni.flywheel.io). In some cases the physiological data (respiratory and cardiac waveforms) from the scanner were not matched to the correct acquisition in Flywheel, or were not uploaded at all. We have determined that such failures occurred most… Read more Update on Physiological Data Association in Flywheel

Hyperband Transition

Executive Summary The GE product Hyperband BOLD and diffusion sequences are a result of close collaboration between GE scientists and engineers with the CNI staff.  The CNI SMS implementation, which we called the “MUX” research sequence, served as a resource and a benchmark for the GE Hyperband product.  Over the last several months Adam and… Read more Hyperband Transition

CNI upgrade planning

Planning for an MRI scanner upgrade at the CNI The MRI scanner we have (GE DVMR 750) is about 8 years old. There have been advances over the years that we incorporated through compute infrastructure and software. It is now time for us to consider the opportunity for a hardware upgrade. In anticipation of the hardware… Read more CNI upgrade planning

Flywheel: Part Four

Flywheel We are on track to switch over to Flywheel on Saturday, September 1.  As of that day, new data collected at CNI will not be placed in NIMS.  New data will be sent  to Flywheel directly (https://cni.flywheel.io).  NIMS will be kept online as legacy only. Logins for the Flywheel site is managed by Stanford authentication, via Google. So to login… Read more Flywheel: Part Four

Flywheel: Part Three

Thanks to all of you who have started to take a look at the Flywheel data management system. A few notes and reminders. 1.  We are still on track for a September 1 change over.  Having said this, Michael is considering transitioning a little bit sooner.  The reason is that the very heavy use of… Read more Flywheel: Part Three

NIMS transition to Flywheel: Part Two

Main point The Flywheel data management system has been running smoothly for several months at the CNI.  The main purpose of this message is to encourage you to explore Flywheel (https://cni.flywheel.io). A number of groups have already switched from NIMS to take advantage of Flywheel’s features. After Michael completes further testing, which we anticipate to be around September 1, we will… Read more NIMS transition to Flywheel: Part Two

NIMS Transition to Flywheel: Part One

BACKGROUND When planning the CNI we committed to providing the community with data management services. As many of you know, most MRI centers do little more than hand the user a DVD at the end of the session, and wish them well. CNI users are supported much more extensively. Data acquired on our scanner are… Read more NIMS Transition to Flywheel: Part One

CNI scanner upgrade to DV26

After weeks of testing, the CNI will upgrade the scanner’s software to DV26 on Monday, Nov 12, 2017. All existing protocols will be migrated to the new platform, and we fully expect they will perform as they do on the current platform. Data will continue to be stored in NIMS as they are now as… Read more CNI scanner upgrade to DV26

Laima measures GABA

You may have been wondering about Laima’s experimental work over the last few years.  You can now read about it in a paper co-authored by folks who work at the CNI, GE, and Lucas.  Nice collaboration! GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence Meng Gu, Ralph Hurd, Ralph Noeske, Laima Baltusis, Roeland Hancock, Matthew D. Sacchet, Ian H. Gotlib, Frederick T. Chin, Daniel M. Spielman… Read more Laima measures GABA

Upgrade Plan for DV26

Executive summary We will be upgrading the GE software and computational infrastructure in late September (from DV25 to DV26). The reasons and implications for your projects are explained below in detail. To migrate the CNI sequences to this new environment, the CNI development team needs time on the scanner (we estimate about 12 hours).  As… Read more Upgrade Plan for DV26

Optimizing image quality: Fieldmaps and shimming

Acquiring a high quality fieldmap of the mean magnetic field is crucial to obtaining a good measurement.  Making sure you set the parameters so that this field map is obtained as part of your protocol is something we help you with.  There are cases, including new sequences, where this can require some extra attention. The… Read more Optimizing image quality: Fieldmaps and shimming

Updates for multiband reconstruction

The CNI has recently introduced a new option for reconstructing SMS (aka, multiband or mux) scans. The default reconstruction method in the SMS reconstruction pipeline is currently 1D-GRAPPA (Blaimer M. et al. MRM 2013). Based on recent research and testing, we believe that the split-slice-GRAPPA (Cauley SF, et al. MRM 2014) reconstruction algorithm does a better… Read more Updates for multiband reconstruction

Planning for hardware upgrades

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… Read more Planning for hardware upgrades

High Order Shim Errors (UPDATE)

Gary Glover kindly shared his fix for this issue and we have installed it on the CNI scanner. So you no longer need to worry about the HO Shim checkbox described below. Your shims will be preserved regardless of the checkbox state (although it doesn’t hurt to have it checked).   Hello CNI users, After… Read more High Order Shim Errors (UPDATE)

SMS, EPI and tSNR (long)

Bob, Hua and the CNI team are working with the community to improve our methods.  The text below – excerpted from a recent exchange with the Wagner lab – illustrates the tools we use to exchange data and computational methods.  This software infrastructure is an important part of the CNI research and development mission. The story below illustrates how… Read more SMS, EPI and tSNR (long)