CNI Blog

February 19th, 2016

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…

Posted in Computing, Data Acquisition, Flywheel, NIMS | Leave a comment

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…

Posted in Computing, Data Acquisition, Flywheel, NIMS, Uncategorized | Leave a comment

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…

Posted in Computing, Data Acquisition, Flywheel, NIMS, Uncategorized | Leave a comment

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…

Posted in CNI History, Computing, Data Acquisition, Flywheel, NIMS | Leave a comment

2017 Recap and Upcoming at CNI

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, read more…

Posted in Hardware, NIMS | Leave a comment

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…

Posted in Data Acquisition, Hardware | Leave a comment

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…

Posted in Data Acquisition, Data Processing | Leave a comment

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…

Posted in Data Acquisition, Data Processing, SMS | 1 Comment

Choosing an MRI protocol for your experiment

The CNI’s Wiki pages offer general advice about how to set up your scan protocols and save the information for later use. The wiki pages take you through the template protocols we think are most widely used. These protocols can be found on the the scanner console, saved under “CNI/head” within the protocol pool. The read more…

Posted in Uncategorized | Leave a comment

Bob Dougherty farewell

Please come by the CNI this Friday (May 5th) at 5-6:30pm to share some nibbles and to wish Bob well;  he will  be moving out of the CNI to his new office space at Mindstrong. A good time will be had by all.   Laima, Adam, Michael, Hua, and Brian

Posted in Uncategorized | Leave a comment

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…

Posted in Data Acquisition, Data Processing | Leave a comment

CNI – A new team

Hi Everyone, About three weeks ago Bob Dougherty let the CNI board know that he was considering taking a position in an interesting new company, Mindstrong Health, a startup in health management. We tried to change Bob’s mind, but it is strong; we were not successful. Bob’s last official day at the CNI is March 31st, though read more…

Posted in CNI History | Leave a comment

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…

Posted in Data Acquisition, NIMS, SMS | 1 Comment

CNI 5th Year – Thanks and links to videos of the presentations

The CNI Team sends a thanks to the many of you who took the time to come to the talks and celebrate the CNI’s fifth year.  We hope you enjoyed the morning. A special thanks to Nisa Cao, who organized the room, food, and posters, with great help from Roz Grayson and Porsche Williams.  Nisa and the read more…

Posted in Uncategorized | Leave a comment

CNI Fifth Year Celebration

Friday, October 14th – Room 041 Jordan Hall The CNI team invites you to join us for a celebration to mark our first five years of operation.  The event will take place the morning of October 14th, the day after the SNI Symposium. Register here Schedule – Friday, October 14, 2016 9:00 –  Coffee 9:30 read more…

Posted in Uncategorized | Leave a comment

CNI – Celebrating Five Years (Save the Date, October 14th)

Save the Date:  The morning of Friday, October 14th The CNI team invites you to join us for a celebration to mark our first five years of operation.  The celebration will take place the morning of October 14th.  We have not yet secured a room, but we remain hopeful ;-).  The time is a bit uncertain because the room read more…

Posted in Uncategorized | Leave a comment

Data management and storage at the CNI

In planning the CNI environment, we made a risky decision: We committed to providing the community with data management services. Many of you know that most MRI centers do no more than hand the user a DVD at the end of the session, and wish them well. Or perhaps they allow the user to copy the data read more…

Posted in CNI History, Computing, NIMS | Leave a comment

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…

Posted in Data Acquisition, Hardware | Leave a comment

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…

Posted in Data Acquisition | Tagged , , , | Leave a comment

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…

Posted in Computing, Data Acquisition, Data Processing | Tagged , , , | Leave a comment

Lululemon clothes: MRI safe?

This recently came across to us, so we thought we would pass it on and remind users of the importance of having subjects be aware of their clothing and suggest that they change into scrubs prior to getting in the scanner if there are any concerns. “The comfortable, stretch, barely-there yoga pants all girls know read more…

Posted in MR Safety | Tagged | Leave a comment

New ‘MR Unsafe’ contact lens, Triggerfish, used to monitor intraocular pressure

The US Food and Drug Administration (FDA) has approved the Triggerfish (Sensimed AG, http://www.sensimed.ch/en/) contact lens sensor that provides an automated recording of continuous eye pressure changes over the course of 24 hours. “The Triggerfish gives the clinician 24-hour continuous monitoring of changes in [intraocular pressure (IOP)] patterns that otherwise could not be obtained,” William read more…

Posted in MR Safety | Tagged , , | Leave a comment

Welcome to the blog!

Welcome to the CNI blog! We plan to use this format to share with the CNI user community information about our activities. We are excited to begin and to help communicate between the CNI staff and users. If you have questions or would like to suggest post topics please let us know. Some topics we’ll be focusing on are: read more…

Posted in CNI Welcome | Leave a comment