Archive for the ‘CNI History’ Category

NIMS Transition to Flywheel: Part One

February 9th, 2018

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 immediately transferred to the Neurobiological Image Management System (NIMS). Once in NIMS, the data can be reconstructed and converted into the formats that most of our community uses (e.g., NIfTI). These are the data that most users download and use in their research.

Over the years the CNI community has accumulated a great deal of data. NIMS contains the work of about 900 researchers. These data comprise more than 15,000 sessions from more than 6,000 subjects. There are more than 45,000 fMRI scans, nearly 100,000 anatomical scans, around 5000 diffusion scans and over 500 spectroscopy scans.

The CNI remains committed to supporting the research of its user community by providing state-of-the art data management. To this end we are excited about transitioning from NIMS, our home-grown data management system, to Flywheel.

THE ISSUES

Over the years there have been a series of updates to NIMS to accommodate the growing data set. In addition to updates to the NIMS software itself there have been several hardware upgrades over the last few years, including both increased storage and increased computational power; we were fortunate receive grants to support improvements from the Neurosciences Institute. At present NIMS is comprised of a 200TB main file server and a 200TB off-site backup file server, three compute servers (with more than 80 cores, 2TB of RAM, and 14TB of SSD scratch), and a powerful web server, all interconnected by a 10 Gigabit network. The NIMS hardware and associated software are maintained by Michael and the CNI staff.

The support, both physical and financial, of this system is a burden on the CNI. Some of you have may have experienced the limitations of NIMS with regard to data reconstructions, or the limited feature set around search, sharing, and permissions, or downloading bulk datasets, or other missing features that fall into the “Wouldn’t it be nice if…” category.

THE SOLUTION

Over the last few years a number of us (Wandell, Schaefer, Dougherty, Perry, and others) were supported by the Simons Foundation to design the next generation of NIMS. This project (The Project on Scientific Transparency) has also been supported by and integrated with the work being done by Russ Poldrack and Chris Gorgolewski (OpenfMRI) – supported by the Arnold Foundation. This joint effort culminated in the development of an open-source framework to support the next generation of data management – SciTran.

Flywheel has adopted SciTran and engineered a modern user interface and infrastructure that makes it easy to use, maintain, and scale. Flywheel has a multitude of new features over NIMS; runs on Google Cloud Platform; and has a sustainable support strategy.

We will be describing Flywheel more fully in the coming weeks, first reaching out to lab managers and individual groups with the goal of rolling it out to the user community broadly in the coming months. We look forward to working with all of you to make the transition smooth and to help you take advantage of new opportunities that are enabled by the next generation system.

 

See you around the magnet!
- The CNI Team

Data management and storage at the CNI

May 31st, 2016

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 from the center to their lab over the Internet.  CNI users are supported much more extensively.

Data acquired on our scanner are immediately transferred from the GE system to the Neurobiological Image Management System (NIMS), a database. As they are placed in the database, the MRI data are converted into the formats (such as NIfTI) that most of our community uses.  These are the data that you typically download from a browser.

The full set of MRI data are kept online, backed-up, and available forever. The data are stored in an organized format that your collaborators can appreciate and understand. You can search through the entire database to discover what is there. You can perform simple visualizations and check image quality of your own data. The NIMS software you are using was designed and implemented by Bob Dougherty, Gunnar Schaefer and Reno Bowen.

In its 5th year of operation, the CNI has accumulated a great deal of data.  We are storing the work of about 700 people (trained by Laima). The data comprise more than 11,000 sessions and more than 6,000 subjects. There are more than 45,000 fMRI scans, nearly 10,000 anatomical scans, 5000 diffusion scans and 500 spectroscopy scans. You can search through the system and request access to scans carried out by other labs. Nobody is forced to share their data; but if you would like to share with another scientist, and your IRB permits it, then you can do so with a few clicks.

Over the years there have been a series of updates to the system to accommodate the growing data set.  There have been several hardware upgrades over the last few years, including both increased storage and increased computational power. The CNI data management system now includes a 200 Terabyte main file server with 200TB of off-site backup storage, three compute servers with a total of 80 cores, 1.9 TB of RAM, and 14 TB of fast SSD scratch storage, and a powerful web server, all interconnected by a 10 Gigabit network. The NIMS hardware and software are being maintained by Michael Perry and Bob.

Over the last three years a number of us (Gunnar Schaefer, Michael Perry, Bob Dougherty, Renzo Frigato) have been supported by the Simons Foundation to design the next generation of this software.  This work has also been supported by and integrated with the work being done by Russ Poldrack and Chris Filo, supported by the Arnold Foundation.  The next generation of software has many new features, and we will start to tell the story of the next generation of data management software during the coming months.