Main Page - Revision history

Huawu at 20:39, 18 March 2026

2026-03-18T20:39:43Z

← Older revision		Revision as of 20:39, 18 March 2026
Line 6:		Line 6:

	* General information is on the [http://cni.su.domains/ CNI administrative site (wordpress)]		* General information is on the [http://cni.su.domains/ CNI administrative site (wordpress)]
	* To schedule time on the facilities, see the [https://cni.~~stanford~~.~~edu/scheduler~~ CNI resource scheduler].		* To schedule time on the facilities, see the [https://stanford-cni.calpendo.com CNI resource scheduler].

	'''If you are experiencing problems with the scanner or the peripherals, please consult the [[Troubleshooting\|Troubleshooting]] section.'''		'''If you are experiencing problems with the scanner or the peripherals, please consult the [[Troubleshooting\|Troubleshooting]] section.'''

Huawu: Reverted edit by DeneenZas3473804 (talk) to last revision by Wandell

2025-06-12T23:13:11Z

Reverted edit by DeneenZas3473804 (talk) to last revision by Wandell

Show changes

DeneenZas3473804 at 07:04, 8 June 2025

2025-06-08T07:04:32Z

Show changes

Wandell at 21:06, 21 September 2023

2023-09-21T21:06:04Z

← Older revision		Revision as of 21:06, 21 September 2023
Line 5:		Line 5:
	Follow [[Getting Started \| this Getting Started link]] if you are new to the CNI and would like to learn about the basic facilities and how to get access and help in using the CNI facilities.		Follow [[Getting Started \| this Getting Started link]] if you are new to the CNI and would like to learn about the basic facilities and how to get access and help in using the CNI facilities.

	* General information is on the [http://cni.~~stanford~~.~~edu~~/ CNI administrative site (wordpress)]		* General information is on the [http://cni.su.domains/ CNI administrative site (wordpress)]
	* To schedule time on the facilities, see the [https://cni.stanford.edu/scheduler CNI resource scheduler].		* To schedule time on the facilities, see the [https://cni.stanford.edu/scheduler CNI resource scheduler].

Wandell at 00:15, 23 August 2023

2023-08-23T00:15:53Z

← Older revision		Revision as of 00:15, 23 August 2023
Line 30:		Line 30:

	The first CNI project was construction of the MR facility in the basement of Building 420. The MR scanner was delivered on November 13th, 2010 and began running within a year.		The first CNI project was construction of the MR facility in the basement of Building 420. The MR scanner was delivered on November 13th, 2010 and began running within a year.

			In addition to the MRI scanner, there is a mock scanner for training, experimental testing rooms, and integrated experimental equipment (displays and EEG). (See [[Facilities and Resources]] for more details and text useful when preparing sections of NIH or other grants.)

	~~In recent years the~~ scanner ~~has been~~ heavily used. We train about 100 new users each year		= Data Management =

			The scanner is heavily used. We train about 100 new users each year

			The [[ Flywheel \| Data Management ]] page contains information about how we use Flywheel to store the data collected at the CNI, and to run certain data analyses.

	We have some summary statistics for the last few years gleaned from the Flywheel site that has been up since 2017.		We have some summary statistics for the last few years gleaned from the Flywheel site that has been up since 2017.
Line 42:		Line 48:
	** 250,000 functional MR files		** 250,000 functional MR files

	~~In addition to the MRI scanner, there is a mock scanner for training, experimental testing rooms, and integrated experimental equipment (displays and EEG). (See [[Facilities and~~ Resources~~]] for more details and text useful when preparing sections of NIH or other grants.)~~		= Computational Resources =

	~~= Computational Resources =~~
	At startup time (2011), the CNI received funding from [http://biox.stanford.edu/biox/neuro.html BIO-X Neuroventures] for what was then a high-powered compute server which will be used to provide computational resources to CNI users. That system evolved to use Linux containers.		At startup time (2011), the CNI received funding from [http://biox.stanford.edu/biox/neuro.html BIO-X Neuroventures] for what was then a high-powered compute server which will be used to provide computational resources to CNI users. That system evolved to use Linux containers.

Line 52:		Line 57:

	In 2023 the CNI received funding from [https://csharp.stanford.edu/ C-ShARP] to upgrade our computational facilities with advanced GPUs. These are being installed and will be heavily used for advanced reconstruction methods, particularly for quantitative methods developed by Kawin Setsompop's group.		In 2023 the CNI received funding from [https://csharp.stanford.edu/ C-ShARP] to upgrade our computational facilities with advanced GPUs. These are being installed and will be heavily used for advanced reconstruction methods, particularly for quantitative methods developed by Kawin Setsompop's group.

	~~= Data Management =~~

	~~The [[ Flywheel \| Flywheel ]] page contains information about how we use Flywheel to manage all the data collected at the CNI.~~

Wandell: /* Computational Resources */

2023-08-23T00:13:05Z

Computational Resources

← Older revision		Revision as of 00:13, 23 August 2023
Line 45:		Line 45:

	= Computational Resources =		= Computational Resources =
	At startup time, the CNI received funding from [http://biox.stanford.edu/biox/neuro.html BIO-X Neuroventures] for a high-powered compute server which will be used to provide computational resources to CNI users.		At startup time (2011), the CNI received funding from [http://biox.stanford.edu/biox/neuro.html BIO-X Neuroventures] for what was then a high-powered compute server which will be used to provide computational resources to CNI users. That system evolved to use Linux containers.

	In ~~2023~~ we ~~received~~ a ~~new round of funding from~~ [~~https://csharp.stanford.edu/ C-ShARP~~] to ~~upgrade our computational facilities with advanced GPUs~~. ~~These are being installed~~ and ~~will be heavily used for advanced reconstruction methods, particularly for quantitative methods developed by Kawin Setsompop's group~~.		In the early years we implemented a data management systems (NIMS) for storing and distributing all the data collected at the CNI. We also implemented an [[LXC \| LXC Page]] system to support user computations. NIMS was retired in 2017 and the LXC system was retired in 2021.

	~~The CNI has recently started providing LXContainers~~ and ~~is moving away from the previous [[Virtual Machines]] deployment scheme~~.		In 2017 we installed Flywheel, which is a commercialized version of NIMS. That system continues to evolve and holds a great deal of data. It supports cloud-based computations (docker containers, which Flywheel calls Gears).

	~~Please visit~~ the [~~[LXC \| LXC Page]~~] for ~~information about getting started with computational resources~~.		In 2023 the CNI received funding from [https://csharp.stanford.edu/ C-ShARP] to upgrade our computational facilities with advanced GPUs. These are being installed and will be heavily used for advanced reconstruction methods, particularly for quantitative methods developed by Kawin Setsompop's group.

	= Data Management =		= Data Management =

Wandell: /* Computational Resources */

2023-08-23T00:07:56Z

Computational Resources

← Older revision		Revision as of 00:07, 23 August 2023
Line 45:		Line 45:

	= Computational Resources =		= Computational Resources =
	~~The~~ CNI ~~has~~ received funding from [http://biox.stanford.edu/biox/neuro.html BIO-X Neuroventures] for a high-powered compute server which will be used to provide computational resources to CNI users.		At startup time, the CNI received funding from [http://biox.stanford.edu/biox/neuro.html BIO-X Neuroventures] for a high-powered compute server which will be used to provide computational resources to CNI users.

			In 2023 we received a new round of funding from [https://csharp.stanford.edu/ C-ShARP] to upgrade our computational facilities with advanced GPUs. These are being installed and will be heavily used for advanced reconstruction methods, particularly for quantitative methods developed by Kawin Setsompop's group.

	The CNI has recently started providing LXContainers and is moving away from the previous [[Virtual Machines]] deployment scheme.		The CNI has recently started providing LXContainers and is moving away from the previous [[Virtual Machines]] deployment scheme.

Wandell: /* Facilities */

2023-08-23T00:04:41Z

Facilities

← Older revision		Revision as of 00:04, 23 August 2023
Line 29:		Line 29:
	= Facilities =		= Facilities =

	The first CNI project was construction of the MR facility in the basement of Building 420. The MR scanner was delivered on November 13th, 2010.		The first CNI project was construction of the MR facility in the basement of Building 420. The MR scanner was delivered on November 13th, 2010 and began running within a year.
	~~Some numbers~~ about ~~usage~~.
			In recent years the scanner has been heavily used. We train about 100 new users each year

			We have some summary statistics for the last few years gleaned from the Flywheel site that has been up since 2017.

	* We train 100 new users each year
	* We have collected approximately 1700 data sets (one hour sessions at the scanner) each year		* We have collected approximately 1700 data sets (one hour sessions at the scanner) each year
	* We have run about 75,000 jobs per year		* We have run about 75,000 jobs (Flywheel Gears) per year
	* ~~The Flywheel site with CNI data (started in 2017) contains~~ 540,000 files, including		* We are storing 540,000 files, including
	** 50,000 T1 anatomical files		** 50,000 T1 anatomical files
	** 30,000 DWI diffusion files		** 30,000 DWI diffusion files
	** 250,000 functional MR files		** 250,000 functional MR files

	In addition to the MRI scanner, there is a mock scanner for training, experimental testing rooms, and integrated experimental equipment (displays and EEG). (See [[Facilities and Resources]] for more details and text useful when preparing sections of NIH or other grants.)		In addition to the MRI scanner, there is a mock scanner for training, experimental testing rooms, and integrated experimental equipment (displays and EEG). (See [[Facilities and Resources]] for more details and text useful when preparing sections of NIH or other grants.)

Wandell: /* Facilities */

2023-08-23T00:02:05Z

Facilities

← Older revision		Revision as of 00:02, 23 August 2023
Line 29:		Line 29:
	= Facilities =		= Facilities =

	The first CNI project was construction of the MR facility in the basement of Building 420. The MR scanner was delivered on November 13th, 2010. ~~See some [http://share.shutterfly.com/action/welcome?sid=9QZsmrNuyUsTg pictures from that day]. Since the time it was installed, we train~~ about 100 new users each year. We have collected approximately 15,000 data sets (one hour sessions at the scanner) comprising 25,000 anatomical acquisitions (mostly T1-weighted), 6,000 diffusion-weighted acquisitions, and 63,000 fMRI acquisitions.		The first CNI project was construction of the MR facility in the basement of Building 420. The MR scanner was delivered on November 13th, 2010.
			Some numbers about usage.

			* We train 100 new users each year
			* We have collected approximately 1700 data sets (one hour sessions at the scanner) each year
			* We have run about 75,000 jobs per year
			* The Flywheel site with CNI data (started in 2017) contains 540,000 files, including
			** 50,000 T1 anatomical files
			** 30,000 DWI diffusion files
			** 250,000 functional MR files

	In addition to the MRI scanner, there is a mock scanner for training, experimental testing rooms, and integrated experimental equipment (displays and EEG). (See [[Facilities and Resources]] for more details and text useful when preparing sections of NIH or other grants.)		In addition to the MRI scanner, there is a mock scanner for training, experimental testing rooms, and integrated experimental equipment (displays and EEG). (See [[Facilities and Resources]] for more details and text useful when preparing sections of NIH or other grants.)

Wandell at 23:13, 22 August 2023

2023-08-22T23:13:28Z

← Older revision		Revision as of 23:13, 22 August 2023
Line 5:		Line 5:
	Follow [[Getting Started \| this Getting Started link]] if you are new to the CNI and would like to learn about the basic facilities and how to get access and help in using the CNI facilities.		Follow [[Getting Started \| this Getting Started link]] if you are new to the CNI and would like to learn about the basic facilities and how to get access and help in using the CNI facilities.

	* General information is on the [http://cni.stanford.edu/ CNI administrative site]		* General information is on the [http://cni.stanford.edu/ CNI administrative site (wordpress)]
	* To schedule time on the facilities, see the [https://cni.stanford.edu/scheduler CNI resource scheduler].		* To schedule time on the facilities, see the [https://cni.stanford.edu/scheduler CNI resource scheduler].