Systems Overview

The CoNNECT MRI facility consists of several components described below.

Note

FIGURE TO BE INSERTED

Philips 3.0T Ingenia Cx

The CoNNECT MRI facility was created when Dr. Sherwood received funding from the Air Force Office of Scientific Research and State of Ohio Department of Higher Education to purchase and install a 3-Tesla (T) MRI for the enhancement of defense-related research. The MRI scanner installation was completed on March 31, 2022. The Philips 3.0T Ingenia Cx is obviously at the core of the CoNNECT. This MRI is capable of performing state-of-the-art functional and anatomical neuroimaging. Additional MRI components can be found at the equipment section of the CoNNECT laboratory website.

Data Management

Centralized Storage

Centralized storage has been made available.

File Share

A file share has been created in /resshare. Any documents or directories created here will be backed up daily but will also be available on the master and any core nodes.

Data Organization

Data collected and produced for each project will follow BIDS specifications to ensure community standards are upheld, to improve data integrity and conformity, and to improve data consistency and data processing optimization.

Note

Insert BIDS overview, etc including filename structure table here

For example, bids format should follow this structure: _sub-_ses-_acq-_run-_task-_desc-_.ext

Table 1 Available Keys for compliant get_bids_filename from input labels.

Entity	Label Prefix	Description
task	task	A set of structured activities performed by the participant. No two tasks should have the same name.
acquisition	acq	Data acquisition is a continuous uninterupted block of time during which the MRI was acquiring data.
run	run	An uniterupted repition that has the same acquisition parameters and task.
process	proc	Name of process that generated the outputs.
resolution	res	The acq-<label> entity cooresponds to a custom label the user may use to distinguish a different set of parameters used for acquiring the same modality. For example <acq-highres> or <acq-lowres>.
space	space	Useful for describing the source of tranforms from an input image to a target space.
description	desc	Describing acronyms within labeling code.
suffix	NA	A filename consists of a chain of entity instances and a suffix all separated by underscores, and an extension.
extension	ext	The extension depends on the inaging modality and the data format, and can convey further details of the file’s content.

CoNNECT Neuro-Processing Cluster (NPC)

The CoNNECT NPC is a collection of systems that are centrally and locally managed. The resources are all centrally located and under the control of Wright State Computing and Telecommunications (CaTS). The CoNNECT NPC operates on a network isolated from the main WSU campus network.

Jumpbox

The jumpbox is a user-specific virtual machine (VM) running either windows or linux. The jumpbox is NIST and HIPPA compliant. A user accesses their jumpbox VM via VMware Horizon when connected to WSU’s secure network or LAN, or connected to the network via virtual private network (VPN). Users can access the remainder of the CoNNECT NPC via their jumpbox.

Master Node

The master node is the main controller of the CoNNECT NPC. Users access the master node via secure shell (SSH) connections through their jumpbox. The master node has 40 physical cores and 756GB RAM, and is running Ubuntu 20.04.

Core Node(s)

Core nodes are the workhorse of the CoNNECT NPC. The core nodes run the same operating system as the master, Ubuntu 20.04. Currently, there is a single core node with 40 physical cores and 756GB RAM. Processing can be conducted utilizing the core node(s) by supplying the submit option to the programs described within this manual