Overview

The Neuroinformatics Database (NiDB) is designed to store, retrieve, analyze, and share neuroimaging data. Modalities include MR, EEG, ET, video, genetics, assessment data, and any binary data. Subject demographics, family relationships, and data imported from RedCap can be stored and queried in the database.

Features

• .rpm based installation for RHEL 8 and RHEL 9 compatible (not for CentOS Stream)

• Store any neuroimaging data, including MR, CT, EEG, ET, Video, Task, GSR, Consent, MEG, TMS, and more

• Store any assessment data (paper-based tasks)

• Store clinical trial information (manage data across multiple days & dose times, etc)

Features

.rpm based installation & upgrade

Install or upgrade NiDB in minutes on RHEL compatible Linux OS.

Automated import of DICOM data

DICOM data can be automatically imported using the included dcmrcv DICOM receiver. Setup your MRI or other DICOM compatible device to send images to NiDB, and NiDB will automatically archive them. Image series can arrive on NiDB in any order: partial series, or full series to overlap incomplete series.

Store any type of data

Literally any type of imaging data: binary; assessment; paper based; genetics. See full list of . All data is stored in a hierarchy: Subject --> Study --> Series. Data is searchable across project and across subject.

Store clinical trial data

NiDB stores multiple time-points with identifiers for clinical trials; exact day numbers (days 1, 15, 30 ...) or ordinal timepoints (timepoint 1, 2, 3 ...) or both (day1-time1, day1-time2, day2-time1, ... )

Bulk import of imaging data

Got a batch of DICOMs from a collaborator, or from an old DVD? Import them easily

Search and export imaging data

Find imaging data from any project (that you have permissions to...) and export data. Search by dozens of criteria.

Export to multiple formats

Image formats

• Original raw data - DICOM, Par/Rec, Nifti

  • Anonymized DICOM data: partial and full anonymization

• Nifti3d

• Nifti3dgz

Package formats

• squirrel

• BIDS

• NDA/NDAR

Destinations

• NFS share

• Web

• Public download/dataset

• Local FTP

Search and export non-imaging data

Data obtained from pipeline analysis, imported and locally generated measures, drugs, vitals, measures, are all searchable.

Full analysis pipeline system

From raw data to analyzed, and storing result values/images. Utilize a compute cluster to process jobs in parallel. Example below, 200,000 hrs of compute time completed in a few weeks. Hundreds of thousands of result values automatically stored in NiDB and are searchable.

Automated MR quality control

Large number of automatically generated metrics. Metrics are exportable as .csv and tables.

Calendar

Fully featured calendar, running securely on your internal network. Repeating appts, blocking appts, and time requests.

Publications

• Book GA, Anderson BM, Stevens MC, Glahn DC, Assaf M, Pearlson GD. Neuroinformatics Database (NiDB)--a modular, portable database for the storage, analysis, and sharing of neuroimaging data. Neuroinformatics. 2013 Oct;11(4):495-505. doi: 10.1007/s12021-013-9194-1. PMID: 23912507; PMCID: PMC3864015. https://pubmed.ncbi.nlm.nih.gov/23912507/

• Book GA, Stevens MC, Assaf M, Glahn DC, Pearlson GD. Neuroimaging data sharing on the neuroinformatics database platform. Neuroimage. 2016 Jan 1;124(Pt B):1089-1092. doi: 10.1016/j.neuroimage.2015.04.022. Epub 2015 Apr 16. PMID: 25888923; PMCID: PMC4608854. https://pubmed.ncbi.nlm.nih.gov/25888923/

Outdated information Watch an overview of the main features of NiDB (recorded 2015, so it's a little outdated): | |

Documentation

Getting Started

Using NiDB

Advanced

NiDB attempts to ensure HIPAA compliance, but is not completely compliant with all aspects of data privacy.

HIPAA Identifiers

There are 18 types of personally identifiable information (from Health and Human Services website). Data that can be stored in NiDB is highlighted.

• Names

• All geographic subdivisions smaller than a state, including street address, city, county, precinct, ZIP code, and their equivalent geocodes, except for the initial three digits of the ZIP code if, according to the current publicly available data from the Bureau of the Census:

  • The geographic unit formed by combining all ZIP codes with the same three initial digits contains more than 20,000 people; and

  • The initial three digits of a ZIP code for all such geographic units containing 20,000 or fewer people is changed to 000

• All elements of dates (except year) for dates that are directly related to an individual, including birth date, admission date, discharge date, death date, and all ages over 89 and all elements of dates (including year) indicative of such age, except that such ages and elements may be aggregated into a single category of age 90 or older

• Telephone numbers

• Vehicle identifiers and serial numbers, including license plate numbers

• Fax numbers

• Device identifiers and serial numbers

• Email addresses

• Web Universal Resource Locators (URLs)

• Social security numbers

• Internet Protocol (IP) addresses

• Medical record numbers

• Biometric identifiers, including finger and voice prints

• Health plan beneficiary numbers

• Full-face photographs and any comparable images

• Account numbers

• Any other unique identifying number, characteristic, or code, except as permitted by paragraph (c) of this section [Paragraph (c) is presented below in the section “Re-identification”]; and

• Certificate/license numbers

PHI on NiDB

The following pieces of information are stored on NiDB. Not all are required.

Ways to reduce PHI exposure