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Human Imaging Database

An extensible database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large. The HID can be extended to contain relevant information concerning experimental subjects, assessments of subjects, the experimental data collected, the experimental protocols, and other metadata normally included with experiments. This large, multi-site, publicly available data repository rich in fMRI, structural imaging, and clinical data is available so that the research community can develop and test novel hypotheses. Publicly available datasets include: * BrainScape_BS002: This dataset includes seventeen healthy subjects with four resting state fixation scans plus one T1 scan and one T2 scan. The data were collected as part of a study on the behavioral effects of spontaneous BOLD fluctuations. * BrainScape_BS003: This dataset includes ten healthy subjects scanned 3 times with 3 conditions: eyes open, eyes closed, and fixating in addition to two anatomical scans (T1 and T2). * fBIRNTravelingSubject2003: This dataset includes five healthy subjects imaged twice at each of ten FBIRN MRI scanners on successive days. Functional and structural imaging, behavioral, and demographic data are available from 100 scanning sessions on these subjects. * fBIRN PhaseII: The Phase II multi-site clinical imaging study consists of approximately 250 subjects, both chronic schizophrenics and age- and gender- matched controls. The MRI data include structural and fMRI images from two separate scanning visits for each subject, including the Sternberg Item Recognition Paradigm and the Auditory Oddball paradigm, a breath hold task, and a sensorimotor task. The clinical assessments include behavioral measures, handedness and demographic measures, SES, smoking measurements, North American Adult Reading Test (NARRT), and clinical severity assessments for the clinical subjects. Currently data from three sites are released to the general research community; the remainder are awaiting IRB approvals for public data sharing.

URL: http://www.birncommunity.org/tools-catalog/human-imaging-database-hid/

Resource ID: nif-0000-00269     Resource Type: Resource     Version: Latest Version

Keywords

imaging, fmri, clinical, behavior, biomedical imaging data, mri, auditory oddball paradigm, behavioral effect, behavioral measure, bold fluctuation, breath hold task, clinical assessment, clinical severity assessment, demographic measure, handedness, healthy, human, image, north american adult reading test, schizophrenia, sensorimotor task, ses, smoking measurement, sternberg item recognition paradigm, t1, t2, data set

Listed By

NITRC

Old URLs

http://fbirnbdr.nbirn.net:8080/BDR/

Species

human

Abbreviation

HID

Synonyms

Human Imaging Database (HID) System, Function BIRN Data Repository, fBIRN Data Repository

Parent Organization

Additional Resource Types

Database, Data Repository, Data Management Software, Source Code, Image Repository

Availability

BSD License, BIRN License

Related Disease

Schizophrenia

Supercategory

Resource

Original Submitter

Anonymous

Version Status

Curated

Submitted On

12:00am April 9, 2012

Originated From

SciCrunch

Changes from Previous Version

  • Description was changed
  • Additional Resource Types was changed

Version 2

Created 2 weeks ago by Christie Wang

Version 1

Created 3 years ago by Anonymous

Derived Data Storage and Exchange Workflow for Large-Scale Neuroimaging Analyses on the BIRN Grid.

  • Keator DB
  • Front Neuroinform
  • 2009 14

Organizing and annotating biomedical data in structured ways has gained much interest and focus in the last 30 years. Driven by decreases in digital storage costs and advances in genetics sequencing, imaging, electronic data collection, and microarray technologies, data is being collected at an ever increasing rate. The need to store and exchange data in meaningful ways in support of data analysis, hypothesis testing and future collaborative use is pervasive. Because trans-disciplinary projects rely on effective use of data from many domains, there is a genuine interest in informatics community on how best to store and combine this data while maintaining a high level of data quality and documentation. The difficulties in sharing and combining raw data become amplified after post-processing and/or data analysis in which the new dataset of interest is a function of the original data and may have been collected by multiple collaborating sites. Simple meta-data, documenting which subject and version of data were used for a particular analysis, becomes complicated by the heterogeneity of the collecting sites yet is critically important to the interpretation and reuse of derived results. This manuscript will present a case study of using the XML-Based Clinical Experiment Data Exchange (XCEDE) schema and the Human Imaging Database (HID) in the Biomedical Informatics Research Network's (BIRN) distributed environment to document and exchange derived data. The discussion includes an overview of the data structures used in both the XML and the database representations, insight into the design considerations, and the extensibility of the design to support additional analysis streams.

A national human neuroimaging collaboratory enabled by the Biomedical Informatics Research Network (BIRN).

  • Keator DB
  • IEEE Trans Inf Technol Biomed
  • 2008 19

The aggregation of imaging, clinical, and behavioral data from multiple independent institutions and researchers presents both a great opportunity for biomedical research as well as a formidable challenge. Many research groups have well-established data collection and analysis procedures, as well as data and metadata format requirements that are particular to that group. Moreover, the types of data and metadata collected are quite diverse, including image, physiological, and behavioral data, as well as descriptions of experimental design, and preprocessing and analysis methods. Each of these types of data utilizes a variety of software tools for collection, storage, and processing. Furthermore sites are reluctant to release control over the distribution and access to the data and the tools. To address these needs, the Biomedical Informatics Research Network (BIRN) has developed a federated and distributed infrastructure for the storage, retrieval, analysis, and documentation of biomedical imaging data. The infrastructure consists of distributed data collections hosted on dedicated storage and computational resources located at each participating site, a federated data management system and data integration environment, an Extensible Markup Language (XML) schema for data exchange, and analysis pipelines, designed to leverage both the distributed data management environment and the available grid computing resources.