CTSC Imaging Informatics Initiative
Contents
Back to CTSC_CrossSiteImagingIdeas
Note: This is a work in progress
Overview
The Harvard Catalyst Medical Imaging Informatics Bench to Bedside (mi2b2) Initiative is preparing to provide services for setting up imaging data management systems (IDMS) to support research and clinical efforts involving imaging for Harvard Catalyst affiliated investigators. Two simultaneous (and potentially conflicting) priorities are to 1) provide optimal, customized hardware and software tools for each investigator/ laboratory and 2) to harmonized these solutions to allow for aggregation of the raw and derived medical imaging data for subsequent sharing beyond the investigator/ laboratory.
XNAT has been identified as a potential software solution for providing the core functionalities of a Harvard Catalyst IDMS.
A typical IDMS service engagement will include the following steps:
- Requirement gathering
- Gap analysis
- Infrastructure setup
- Data modeling
- IDMS installation and setup
- Data loading
- Testing and evaluation
- Ongoing data entry, data loading/transfer, and system monitoring and maintenance
- System upgrade
mi2b2 Phases
Planning and Information Gathering
The goals of current phase of the initiative are to:
- Gather concrete and specific requirements for imaging data transfer and management from a number of high-volume imaging projects led by Harvard Catalyst-affiliated investigators that are generating valuable derived image data with the intention to share that data beyond their own laboratory;
- Generate a list of overlapping requirements from these specific investigators;
- Prioritize the projects to determine next steps;
- Deploy a demo IDMS based on the default XNAT source code;
- Assess the effort required to extend XNAT code to support the features identified.
Prototype Development
CHB
- Grant Lab
MGH
- Dickerson Lab
Production System Development for Selective projects
CHB
MGH
BWH
Use Cases
(Template
- Mission
- Description of big picture, goal(s) of project
- Participants
- Data Types
- Project
- Imaging Modalities
- Genetic
- Storage needs
- Workflow
- Other software to be integrated (e.g., Osirix)
- other features
- Data transfer
- Data Management)
The use cases presented here are based on on-going informal interviews with various labs and email communications.
Clinical
Research
- Ellen Grant, CHB
- Stephan Voss, CHB
- Simon Warfield, CHB
- Bill Hanlon, DF/HCC
- COPD Gene Project, BWH
- Brad Dickerson
Project Prioritization Criteria
Possible criteria include:
- Impact
- Number of users
- Duration of the project
- Amount of data (# of subjects, # of scans ...)
- Success Potential
- Commitment of PI
- Feasibility: is it a good fit for using XNAT?
- Availability of project support at each stage of the effort, including requirement gathering, data collection, system testing, continuing IT and informatics support.
Current Status
Test installations of XNAT (1.4 release candidate 2) were done on Windows XP and Linux in VMware. Minor issues in the setup process needs to be fixed to make successful installation on Windows Vista.
Requirement gathering from several research and clinical projects have been conducted.
XNAT 1.4R2 setup/installation process semi-automated.
XNAT extension prototype built.
Explored ways of extracting and loading additional DICOM fields.
Other Software
In addition, an evaluation of dcm4chee|[1] (a DICOM Implementation in JAVA) is in progress. Simon's group runs an instance of dcm4chee. XNAT's DicomServer and DicomBrowser are based on dcm4che.
The Globus MEDICUS (Medical Imaging and Computing for Unified Information Sharing)|[2] has been proposed to provide an image sharing solution.
Reporting and database management of radiological data for clinical trials offered by http://tumormetrics.org/
Evorad Medical Imaging Workstation from http://www.evorad.com/
List of image visualization and analysis software
Neuroimaging
NITRC Funded by the National Institutes of Health Blueprint for Neuroscience Research, NITRC facilitates finding and comparing structural and functional neuroimaging tools and resources. Collecting and pointing to standardized information about tools, this site can help you find the right structural or functional neuroimaging tool or resource and help you decide whether it can help in your research
Commercial
PACS
Fuji Synapse Used at CHB for MR and CT.
Hermes Used at CHB and DFCI for nuclear medicine
GE Centricity system Used at BIDMC, BWH, MGH and DFCI
Amicas web-based application it uses compression techniques to deliver images to the desktop PC for clinical review. It is used primarily by referring clinicians. Used at MGH
AGFA IMPAX Used at MGH.
Workstations
Toshiba Voxar Works on PC. Used at CHB
Merge efilm Works on PC. Used at CHB and MGH
GE Advantage Used at BIDMC, MGH and CHB for postprocessing of CT and MR data.
TeraRecon AquariusNET server connected with PACS to allow clinicians to analyze and segment volumes from routine desktop computers (rather than dedicated workstations). Used at BIDMC and MGH
Siemens Leonardo Used at BIDMC for Interventional Angiography & Interventional Neuroradiology
MedX, designed especially for medical imaging researchers and system developers. Works on Linux desktop systems. Used at MGH (neurosurgery)
Vital Vitrea for visualization of CT and MR data. Used at CHB, MGH and BIDMC.
Image management
AccelaRAD Virtual Radiology Network (VRN) enables multi-site radiology groups to perform remote reading across geographic boundaries with greater control over report turnaround times and distribution to clients and referring doctors. Used at CHB
Open source
OsirX OsiriX is at the same time a DICOM PACS workstation for imaging and an image processing software for medical research (radiology and nuclear imaging), functional imaging, 3D imaging, confocal microscopy and molecular imaging. For MAC computers. Used at CHB and MGH
myPACS radiology e-teaching files. Used at CHB
k-PACS DICOM Viewing Software for research only. Used at CHB
FSL is a comprehensive library of analysis tools for fMRI, MRI and DTI brain imaging data. Used at CHB, MGH and BWH for research.
MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. Used at BWH
ConQuest Radiology Micro PACS. Used as the Neuro OR desktop micro PACs server at MGH.
Research software from Children's Hospital
STAPLE Simultaneous Truth and Performance Level Estimation. Algorithm for assessing a collection of segmentations of an image.
Research software from Brigham and Women's Hospital
3D Slicer is a multi-platform, free open source software (FOSS) for visualization and image computing.
Research software from Massachusetts General Hospital
Freesursfer is a set of automated and semi-automated tools for the segmentation, reconstruction, and processing of surface-models of the human cerebral cortex. Used for MRI data.