As part of our NCBIB efforts, once new pulse sequences and analysis approaches have reached sufficient maturity to allow use by non-experts, we will make our technologies available to other researchers and clinicians in the country and worldwide.
For our data acquisition approaches, the software is often vendor specific and research agreements with the vendor are generally needed. So please contact the principle investigators of the Resource for these, who will put you in contact with the particular project investigators, or contact the project investigators directly through the “about us” page and “people” pages within that.
For analysis software, some may be made available as freeware through github, and may be improved further by others, others can just be run as compiled software. Below are links to our currently available software, in alphabetical order.
Acute-stroke Detection Segmentation (ADS) Tool: A tool for detection and segmentation of ischemic acute and sub-acute strokes in brain diffusion weighted MRIs. The method is fast: the lesion inference takes 20~30 seconds in CPU and the total processing, including registration and generation of results/report takes ~ 2.5 mins. The outputs, provided with a single command line, are: the predicted lesion mask, the lesion mask and the image inputs (DWI, B0, ADC) in standard space, MNI, and the quantification of the lesion per brain structure and per vascular territory.
Arterial Brain Atlas: Atlas of brain arterial territories based on lesion distributions in 1,298 acute stroke patients. The atlas covers supra- and infra-tentorial regions and contains hierarchical segmentation levels created by a fusion of vascular and classical anatomical criteria. This deformable 3D digital atlas can be readily used by the clinical and research communities, enabling automatic and highly reproducible exploration of large-scaled data.
Blood T2, T1, Hct, and Oxygenation Calculator: Calculates blood parameters for field strengths from 1.5 – 11.7T, including T1 and T2 when hematocrit fraction (Hct) and oxygen saturation fraction (Y) are available and vice versa.
MRI Cloud: is a large program/data infrastructure that provides both data processing and so-called multi-atlases (multiple ages and brain shapes) for many MRI contrasts. These include contrasts such as ASL, CVR/CBV, and Quantitative Susceptibility Mapping (QSM), as well as anatomical atlases based on T1-MPRAGE and DTI, and functional MRI, all of which can be combined. MRI Cloud also includes a simulation software “MRSCloud” that allows full density-matrix simulations of MRS experiments to generate complete basis sets of conventional and spectral-editing sequences.
Neuroconductor: This project is a software repository and continuous integration service for R packages related to the processing and analysis of imaging and neuroscience data. This resource has grown to over 100 listed packages, including several dedicated to the analysis of MRICloud data.
OSPREY: Package for Linear-Combination (LC) modeling for metabolite level estimation
QSM Analysis Tools: Data processing for conventional and deep learning based Quantitative Susceptibility Mapping (QSM) analysis using MR magnitude and phase data acquired using gradient echo (GRE) MRI