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Resource for Quantitative Functional MRI

Peter C. M. van Zijl, Ph.D.
P41EB015909
Active

Center Overview

This Resource is an interdepartmental and interdisciplinary laboratory combining facilities of the F.M. Kirby Research Center for Functional Brain Imaging at the Hugo Moser Research Institute at Kennedy Krieger (KKI) and the Center for Imaging Science (CIS) at Johns Hopkins University (JHU). It provides expertise for the design of quantitative magnetic resonance imaging (MRI) and spectroscopy (MRS) data acquisition and processing technologies that facilitate the biomedical research of a large community of clinicians and neuroscientists in Maryland and throughout the USA. These methods allow noninvasive assessment of changes in brain anatomy as well as in tissue metabolite levels, physiology, and brain functioning while the brain is changing size during early development and during neurodegeneration, i.e. the changing brain throughout our life span. The Kirby Center has 3 Tesla and 7 Tesla state of the art scanners equipped with parallel imaging (8, 16, and 32-channel receive coils) and multi-transmit capabilities. CIS has an IBM supercomputer that is part of a national supercomputing infrastructure.

Impact on Human Health

The mission of the resource is to develop quantitative imaging biomarkers of disease for tracking changes in brain anatomy, function, metabolism and physiology, which can be used for diagnosis, prognosis, and the monitoring of therapy. These developments are headed by the technical research and development project PIs, Drs. Barker, Pekar, Caffo, Mori and Miller. Specifically, the focus is on noninvasive approaches that do not require infusion of paramagnetic contrast agents and on the rapid translation of such methods for use in human disease. These developments are driven by the needs of our associated biomedical projects, which focus on topics such as learning disabilities, impaired brain development, inherited metabolic disorders, attention deficit, neurodegeneration, multiple sclerosis, schizophrenia, and cancer.

Resources

ResourceDescriptionSupported PlatformsSupported FormatsData TypeData Size (compressed)
CA Portal: The Computational Anatomy Portal
Resource for Quantitative Functional MRI
NIBIB

For analyzing and interpreting anatomical images.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
CEST Z-spectral simulations
Resource for Quantitative Functional MRI
NIBIB

Uses Bloch equations to simulate Z-spectra for 2-pool system

Web-Based N/A N/A
CIS Software
Resource for Quantitative Functional MRI
NIBIB

For analyzing and interpreting anatomical images.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
CSX3
Resource for Quantitative Functional MRI
NIBIB

MRS and MRSI Analysis. csx3 is free software available for download that processes and displays MR spectroscopic and spectroscopic imaging (MRSI) datasets. It is particularly designed for the quantitative analysis and visualization of MRSI data.

Linux, Mac OSX, Unix DICOM, GE, Philips, Siemens,...(more) N/A N/A
Gannet
Resource for Quantitative Functional MRI
NIBIB

GABA-Edited MRS Analysis Gannet is free software available for download that processes and displays GABA-edited MRS datasets. It is designed for the quantitative batch-analysis and visualization of GABA-edited data with minimal user intervention.

GE, Philips, Siemens, spectroscopy...(more) N/A N/A
IMAX3
Resource for Quantitative Functional MRI
NIBIB

MRS and MRSI Analysis. csx3 is free software available for download that processes and displays MR spectroscopic and spectroscopic imaging (MRSI) datasets. It is particularly designed for the quantitative analysis and visualization of MRSI data.

Linux, Mac OSX, Unix DICOM, GE, Philips, Siemens,...(more) N/A N/A
LDDMM Suite
Resource for Quantitative Functional MRI
NIBIB

For analyzing and interpreting anatomical images.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
MriStudio
Resource for Quantitative Functional MRI
NIBIB

Inter-Subject MRI Co-Registration, DTI Processing, ROI Analysis to process large multimodal datasets between subjects by coregistering them to an atlas. MriStudio consists of DtiStudio, DiffeoMap, and RoiEditor. DtiStudio processes DTI data for tensor calculation and fiber tractography. DiffeoMap performs image transformation. RoiEditor applies atlas templates for automated image segmentation based on the results of DiffeoMap.

Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
Parallel HDICA
Resource for Quantitative Functional MRI
NIBIB

High dimensional ICA analysis. Implements ICA for large dimensional data sets using Sun Grid Engine.

NifTI (.nia), NifTI (.nii,...(more) N/A N/A
SMART
Resource for Quantitative Functional MRI
NIBIB

Statistical Analysis. Downloadable subroutines for a variety of imaging analysis tasks as well as video tutorial on visualization and software useage.

Linux, Mac OSX, Windows NifTI (.nia), NifTI (.nii,...(more) N/A N/A
XNAT in CAWorks
Resource for Quantitative Functional MRI
NIBIB

Imaging Informatics for common management, productivity, and quality assurance for imaging and associated data.

Linux, Mac OSX, Windows VTK (.vtk) N/A N/A
Anatomical Image Datasets
Resource for Quantitative Functional MRI
NIBIB

Segmented Subvolumes

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) MRI 0 - 500MB
Diffusion Tensor Imaging Databases
Resource for Quantitative Functional MRI
NIBIB

Human Brain Atlas, Normal Human Volunteer Database, Developmental Databases

Analyze (.hdr), Analyze (.img.gz),...(more) DTI 8GB - 16GB
Kirby 21
Resource for Quantitative Functional MRI
NIBIB

A multi-modal MRI reproducibility data resource: MPRAGE, FLAIR, DTI, RS fMRI, B0 maps, B1 maps, ASL, VASO, T1 mapping, T2 mapping, Magnetization Transfer

NifTI (.nia), NifTI (.nii,...(more) MRI 2GB - 8GB