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Resource for MRI of Neurodegenerative Disorders

Michael W. Weiner, Ph.D.
P41EB015904
N/A
Retired

Center Overview

The Center for Imaging of Neurodegenerative Diseases (CIND) develops and validates new imaging methods for detecting brain abnormalities in neurodegenerative diseases, including Alzheimer's disease, vascular dementia, frontotemporal dementia, Parkinson's disease, as well as epilepsy, depression, and other conditions associated with nerve loss in the brain. As people around the globe live longer, the impact of neurodegenerative diseases is expected to increase further with dire social and economical consequences for societies if no effective treatments are developed soon. The development at CIND is aimed to improve magnetic resonance imaging (MRI). The ultimate goal of the scientific program is to identify imaging markers that improve accuracy in diagnosing neurodegenerative diseases at early stages, achieve more reliable prognoses of disease progression, and facilitate the discovery of effective treatment interventions.

In addition to addressing the general needs for studying neurodegenerative diseases, another focus of CIND concerns brain diseases associated with military service and war combat, such as post traumatic stress disorder (PTSD), brain trauma, gulf war illness and the long-term effects of these conditions on the mental health of veterans. The symbiosis between CIND and the Veterans Administration Medical Center in San Francisco makes this program uniquely suited to serve military veterans.

Impact on Human Health

The mission of CIND is to improve medical imaging techniques for more accurate clinical diagnosis of neurodegenerative diseases and related conditions as well as for an early detection of these diseases, monitoring their progression and assessing potential treatment effects. For more than 20 years, CIND researchers have studied brain changes in neurodegenerative diseases, including alterations in brain macro- and micro structure, physiology, function and metabolism. CIND has been a leader in the field bringing together imaging scientists and clinical investigators to focus on studies of neurodegenerative diseases and brain aging.

To facilitate these studies, CIND researchers are developing new MRI methods that promise added clinical value. For instance, higher spatial resolution in structural MRI is showing promise for more accurate measurements of cortical thickness and small brain structures, such as the hippocampal subfields, which are particularly vulnerable to neurodegeneration. In diffusion MRI, a unique method to assess white matter microstructure, the development of new concepts for image reconstruction based on statistical modeling promises substantial gains in sensitivity. For studies of brain perfusion and function, new methods are being implemented based on arterial spin labeling to capture changes in cerebral blood flow and blood oxygenation more efficiently. Furthermore, for improvements in image reconstruction, concepts are being developed that incorporate statistical prior information, i.e. from high-resolution anatomical, into the reconstruction process, thereby boosting image resolution for perfusion and functional MRI toward unprecedented clarity. Lastly, new protocols for joint analyses of structural, diffusion, perfusion and functional MRI data are being designed in conjunction with multivariate statistical concepts to improve the sensitivity and specificity of MRI to detect neurodegeneration.

Researchers of CIND are key partners in many national and international collaboration. For instance, Dr. Weiner of CIND is the Principal Investigator of the Alzheimer's disease Neuroimaging Initiative (ADNI), funded by NIH. CIND also performs the analysis of structural and perfusion MRI data for ADNI. Aside from ADNI, CIND supports imaging for major other clinical programs sponsored by either NIH, the Department of Defense, or private foundations, such as a program project on Frontotemporal Lobar Degeneration, the Frontotemporal Lobar and Tauopathies imaging initiatives, and the international Parkinson's Progression Imaging Initiative (PPMI).

Resources

ResourceDescriptionSupported PlatformsSupported FormatsData TypeData Size (compressed)
Brain
Resource for MRI of Neurodegenerative Disorders
NIBIB

This program identifies the largest contiguous solid within a T2 image.

Windows HDF N/A N/A
CGoct3D
Resource for MRI of Neurodegenerative Disorders
NIBIB

CGoct3D is a program to perform K-Bayes optimization of multi-slice ASL-perfusion datasets.

Binary N/A N/A
DicomToHdf
Resource for MRI of Neurodegenerative Disorders
NIBIB

This program converts Dicom data to HDF version 4.2 format. The windows command-line version of the dicom2 program is used to translate the Dicom header. Dicom files from the parent directory are cataloged and combined into a single HD volume when possible.

Windows DICOM N/A N/A
FourPhasePerf
Resource for MRI of Neurodegenerative Disorders
NIBIB

The FourPhasePerf program is a Matlab program designed to obtain quantitative measures of cerebral blood flow from arterial spin labeling (ASL) MRI data.  It calculates hemodynamic parameters based on a four phase ASL model.  In this dual-compartment distributed perfusion model, the bolus arrival time is decomposed into transit delays through large arteries and delays through smaller arteries and arterioles, expressed as arterial-arteriole transit time (aaTT), before the spin labels reach the capillary bed and perfusion...

Linux, Mac OSX, Windows ASL values of a...(more) N/A N/A
Import
Resource for MRI of Neurodegenerative Disorders
NIBIB

This program converts Siemens VISION system MR images (ACR-NEMA) to HDF format.

Windows ACR-NEMA N/A N/A
MatCoil
Resource for MRI of Neurodegenerative Disorders
NIBIB

MATCOIL is a program written in Matlab with GUI interfaces that enables both single surface coils and surface coil configurations to be designed, and the resulting B1 fields and sensitivity fields to be calculated and displayed. Additional parameters, such as tip angle, and vector field plots of the B1 field, are also available. The coil shapes may be varied from circular, to elliptical, to rectangular, and may be planar or wrapped about a circular cylinder.  In addition,...

Linux, Mac OSX, Windows Matlab N/A N/A
MatMRI
Resource for MRI of Neurodegenerative Disorders
NIBIB

The MATMRI program is written in Matlab and calculates magnetization transfer (MT) effects in MP RAGE experiments based saturation of the bound pool as calculated and discussed by Henkelmann et al. (Magn Reson Med 19997; 37, 866) and on the formulations for transfer of MT provided by Helms and Hagberg (Concepts Magn Reson 2004; 21, 37).  The program is presently being re-written, and some features may not work.  Contact Dr. Matson for details.

Linux, Mac OSX, Windows Matlab N/A N/A
MatPulse
Resource for MRI of Neurodegenerative Disorders
NIBIB

MATPULSE is a program written in Matlab with GUI interfaces that enables calculation of Shinnar-LeRoux (SLR) frequency selective RF pulses. The program also provides pulse re-mapping (the MATPULSE version of VERSE), and includes a Bloch equations section, and a variety of other calculations, including gradient refocusing, and calculation of the effects due to relaxation. Additional features include pulse concatenation, root reflection, calculation of the effects  of flow, and optimization of pulses with immunity to B1...

Linux, Mac OSX, Windows Matlab N/A N/A
Poisson Disk Distributrion for Sparse Sampling in MRI
Resource for MRI of Neurodegenerative Disorders
NIBIB

The program p_disk_dist.m is a Matlab program for calculation of a Poisson disk distribution on a Cartesian frame. The program includes a Matlab GUI interface for ease of use. A Poisson Disk distribution is superior to a random distribution for use as a sparse sampling pattern for MRI. The program supports a variety of options for tailoring the distribution to the desired pattern density.

Linux, Mac OSX, Windows Matlab N/A N/A
Results
Resource for MRI of Neurodegenerative Disorders
NIBIB

This program supports a broad range of processing, including logical operations, rigid body transformations, etc.

Windows HDF N/A N/A
Scalar_voxMediation
Resource for MRI of Neurodegenerative Disorders
NIBIB

scalar_voxMediation is a command line tool that will test for the mediation effect, when the independent variables are scalar and the dependent variables are maps (perfusion, deformation, FA, etc.). It assumes that you have already done a voxel-wise analysis of the simple models, then computes the Sobel test for the mediation effects. Note: This program is no longer supported by the CIND.

Windows N/A N/A
Segment
Resource for MRI of Neurodegenerative Disorders
NIBIB

This program used K-means cluster analysis to produce a 3 tissue classification from a trio of images (T1-weighted, T2_weighted, and PD-weighted). The clustering procedure is identical to the SAS "Fastclus" procedure. It assumes that all 3 inputs are in register.

Windows HDF N/A N/A
Sicore
Resource for MRI of Neurodegenerative Disorders
NIBIB

This program transforms a segmented image down to the resolution of spectroscopic imaging (SI) or single voxel spectroscopy data, taking into account the SI point spread function, RF pulse profiles, and metabolite chemical shifts. Tissue type contributions to individual voxels are reported.

Windows HDF N/A N/A
Tailored Constant Density to Variable Density Spiral
Resource for MRI of Neurodegenerative Disorders
NIBIB

This Matlab program (spiral_vdsn.m) generates a constant density spiral starting from the center of k-space out to a selected portion of k-space, and then switches over to a variable density spiral. In this scheme, only the outer regions of k-space are under-sampled. The program uses a Matlab GUI to generate a user-friendly interface. Inputs to the program include the image matrix size, the field of view, the variable density parameter (alpha) for the outer regions...

Linux, Mac OSX, Windows N/A N/A
tMCimg
Resource for MRI of Neurodegenerative Disorders
NIBIB

tMCimg uses a Monte Carlo algorithm to model the transport of photons through 3D highly volumes with spatially varying optical properties and arbitrary boundary conditions.

Linux, Mac OSX, Windows N/A N/A
ValMap
Resource for MRI of Neurodegenerative Disorders
NIBIB

ValMap is a command line voxel-wise statistical analysis program for images. Images can be gray matter density, jacobian images, etc. The linear model is implemented, i.e. designs that can be modeled as Y=AB, where Y is a vector or matrix of dependent variables, B is a vector or matrix of parameters to be estimated, and A is a design matrix. Note: This program is no longer supported by the CIND.

Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
NMR Animations
Resource for MRI of Neurodegenerative Disorders
NIBIB

The NMR_Animations Powerpoint (nmr_Animations.pptx) presentation illustrates the vector model for NMR under the action of first, the main magnetic field, and second, an applied off-resonance RF pulse from the viewpoint of the rotating frame.

Linux, Mac OSX, Windows N/A 0 - 500MB
Pseudo-Continuous Arterial spin Labeling
Resource for MRI of Neurodegenerative Disorders
NIBIB

ASL.pptx shows animations of the progression of the magnetization of flowing spins under the action of pseudo-continuous arterial spin labeling (ASL) pulses.  Inversion and two versions of null pulses are shown. The pulses are described in Nezamzadeh, et al. J Magn Reson Imaging 31, 1419, 2010.

Linux, Mac OSX, Windows N/A 0 - 500MB