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MRI is a noninvasive technique that does not use x-rays or radioactive molecules. It involves passing a temporary magnetic field through the brain, and using the brain tissues' inherent physical properties to create a tissue density map which is then translated into an image. MRI is especially helpful in diagnosing tumors or other abnormalities of the tissue in the brain. In recent years, MRI has become a useful tool in clinical research. PNI uses MRIvolumetry and morphometry extensively to assess structural differences between normal individuals and abnormal patient populations.

The main challenge to volumetric and morphometric techniques is that there is fairly large heterogeneity in neuroanatomy between individuals.

Manual Segmentation
At PNI, we use a variety of manual segmentation methods implemented within our software Measure (and soon to be implemented in the new Java-based platform, MIPAV). Protocols for structural measurements are available here.

Voxel-Based morphometry
VBM is a simple voxel-by-voxel comparison based on the General Linear Model conducted on co-registered images to assess structural differences across groups.

 

Software Library
MEASURE
Measure is visualization and measurement tool for structural MRI data. It was written in 1997 by Patrick Barta, M.D. Measure provides a user-friendly environment for conducting neuroanatomical volumetric measurement using occupancy and grid (Cavalieri) methods. Measure is a 32-bit Window application that runs in 256 colors. To request a copy of Measure or a renewed license, please contact Guillermo Verduzco.
BLOX
The purpose of the project is to develop a quantitative medical imaging and visualization program for use on brain MR, DTI and MRS data. It is a joint project between PNI and the Kennedy Krieger Institute. Blox is a freesource Java tool, available for download from its sourceforge webpage.
MIPAV
The 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. MIPAV is a Java application, developed at the BIRSS at the National Institutes of Health by Matthew McAuliffe and his project team. PNI collaborates with this team to develop new tools within this programming environment.
BRAINSTRIP
Brainstrip was developed as a plug-in to MIPAV by the Medical Image Analysis Lab in the Department of Radiology at the Johns Hopkins School of Medicine. This utilitiy provides a suite of tools for accurate and reliable semi-automated brain extraction. It is based on two-level thresholding and the application of morphological operators, followed by simple manual post-processing. Data on validity and reliability is currently in press.
ATLAS_TRANSFORM
The Atlas Transformation Wizard is a plug-in to MIPAV, also developed by the MedIC lab. It provides an atlas-based labeling in the Talairach or MRI coordinate space, and allows the identification of subregions of the brain, and measurement of their volume . Reliability and validity data for this method are currently in press.
FANTASM
Fantasm (Fuzzy and Noise Tolerant Adaptive Segmentation Method) is a robuse tissue classification tool written by Dzung Pham of the MedIC lab. It is an extension of the fuzzy C-means algorithm. It is implemented as plug-in to MIPAV. For more information on this method, click here.
ABSEG (Atlas-Based Segmentation)
ABSEG was developed by Adam Dziorny as a plug-in to MIPAV, re-implementing an algorithm for whole brain segmentation based on Atlas priors by Bruce Fischl at MGH. The software provides a tool for the automated labeling of neuroanatomical structures in the human brain. This algorithm combines spatial and intensity information to improve registration to manually created atlases. This tool is still undergoing testing. For more information about this tool, please contact Scott Yeagy.

Other MRI Processing and Visualization Packages