PET-MRI Tools

Author: József VARGA, 2000-

Developed at the Johns Hopkins University, Baltimore, MD, and the University of Debrecen, Hungary
This material is based upon work supported by the National Science Foundation under Grant No. 0000843.

E-mail:

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•  Features

•  Requirements

•  Elements integrated

•  Release

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 PET-MRI Tools is a software collection running under Windows operation systems, for processing medical images of various modalities, including positron and single photon emission tomography (PET and SPECT), magnetic resonance imaging (MRI) and X-ray computed tomography (CT).

 The software was developed to be used for research purposes at academic institutes. It integrates elements (packages) developed by various persons and research groups, as listed below; see the listed references for their respective copyright notes. These packages are offered to be used on the same conditions as the original packages. Most of these packages were originally developed under UNIX, and they have been ported to Windows operating system by JV.

Functions included:

•  File type conversions
•  Displaying image files
•  Spatial coregistration
•  Reslicing of image volumes
•  Drawing regions (volumes) of interest
•  Creating time-activity curves
•  Analysis of time-activity curves
•  Segmenting MRI images
•  Partial volume correction
•  MatLab Automation Tools

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Requirements:

-        Windows 95, 98, NT 4.0, 2000, XP or Windows 7* operating system
(*not fully tested, as only a newer version of MatLab may be run under Windows 7)

-        Matlab R12.1 (version 6.1) installed, including the following packages:

o       Image Processing Toolbox

o       Optimization Toolbox

The package was developed in a bilingual (C/C++ and MatLab) environment, and contains the following types of elements:

Type:	Extension:
Windows executable	.exe
Windows batch file	.bat
MatLab function source code	.m
MatLab preprocessed function	.p
MatLab MEX file	.dll
MatLab data file	.mat
Menu resource file	.mnu

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Elements integrated from other software packages:

		Name	Description	From	Reference
	I.	C libraries
	I.1	NetCDF	Network Common Data Form	Unidata	http://www.unidata.ucar.edu/packages/netcdf/
	I.2	MINC	Medical Image NetCDF	BIC	http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC http://www.nitrc.org/frs/?group_id=129 http://en.wikibooks.org/wiki/MINC
	I.3	Volume_io	Manipulating multidimensional MINC data sets	BIC	http://www.bic.mni.mcgill.ca/~david/volume_io/volume_io.html
	I.4	MINC_Win	NetCDF, MINC and Volume_io adaptation for Windows	JV	Download
	II	MatLab libraries & programs
	II.1	NetCDF Toolbox	I/O for NetCDF data	Charles R. Denham USGS	http://www.unidata.ucar.edu/packages/netcdf/software.html#NC4ML5
	II.2	EMMA	Extensible Matlab Medical Image Analysis	Mark Wolforth & Greg Ward, BIC	http://www.bic.mni.mcgill.ca/users/wolforth/EMMA/
III.a		Standalone executables
	III.1	MatWrap	MatLab wrap file generator for C	Gary Holt	http://lnc.usc.edu/~holt/matwrap/index.html
	III.2	AIR	Automatic Image Registration	UCLA (Woods method)	http://bishopw.loni.ucla.edu/AIR5/index.html
	III.3	MINC-AIR	MINC interface for AIR	BIC	Greg Ward greg@bic.mni.mcgill.ca
	III.4	MINC resample	Transformation and reslicing MINC data	BIC	http://www.imaging.robarts.ca/Software/mni_software/minc/man/mincresample.html
	III.5	MINCinfo	Prints information from a MINC file	BIC	http://www.imaging.robarts.ca/Software/command_line_tools/node13.html
	III.6	NCDump	Prints information from a NetCDF file	Unidata	http://www.unidata.ucar.edu/software/netcdf/docs/ncdump-man-1.html
	III.8	AFCM	Adaptive Fuzzy c-means segmentation	Dzung Phom	IEEE Trans. On Medical Imaging 18/9:737-752, 1999.
	III.9	BET	Brain Extraction Tool (from MRI)	Steve Smith	http://www.fmrib.ox.ac.uk/analysis/research/bet/

 Abbreviations: