| The UCLA Brain mapping center makes available a variety of software tools for academic use by scientific investigators. Users are requested to acknowledge such use in all publications, and to keep the authors informed of any modification to source code that extend the functionality. Commerical reproduction is forbidden without prior consent of the authors. |
Some of the programs that we have written are available in object (executable) form. You can find Apple or Sun targets at these links. Please note that the links for Sun have been kindly provided by Theo Van Erp.
Correlation coefficient calculation for fMRI Experiments: CC_gr"CC_gr" is a tool for the calculation of the coefficient of correlation between the intensities of each pixel in a time series of images with a reference vector. The reference vector is in turn a text file of the weights to associate with each image in the time series. CC_gr makes liberal use of the ImgLib library included below. It is very fast and memory efficient. Currently, it will read in the native data types on the ANMR apd2 console, the General Electric Signa(r) genesis format and the MGH NMR center file types (xx.bshort, xx.buchar, xx.bfloat). It writes out files of type xx.CC_gr.bfloat, as well as a processing record file and a color overlay file. The overlay file is a file of 1-byte/pixel images. To view these, you can download our file TwoColorLUTs to use with the public domain program NIH Image, available by web at the NIH image home page. The wonderful program "xds", developed by Tim Davis also supports the import of such color maps. CC_gr is available as Shareware -- Commercial use is not permitted without prior consent of Mark Cohen. It would be generous to receive a citation and a copy of any articles that use the tools. CC_gr is distributed as ANSI C source code. Late-breaking flash: Our patent office requires that downloads of this software are by individual request only (sorry). Please report any bugs or problems to Mark Cohen |
t-statistic mapping calculation for fMRI Experiments: T_gr"T_gr" is a tool for the calculation of the t-statistic comparing the intensities of each pixel in a time series of images with a reference vector. The reference vector is in turn a text file of the weights to associate with each image in the time series. T_gr makes liberal use of the ImgLib library included below. It is very fast and memory efficient. Currently, it will read in the native data types on the ANMR apd2 console, the General Electric Signa(r) genesis format and the MGH NMR center file types (xx.bshort, xx.buchar, xx.bfloat). It writes out files of type xx.T_gr.bfloat, as well as a processing record file and a color overlay file. The overlay file is a file of 1-byte/pixel images. To view these, you can download our file TwoColorLUTs to use with the public domain program NIH Image, available by web at NIH image home page. The wonderful program "xds", developed by Tim Davis also supports the import of such color maps. T_gr is available as Shareware -- Commercial use is not permitted without prior consent of Mark Cohen. It would be generous to receive a citation and a copy of any articles that use the tools. T_gr is distributed as ANSI C source code. Late-breaking flash: Our patent office requires that downloads of this software are by individual request only (sorry). Please report any bugs or problems to Mark Cohen |
Reference vector creation fMRI Experiments: CprotoCproto"Cproto" is a tool for the creation of ascii reference vectors for use with tools such as CC_gr or T_gr. The user enters in a series of image numbers and weights and the tool calculates the appropriate reference vector. Cproto is available as Shareware -- Commercial use is not permitted without prior consent of Mark Cohen. It would be generous to receive a citation and a copy of any articles that use the tools. Cproto is distributed as ANSI C source code. Late-breaking flash: Our patent office requires that downloads of this software are by individual request only (sorry). Please report any bugs or problems to Mark Cohen |
Color overlay creation for fMRI Experiments: Overlay"Overlay" is a tool for the creation of colorized images that overlay statistical maps onto anatomical images. Generally, the maps are created by a tool such as CC_gr or T_gr as floating point images. It reads in the statistical image and a "base image" (usually an anatomical image) and merges the two. Pixels in the base image are represented by values from 1 to 127. Those in the overlay image are represented in the range from 128 to 254. The values of 0 and 1 are not used, because on the Macintosh computer (which we use almost exclusively) these values are reserved. You can use NIH Image, available by web at NIH and our program TwoColorLUTs to view the merged images. The wonderful program "xds", developed by Tim Davis also supports the import of such color maps. Overlay makes liberal use of the ImgLib library included below. Currently, it will read in the native data types on the ANMR apd2 console, the General Electric Signa(r) genesis format and the MGH NMR center file types (xx.bshort, xx.buchar, xx.bfloat). It writes out files of type xx.buchar, as well as a processing record file. Overlay is distributed as ANSI C source code. Overlay is available as Shareware -- Commercial use is not permitted without prior consent of Mark Cohen. It would be generous to receive a citation and a copy of any articles that use the tools. Late-breaking flash: Our patent office requires that downloads of this software are by individual request only (sorry). Please report any bugs or problems to Mark Cohen |
Two Color Lookup tables for viewing color overlay images: Two Color LUTsThis is a macro for use with the program NIH image (available at NIH). To use it, from the Special menu on Image, select Load Macros... and read in this file. This will install the lookup tables on the Special menu. Simply select the lookup table you like. Note that the files created by T_gr and CC_gr can use only the "auto_red_blue" lookup table. Two Color LUTs is available as Shareware -- Commercial use is not permitted without prior consent of Mark Cohen. It would be generous to receive a citation and a copy of any articles that use the tools. Two Color LUTs is distributed as an ASCII text file. Please report any bugs or problems to Mark Cohen |
MacStim: A program for the presentation of stimuliMacStim is a program that runs on Macintosh computers and allows the flexible and accurate presentation of visual, auditory or other stimuli to subjects for perceptual and cognitive experiments. It incorporates precise timing, easy use and robust performance; in addition, its author, David Darby, continues to make good on his promises of support. We are avid users of this software. The program is designed for use in the environment of magnetic resonance imaging, but might serve equally well in psychophysical testing labs. The current release version is usually available from our site.
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Stimuli for fMRI Experiments: Rings"Rings" is a small application that generates a variety of simple visual stimuli for use in psychophysical experiments. It will produce flashing checkerboards, expanding rings and squares, and drifting gratings, at a broad selection of rates and sizes. Runs on Macintosh computers under system 7.5 or greater. Rings is available as Shareware -- Commercial use is not permitted without prior consent of Mark Cohen. It would be generous to receive a citation and a copy of any articles that use the tools. |
UCLA Image Processing Library: ImgLib"ImgLib" is a set of C language routines that may find general use for image processing. They are available as Shareware -- any commercial use must be cleared in advance with Mark Cohen email: mscohen@ucla.edu prior to use. You may wish to download this library form time to time to get updates. Please report any errors and share any additions with us. There are no guarantees here.
The headers for ImgLib, Target.h VLib.h, MathLib.h, ImgLibError.h and analyzeUtil.h are also available. Please report any bugs or problems to Mark Cohen |
Carnegie Mellon University Command Line Parser: getopt.c, getopt.h"getopt" is a set of C language routines that are used for command line processing. Some computer systems have this as a standard function. To check whether you have it, on the command line type 'man getopt'. As some of our programs use this function, you may need to compile "getopt" first. |
The Automated Image Registration (AIR) package is primarily designed to solve several different registration problems that arise in tomographic data sets:
Automated Image Registration Home Page AIR Automated Image Registration is ©1993-99 Roger P.Woods |
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©1997-2001 Mark S. Cohen, Ph.D.
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