BIAC Software Tools 0.92 Readme This is a preliminary distribution of several useful MATLAB functions used at BIAC for visualizing image data. They are provided as-is in the hope that they will be useful, and are distributed with the understanding that there is no guarantee whatsoever that these tools will perform as promised, and without any guarantee of support. As this is a preliminary distribution, we request that you do not redistribute this software to third parties, and instead point any interested third parties to the original distribution site. See copyright for details. Below are instructions on how to set up the software and how to test it. Tested Platforms These tools are expected to work out-of-the-box in MATLAB 6.1 and 6.5 running on Windows [x86], AIX 5.2 [PPC], or Red Hat Linux (version 7 or greater) [x86] systems. Other systems and versions may work but may require you to compile particular functions for your platform. See compiling below for more info. Setup To use this on a supported UNIX variant (includes compiled mex files for RedHat Linux, and AIX): 1. Unzip the distribution (if you're reading this file, you've probably already done this) 2. Start MATLAB 3. In MATLAB, add the appropriate directories to your path: addpath /my/extracted/dir/biactools/matlab/mr addpath /my/extracted/dir/biactools/matlab/general Alternatively, you may edit the startup.m script to point to your matlab directory and run it instead. This has not been tested extensively. To use this on Windows: 1. Unzip the distribution (if you're reading this file, you've probably already done this) 2. Go to the "System" Control Panel, find the Advanced tab, and click on the "Environment variables" button. Now add a new environment variable by clicking on "New". Type "PATH" into the variable name field, and type the full pathname for the lib\ subdirectory in the extracted distribution, for example: c:\my\extracted\dir\biactools\matlab\lib Click OK. You will only have to do this step once. 3. Start MATLAB 4. In MATLAB, add the matlab directory to your path: addpath c:\my\extracted\dir\biactools\matlab\mr addpath c:\my\extracted\dir\biactools\matlab\general Alternatively, you may edit the startup.m script to point to your matlab directory and run it instead. This has not been tested extensively. Testing We have included a sample data set for you to try. In MATLAB, navigate to the "testdata" subdirectory of the extracted distribution. Once there, type this: showsrs2(readmr('test.bxh')) This should bring up a one-volume uniform spherical phantom in the visualization program showsrs2. Alternatively, you can specify the full path to test.bxh in the line above. If you do not have XML support, you will not be able to read BXH files. Instead, try: showsrs2(readmr('test.hdr')) This will read the same data using an Analyze7.5 header. Compiling If you are running MATLAB on a platform for which we have not provided binaries, you will need to compile them yourself. Three scripts, buildmex.bat (for Windows), buildmex.sh (for UNIX-based platforms), and buildmex.m (for either) have been provided (in the 'general' directory) to help you do this. If you are interested in the BIAC tools' XML support, you will need to have an installation of libxml2 (and its dependencies) in order to compile readxml.c and writexml.c. On Windows you will require two DLLs: libxml2.dll and iconv.dll. On UNIX-based machines you will need libxml2 and libz (required Linux RPMs are libxml2, libxml2-devel, and zlib). Sources for these are available at http://www.xmlsoft.org/, and Win32 binaries are available at http://www.zlatkovic.com/projects/libxml/index.html