______________________________________________________________________________ VLSM Voxel-based Lesion Symptom Mapping Version 1.6 August 2, 2005 Copyright 2002 - 2005 Stephen Wilson ______________________________________________________________________________ VLSM is a technique for analyzing the relationship between lesion data and continuous behavioral measures. The set of MATLAB functions which implement VLSM are also referred to as VLSM. The documentation consists of the brief guide below to getting started, as well as more detailed information about each function which can be viewed by typing 'help function-name' in MATLAB. To display the present file from within MATLAB, you can type 'help vlsm'. A helpful tip for viewing MATLAB help files in general is to type 'more on' before you start, which gives you just one screenful at a time. VLSM is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details. This can be found at http://www.gnu.org/copyleft/gpl.html. If you use VLSM, we would appreciate it if you would cite the following paper: Bates, E., Wilson, S. M., Saygin, A. P., Dick, F., Sereno, M. I., Knight, R. T., & Dronkers, N. F. (2003). Voxel-based lesion-symptom mapping. Nature Neuroscience, 6, 448-450. Installation and startup ________________________ VLSM requires MATLAB version 6.0 or later. Many operations may work under earlier versions of MATLAB, but some functions required for full functionality are only found in version 6.0 or later. Two toolboxes are also required: the statistics toolbox and the image processing toolbox. Again, it may be possible to conduct analyses without these toolboxes, but some functionality will be lacking. The VLSM directory can be stored wherever you want. If you are installing VLSM from a compressed file, extract the VLSM folder and place it in any convenient location. You do, however, have to tell MATLAB where to find the VLSM functions by adding the 'vlsm' directory to its search path. You also need to add the following subdirectories: 'coords', 'files', 'spm-based', 'stats' and 'utils'. This can be accomplished by starting MATLAB and choosing 'Set Path' from the 'File' menu, then adding the directories to the path and saving it. Details can be found in the MATLAB documentation. Once you have added the VLSM directories to the MATLAB path, you can run VLSM functions by typing them at the MATLAB command prompt. There is no need to "start up" VLSM, you just start using VLSM functions. However, the first time you use a VLSM function in a MATLAB session, some information such as the version number and the copyright notice is displayed. Overview of a VLSM analysis ___________________________ There are generally five steps to conducting a VLSM analysis: 1. Open a set of lesion files for the patients of interest with the function VLSM_OPENPATIENTSET. 2. Open a file containing behavioral data for the patients of interest with the function VLSM_OPENBEHAVDATA. 3. Create a VLSM overlay with VLSM_OVERLAY. 4. Display the resulting overlay with VLSM_DISPLAY. 5. Export the figure to a TIFF file viewable in other applications with VLSM_EXPORT. The reason that the process is broken up into these steps is for flexibility. Often, you might want to conduct a number of analyses based on the same patients and behavioral data file. To do this, you would carry out steps 1 and 2, then carry out step 3 multiple times. Another possibility is to skip steps 4 and 5, and view (and possibly export) the overlay images with another image processing package such as MRIcro, SPM or AFNI. For more information on each of the steps above, type 'help function-name' in MATLAB for each of the five functions, e.g. start with 'help vlsm_openpatientset'. There are numerous other functions which you may find useful. They all contain documentation (however minimal) which can be accessed with the 'help' command. Good luck! Contact details _______________ Questions about the VLSM software should be directed to: Stephen Wilson Neuroscience Interdepartmental Program University of California, Los Angeles 1320 Gonda Center 695 Young Drive South Los Angeles, CA 90095-1761