VAMCA OHBM 2009 Annual Meeting Version (updated on 8/20/2010) -------------------- VAMCA ("Visualization And Meta-analysis on Cortical Anatomy") is an open source meta-analysis, visualization, and significance testing toolbox for MatLab, and it can be run on many kinds of hardware. It is a command-line program that can be used to display MNI or Talairach coordinates on a mean cortical surface displayed in any one of 4 views. Two groups of coordinates can be displayed on the surface and they can be tested to see if they are not in the same location or in the same regions of interests. The toolbox works with Matlab versions 5.3-7.x and is a stand-alone package. -------------------- The vamca.zip file that you have downloaded is the CNS Annual Meeting 2008 version and contains the following main files: Documentation: - vamca.readme: this one! - VAMCA Tutorial.pdf: a short tutorial to get started with VAMCA. - vamca.txt: some meager documentation on program options. - VAMCAmethod.pdf: a poster on how VAMCA performs it magic. - VAMCAauditory.pdf: a sample meta-analysis using VAMCA. - VAMCA_TBI.pdf: another sample meta-analysis in poster form. - VAMCAfuturedirections.pdf: poster outlining features to be added to VAMCA. - vamca.lic: the VAMCA license/disclaimer. - vamca.html: some info about VAMCA's database and visualization. Source and Executables: - vamca.m: the VAMCA MatLab function - type "help vamca" in Matlab to get some help on the options available. - dovamca.m: a sample VAMCA calling function - this is the one to try first: type "dovamca" at the MatLab prompt after unzipping the .zip file and moving to the /vamca directory. Sample Data Files - "HUMAN_inputMNI.txt": Human sounds - "NONHUMAN_inputMNI.txt": Non-human sounds These two 3D coordinate files help you reproduce Example 1 in the VAMCAmethod.pdf poster (find the command in "dovamca.m" using them). - "vis-sacc.txt": Visually triggered saccades with uniform weighting - "vis-sacc2.txt": Visually triggered saccades with per-experiment weighting - "vis-sacc3.txt": Visually triggered saccades with #-of-subjects weighting - "vol-sacc.txt": Voluntarily triggered saccades with uniform weighting - "vol-sacc2.txt": Voluntarily triggered saccades with per-experiment weighting - "vol-sacc3.txt": Voluntarily triggered saccades with #-of-subjects weighting These six 3D coordinate files help you reproduce Example 2 in the VAMCAmethod.pdf poster (find the command in "dovamca.m" using them). - "Fannon-MT.txt": single-subject fMRI activations likely associated with area MT - "Fannon-V8.txt": single-subject fMRI activations likely associated with area V8 - "Fannon-extra.txt": Extra reference points to plot These three 3D coordinate files help you reproduce Figure 3 in the journal article: Fannon et al, Frontiers in Neuroscience, 1(7), 2007. - "ffa.txt": mean fMRI activations associated with visual face stimuli - "ppa.txt": mean fMRI activations associated with visual building stimuli These two 3D coordinate files help you reproduce a VAMCA version of Figure 6 in the journal article: Hasson et al, Neuron, 37, 2003. - "Stenbacka2007-UpperVis.txt": fMRI activations for the upper visual field - "Stenbacka2007-LowerVis.txt": fMRI activations for the lower visual field These two 3D fMRI coordinate files of central and peripheral visual field stimulation are taken from the journal article: Steinbacka & Vanni, Clin. Neurophys, 118(6), 2007. - "tbiBadAnat.txt": coordinate locations correlated with traumatic brain injury anatomical damage - "tbiMetabolix.txt": coordinate locations of tbi-related hypometabolism The two preceding files are to allow you to replicate the penultimate analysis in the VANCA_TBI.pdf CNS2009 poster. See dovamca.m. --------------------- How to setup and run Vamca 1) Unzip vamca.zip to a new directory convenient for use with MatLab. 2) Fire up MatLab 5.3-7.x 3) Change ('cd') with MatLab to the directory where vamca now lives. 3a) For Linux, Macintosh, or Windows non-XP users, type 'mex Es2.c' at the matlab prompt and follow the prompts (choose any C compiler when asked to do so). 4) Test the system by typing 'dovamca' at the matlab prompt - you should get 3 different plots after waiting a few seconds. 5) Open the file 'dovamca.m' to see how the 'vamca' command works, try out a few other built in analyses by commenting lines in and out, and processing some of your own data. 6) Have fun. --------------------- Troubleshooting: 1) If you get the error message "Undefined function or variable 'Es2' " or any other kind or error message referencing "Es2.dll" from MatLab, then you need to compile a "mex" function in MatLab, and this is easy to do: type "mex Es2.c" at the MatLab prompt and then follow the instructions (choose any C compiler if asked) until it completes compiling (a few seconds). Then try running vamca.m again. vamca.zip comes with a Windows XP Es2.dll file that should obviate the need for performing the compile step, but using VAMCA in Linux or Macintosh or non-XP versions of Windows (or Matlab 5) will require this step. If the above does not work, type "mex -setup" and select an installed C compiler from the list (select "lcc" if you have no other). If no C compiler is installed, trying Googleing to obtain a free Borland C compiler (bcc32.exe) that should be available online.