:orphan: .. _ahelp_3dBRAIN_VOYAGERtoAFNI: ********************* 3dBRAIN_VOYAGERtoAFNI ********************* .. contents:: :local: | .. code-block:: none Usage: 3dBRAIN_VOYAGERtoAFNI <-input BV_VOLUME.vmr> [-bs] [-qx] [-tlrc|-acpc|-orig] [<-prefix PREFIX>] Converts a BrainVoyager vmr dataset to AFNI's BRIK format The conversion is based on information from BrainVoyager's website: www.brainvoyager.com. Sample data and information provided by Adam Greenberg and Nikolaus Kriegeskorte. If you get error messages about the number of voxels and file size, try the options below. I hope to automate these options once I have a better description of the BrainVoyager QX format. Optional Parameters: -bs: Force byte swapping. -qx: .vmr file is from BrainVoyager QX -tlrc: dset in tlrc space -acpc: dset in acpc-aligned space -orig: dset in orig space If unspecified, the program attempts to guess the view from the name of the input. [-novolreg]: Ignore any Rotate, Volreg, Tagalign, or WarpDrive transformations present in the Surface Volume. [-noxform]: Same as -novolreg [-setenv "'ENVname=ENVvalue'"]: Set environment variable ENVname to be ENVvalue. Quotes are necessary. Example: suma -setenv "'SUMA_BackgroundColor = 1 0 1'" See also options -update_env, -environment, etc in the output of 'suma -help' Common Debugging Options: [-trace]: Turns on In/Out debug and Memory tracing. For speeding up the tracing log, I recommend you redirect stdout to a file when using this option. For example, if you were running suma you would use: suma -spec lh.spec -sv ... > TraceFile This option replaces the old -iodbg and -memdbg. [-TRACE]: Turns on extreme tracing. [-nomall]: Turn off memory tracing. [-yesmall]: Turn on memory tracing (default). NOTE: For programs that output results to stdout (that is to your shell/screen), the debugging info might get mixed up with your results. Global Options (available to all AFNI/SUMA programs) -h: Mini help, at time, same as -help in many cases. -help: The entire help output -HELP: Extreme help, same as -help in majority of cases. -h_view: Open help in text editor. AFNI will try to find a GUI editor -hview : on your machine. You can control which it should use by setting environment variable AFNI_GUI_EDITOR. -h_web: Open help in web browser. AFNI will try to find a browser. -hweb : on your machine. You can control which it should use by setting environment variable AFNI_GUI_EDITOR. -h_find WORD: Look for lines in this programs's -help output that match (approximately) WORD. -h_raw: Help string unedited -h_spx: Help string in sphinx loveliness, but do not try to autoformat -h_aspx: Help string in sphinx with autoformatting of options, etc. -all_opts: Try to identify all options for the program from the output of its -help option. Some options might be missed and others misidentified. Use this output for hints only. Compile Date: Oct 13 2022