vbimagemunge

*** DEPRECATION WARNING -- SEE NOTES ***

VoxBo vbimagemunge (v1.8.5/Jun 14 2011)
summary: image munging for VoxBo
usage:
  vbimagemunge [<file> ...] <flags> -- <op> [<op> ...]
flags:
  -h             show help
  -v             show version
image processing operations:
  smoothvox <x> <y> <z>  3D Gaussian smooth
  smoothmm <x> <y> <z>   3D Gaussian smooth
  thresh <val>           zero where <= val
  threshabs <val>        zero where absolute value <= val
  cutoff <val>           zero where >= val
  quantize <val>         set non-zero values to val
  invert                 zet non-zeros to zero, zeros to 1
  combine ...            see below
  convert <new type>     see below
  add <img/num>          add image (if file exists) or scalar
  sub <img/num>          subtract image (if file exists) or scalar
  mult <img/num>         multiply by image (if file exists) or scalar
  div <img/num>          divide by image (if file exists) or scalar
  nminus <img/num>       subtract from img (if file exists) or scalar
  random01               fill entire volume with random 0s and 1s
  remap <file>           file has two values per line: old value and new value
  flipx/flipy/flipz      
  bigendian/littleendian change how the data will be written out
  byteswap               
  zeroleft/zeroright     
  rotate <pitch> <roll> <yaw>
  regionat <x> <y> <z>   find region including voxel at coordinates x,y,z
  splitregions <fname>   output filename (XXX will be replaced by an index)
combining operations:
  sum               sum all volumes
  average           average all volumes
  product           product of all volumes
  multi             combine input masks into a multi-mask
  union             combine input masks by calculating the union
  intersect         combine input masks by calculating the intersection
  count             combine input masks by counting non-zero voxels
  overlapmask       create a color-coded overlap mask of up to 3 masks
  select <n>        randomly select n volumes
  include <range>   include volumes in range, e.g., 0-5,7,9-13 (no spaces)
  exclude <range>   exclude volumes in range, e.g., 0-5,7,9-13 (no spaces)
output/summary operations:
  write <name>            write to single output filename
  writeprefixed <prefix>  prefix each volume's original name and write
  write4d <name>          combine the volumes into a 4d file
  info                    print general info about each 3D volume
  regioninfo              print region info    // vbregion has great methods
notes:
  vbim replaced vbimagemunge and various other mungers.  this program
  is no longer actively maintained.

  vbimagemunge replaces vbmaskmunge, for the most part.

  vbimagemunge takes multiple 3D volumes as input, and applies the
  specified image processing operations, in the order specified.  If a
  4D input volume is specified, it is broken down into 3D volumes.
  
  vbimagemunge has three kinds of operations.  Image processing
  operations are applied to each 3D volume independently.  Combining
  operations apply to the whole set of 3D volumes and typically reduce
  the set to a single volume.  Output/summary operations print out
  information about the volumes as they exist at that point and/or
  write out files.  The operations are applied in the order given.

  For convert, valid new types are: byte, int16, int32, float, and
  double.  Note that VoxBo historically has used more ambiguous names
  for int16 and int32.

  The combine operation implements several methods for re-calculating
  each voxel's value as a combination of surrounding voxels.  It takes
  six arguments.  The first argment is either "fixed" or "moving" (can
  be abbreviated with f/m).  Fixed means that the brain is divided
  into fixed subregions, and each voxel in a given subregion gets the
  same value.  Moving means that each voxel gets a value calculated
  from a region centered at that voxel.  The next three arguments are
  the size of the region in x, y, and z.  The following argument is
  the combination method.  The following methods are supported: sum,
  count (count nonzero), average, pct (percent nonzero), any (1 if any
  voxel in the region is nonzero), sumthresh (1 if the sum exceeds a
  threshold), and averagethresh.  The final argument is the threshold
  for sumthresh and averagethresh (ignored for the other methods, but
  you must still supply a value.  Note that the output is stored in
  the same format as the input, so you may want to convert to a
  different datatype before performing some operations (e.g., many
  masks are stored as byte data, which can only represent integers in
  the 0-255 range).