From VoxBoWiki
VoxBo vbimagemunge (v1.8.5pre8/May 6 2010)
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:
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).
