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VoxBo vbimagemunge (v%1%)
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summary: image munging for VoxBo
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vbimagemunge [<file> ...] <flags> -- <op> [<op> ...]
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image processing operations:
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smoothvox <x> <y> <z> 3D Gaussian smooth
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smoothmm <x> <y> <z> 3D Gaussian smooth
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thresh <val> zero where <= val
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threshabs <val> zero where absolute value <= val
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cutoff <val> zero where >= val
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quantize <val> set non-zero values to val
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invert zet non-zeros to zero, zeros to 1
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convert <new type> see below
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add <img/num> add image (if file exists) or scalar
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sub <img/num> subtract image (if file exists) or scalar
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mult <img/num> multiply by image (if file exists) or scalar
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div <img/num> divide by image (if file exists) or scalar
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nminus <img/num> subtract from img (if file exists) or scalar
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random01 fill entire volume with random 0s and 1s
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remap <file> file has two values per line: old value and new value
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bigendian/littleendian change how the data will be written out
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rotate <pitch> <roll> <yaw>
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regionat <x> <y> <z> find region including voxel at coordinates x,y,z
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splitregions <fname> output filename (XXX will be replaced by an index)
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# NOT YET IMPLEMENTED:
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# orient <from> <to> RPI notation, use -- as from for current orientation
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# removesmallregions <n> // uses function zerosmallregions(cube,double)
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average average all volumes
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product product of all volumes
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multi combine input masks into a multi-mask
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union combine input masks by calculating the union
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intersect combine input masks by calculating the intersection
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count combine input masks by counting non-zero voxels
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overlapmask create a color-coded overlap mask of up to 3 masks
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select <n> randomly select n volumes
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include <range> include volumes in range, e.g., 0-5,7,9-13 (no spaces)
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exclude <range> exclude volumes in range, e.g., 0-5,7,9-13 (no spaces)
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output/summary operations:
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write <name> write to single output filename
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writeprefixed <prefix> prefix each volume's original name and write
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write4d <name> combine the volumes into a 4d file
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info print general info about each 3D volume
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regioninfo print region info // vbregion has great methods
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vbimagemunge replaces vbmaskmunge, for the most part.
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vbimagemunge takes multiple 3D volumes as input, and applies the
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specified image processing operations, in the order specified. If a
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4D input volume is specified, it is broken down into 3D volumes.
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vbimagemunge has three kinds of operations. Image processing
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operations are applied to each 3D volume independently. Combining
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operations apply to the whole set of 3D volumes and typically reduce
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the set to a single volume. Output/summary operations print out
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information about the volumes as they exist at that point and/or
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write out files. The operations are applied in the order given.
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For convert, valid new types are: byte, int16, int32, float, and
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double. Note that VoxBo historically has used more ambiguous names
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The combine operation implements several methods for re-calculating
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each voxel's value as a combination of surrounding voxels. It takes
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six arguments. The first argment is either "fixed" or "moving" (can
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be abbreviated with f/m). Fixed means that the brain is divided
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into fixed subregions, and each voxel in a given subregion gets the
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same value. Moving means that each voxel gets a value calculated
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from a region centered at that voxel. The next three arguments are
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the size of the region in x, y, and z. The following argument is
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the combination method. The following methods are supported: sum,
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count (count nonzero), average, pct (percent nonzero), any (1 if any
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voxel in the region is nonzero), sumthresh (1 if the sum exceeds a
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threshold), and averagethresh. The final argument is the threshold
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for sumthresh and averagethresh (ignored for the other methods, but
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you must still supply a value. Note that the output is stored in
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the same format as the input, so you may want to convert to a
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different datatype before performing some operations (e.g., many
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masks are stored as byte data, which can only represent integers in
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removed
munge/vbimagemunge.hlp
