Provided by: cmtk_2.1.0-1_amd64 bug

NAME

       imagemath - Image operations

DESCRIPTION

       Perform operations on images using stack-based postfix notation.

       Images  can  be  read  from  files  and  pushed onto the stack. Images on the stack can be
       processed and combined via different operators. Results of all  operations  are  put  back
       onto the stack, where they can be further processed or written back to image files.

OPTIONS

   Global Toolkit Options (these are shared by all CMTK tools)
       --help
            Write list of basic command line options to standard output.

       --help-all
            Write complete list of basic and advanced command line options to standard output.

       --wiki
            Write list of command line options to standard output in MediaWiki markup.

       --man
            Write man page source in 'nroff' markup to standard output.

       --version
            Write toolkit version to standard output.

       --echo
            Write the current command line to standard output.

       --verbose-level <integer>
            Set verbosity level.

       --verbose, -v
            Increment verbosity level by 1 (deprecated; supported for backward compatibility).

       --threads <integer>
            Set maximum number of parallel threads (for POSIX threads and OpenMP).

   Input/output operations
       --in <string-vector>
            Read input image(s) to top of stack

       --out <string>
            Write output image from top of stack (but leave it on the stack)

       --set-padding-value <double>
            Set the value that is interpreted as padding value in subsequently read images.

       --unset-padding
            Disable padding. All values in subsequently read images will be interpreted as actual
            data.

   Internal settings
       --float
            Use single precision for computations and results [This is the default]

       --double
            Use double precision for computations and results

   Stack operations
       --pop
            Pop (discard) top image from stack.

       --dup
            Duplicate image on top of the stack.

       --all
            Apply next single-image operation to all images on the stack.

   Single-image operators
       --fill <double>
            Fill top image with constant value (i.e., assign value to all pixels)

       --abs
            Apply abs() function to top image

       --log
            Apply log() function to top image

       --logit
            Apply log(x/(1-x)) function to top image

       --logistic
            Apply 1/(1+exp(-x)) function to top image

       --exp
            Apply exp() function to top image

       --sqr
            Apply square operator to top image

       --sqrt
            Apply square root operator to top image

       --trunc
            Truncate all values in top image to integer

       --one-over
            For each pixel, replace its value x with 1.0/x

       --scalar-mul <double>
            Multiply top image with a scalar value

       --scalar-add <double>
            Add a scalar to each pixel of the top image

       --scalar-xor <integer>
            Bitwise exclusive-or between top level and given scalar value

       --scalar-and <integer>
            Bitwise and operation between top level and given scalar value

       --thresh-below <string>
            Set values below given threshold to threshold.

       --thresh-above <string>
            Set values above given threshold to threshold.

   Image pair operators
       --add
            Add top and second image, place result on stack

       --mul
            Multiply top and second image, place result on stack

       --div
            Divide top image by second image, place result on stack

       --atan2
            Compute atan2() function from tup two image pixel pairs, place result on stack

       --match-histograms
            Scale intensities in one image to match intensities of another. The last image pushed
            onto  the  stack  provides  the reference intensity distribution, the preceding image
            will be modified. Both input images are removed from the stack and the modified image
            is pushed onto the stack.

       --match-mean-sdev
            Scale  intensities  of one image to match mean and standard deviation of another. The
            last image pushed onto the stack provides the reference intensity  distribution,  the
            preceding  image  will  be modified. Both input images are removed from the stack and
            the modified image is pushed onto the stack.

       --match-mean-sdev3
            Scale intensities of an image by a factor and offset computed from two  other  images
            to  match  their  mean  and standard deviations. The last image pushed onto the stack
            provides the reference intensity  distribution,  the  preceding  image  provides  the
            intensity  distribution to match to the reference image's, and the third image on the
            stack will be modified. All three input images are removed from  the  stack  and  the
            modified image is pushed onto the stack.

       --mask-average
            Mask  averaging:  the  top  image  is  taken as a multi-label mask. The pixels in the
            second image are averaged by mask labels, and then replaced with  the  average  value
            for each mask label.

   Operators that contract the entire stack into a single image
       --sum
            Sum all images on stack, place result on stack

       --product
            Compute product of all images on stack, place result on stack

       --average
            Average all images on stack, place result on stack

       --variance
            For each pixel, compute variance over all images on stack, place result on stack

       --combine-pca
            Combine images using PCA by projecting onto direction of largest correlation

       --max-value
            For each pixel, compute maximum VALUE over all images, place result on stack

       --min-value
            For each pixel, compute minimum VALUE over all images, place result on stack

       --max-index
            For each pixel, compute INDEX of image with maximum value, place result on stack

   Operators that contract a stack of label images into a single label image
       --vote
            Merge all images on stack with voting, place result on stack

       --staple <integer>
            Combine  binary maps on the stack using [arg] iterations of the STAPLE algorithm. The
            result of  this  operation  is  the  spatial  map  of  'weights'  W,  which  are  the
            probabilities  of image foreground at each pixel. In 'verbose' mode, estimated expert
            parameters p (sensitivity) and q (specificity) are also written to standard output.

       --contract-labels
            Contract multiple label maps into one by selecting the first (over all images on  the
            stack) non-zero label at each pixel

       --mstaple <integer>
            Combine  multi-label  maps  on  the  stack  using [arg] iterations of the multi-class
            STAPLE algorithm.The result of  this  operation  is  the  combined  maximum-likeliood
            multi-label map.

       --mstaple-disputed <integer>
            Like previous operation, apply multi-class STAPLE algorithm, but restrict computation
            to 'disputed'voxels, i.e., those where the input  label  maps  disagree.  This  often
            improves results by reducing, e.g., background effects.

       --stack-entropy-labels
            Compute stack entropy at each pixel from integer (label) input images

AUTHORS

       Torsten Rohlfing, Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff

LICENSE

       http://www.fsf.org/licensing/licenses/gpl.html

BUGS

       Report bugs at http://nitrc.org/projects/cmtk/

ACKNOWLEDGMENTS

       From  April 2009 through September 2011, CMTK Development and Maintenance was supported by
       the National Institute  of  Biomedical  Imaging  and  Bioengineering  under  Grant  No.R01
       EB008381 (PI: Torsten Rohlfing).