xenial (1) cmtk-imagemath.1.gz

Provided by: cmtk_3.2.2-1.4_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 <double>
            Set values below given threshold to threshold.

       --thresh-above <double>
            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.

   Complex Arithmetic
       --complex-div
            Complex  division,  (a+ib)/(c+id),  assuming  four values were put on the stack in order a, b, c, d.
            Place result on stack, real first, imaginary second (i.e., imaginary is top).

   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,  with  contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B.
       Russakoff, and Yaroslav Halchenko

LICENSE

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

BUGS

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

ACKNOWLEDGMENTS

       CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium  on  Alcohol  and
       Neurodevelopment  in Adolescence (N-CANDA): Data Integration Component. From April 2009 through September
       2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381.