Provided by: minc-tools_2.3.00+dfsg-10_amd64 bug

NAME

       mincmath - perform simple math operations on minc files

SYNOPSIS

       mincmath [<options>] <in1>.mnc [<in2>.mnc...] <out>.mnc

DESCRIPTION

       Mincmath will perform simple, voxel-by-voxel math operations, on one or more minc files of
       the same shape and having the same coordinate sampling, producing a  single  output  file.
       Operations  can  be  unary  (operate  on one file), binary (two input files) or cumulative
       (operate on two or more input files). Cumulative operations can also be performed across a
       specified dimension of the input files.

OPTIONS

       Note  that  options  can be specified in abbreviated form (as long as they are unique) and
       can be given anywhere on the command line.

General options

       -2     Create a MINC 2.0 format output file.

       -clobber
              Overwrite an existing file.

       -noclobber
              Don't overwrite an existing file (default).

       -no_clobber
              Synonym for -noclobber.

       -verbose
              Print out progress information for each chunk of data copied (default).

       -quiet Do not print out progress information.

       -debug Print out debugging information.

       -filelist filename
              Specify a file containing a list of input file names. If "-" is  given,  then  file
              names  are read from the standard input. If this option is given, then there should
              be no input file names specified on the command line. Empty lines in the input file
              are ignored.

       -copy_header
              Copy all of the header information from the first input file (default for one input
              file).

       -nocopy_header
              Do not copy all of the header from the  first  input  file;  copy  only  coordinate
              information (default for more than one input file).

       -filetype
              Create an output file with the same type as the first input file (default).

       -byte  Store output voxels in 8-bit integer format.

       -short Store output voxels in 16-bit integer format.

       -int   Store output voxels in 32-bit integer format.

       -long  Superseded by -int.

       -float Store output voxels in 32-bit floating point format.

       -double
              Store output voxels in 64-bit floating point format.

       -signed
              Use  signed, two's complement integer format. Applies only if the output voxel type
              is specified to be an integer type (one of -byte, -short, -int or -long).

       -unsigned
              Use unsigned integer format. Applies only if the output voxel type is specified  to
              be an integer type (one of -byte, -short, -int or -long).

       -range min max
              Restrict  the  valid  range  of  integer  data.   Applies only if one of the -byte,
              -short, -int or -long options is specified.

       -max_buffer_size_in_kb size
              Specify the maximum size of the internal  buffers  (in  kbytes).  Default  is  4096
              (4MB).

       -dimension dimname
              Specify a dimension along which we wish to perform a cumulative operation.

       -check_dimensions
              Check that all input files have matching sampling in world dimensions (default).

       -nocheck_dimensions
              Ignore any differences in world dimensions sampling for input files .

       -propagate_nan
              Invalid  data  (Not-A-Number  or  NaN)  at  a  voxel in any of the input files will
              produce invalid data in the output file at that voxel (default).

       -ignore_nan
              For cumulative operations, invalid data (NaN) in an  input  file  is  ignored,  ie.
              treated as though it is not present.

       -nan   When an illegal operation is attempted at a voxel (such as divide by zero), invalid
              data (NaN) is stored in the output file (default). Having no valid input data for a
              cumulative  operation  is  also considered an illegal operation when -ignore_nan is
              used.

       -zero  When an illegal operation is attempted at a voxel (such as divide by  zero),  value
              zero is stored in the output file.

       -illegal_value value
              When  an  illegal  operation  is attempted at a voxel (such as divide by zero), the
              specified value is stored in the output file.

Options for specifying constants

       -constant value
              Specify a single constant.

       -const value
              Synonym for -constant.

       -const2 value1 value2
              Specify two constants.

Operations

       -add   Cumulatively add two or more volumes, or add a volume and a constant.

       -sub   Subtract two volumes or a volume minus a constant.

       -mult  Cumulatively multiply two or more volumes, or multiply a volume and a constant.

       -div   Divide two volumes or a volume divided by a constant.

       -invert
              Calculate 1/x at each voxel, where x is the input voxel value. If a constant  c  is
              specified (with -constant), then calculate c/x at each voxel.

       -sqrt  Calculate the square root of a volume.

       -square
              Calculate the square of a volume.

       -abs   Calculate the absolute value of a volume.

       -maximum
              Calculate the maximum of a series of volumes.

       -minimum
              Calculate the minimum of a series of volumes.

       -exp   Calculate c2*exp(c1*x) at each voxel of a volume, where x is the voxel value and c1
              and c2 are constants specified by -constant c1 or -const2 c1 c2. The default  value
              for these constants is 1.0.

       -log   Calculate  log(x/c2)/c1  for each voxel of a volume, where x is the voxel value and
              c1 and c2 are constants specified by -constant c1 or -const2  c1  c2.  The  default
              value for these constants is 1.0.

       -scale Scale  a  volume  either  by multiplying by a single constant (use -constant) or by
              multiplying by the first constant and adding the second (use -const2).

       -clamp Clamp a volume to lie between two values specified with -const2.

       -segment
              Segment (binarize) a volume so that values within the range  specified  by  -const2
              give value 1 and those outside it give value 0.

       -nsegment
              Opposite of -segment: values within the range specified by -const2 give value 0 and
              those outside it give value 1.

       -percentdiff
              Calculate the percent difference between  two  volumes  (normalized  to  the  first
              volume).  If  the  first  volume is less than a threshold (or zero), then the value
              specified by -nan or -zero is used. The threshold  is  specified  using  -constant,
              with a default of zero.

       -pd    Synonym for -percentdiff.

       -eq    Test for equality of two volumes or a volume and a constant.  Values are rounded to
              the nearest integer before performing the test. Output 1 for true and 0  for  false
              at each voxel.

       -ne    Test  for inequality of two volumes or a volume and a constant.  Values are rounded
              to the nearest integer before performing the test.  Output 1 for  true  and  0  for
              false at each voxel.

       -gt    Test  for volume 1 > volume 2 or a volume > a constant. Output 1 for true and 0 for
              false at each voxel.

       -ge    Test for volume 1 >= volume 2 or a volume >= a constant. Output 1 for  true  and  0
              for false at each voxel.

       -lt    Test  for volume 1 < volume 2 or a volume < a constant. Output 1 for true and 0 for
              false at each voxel.

       -le    Test for volume 1 <= volume 2 or a volume <= a constant. Output 1 for  true  and  0
              for false at each voxel.

       -and   Test  for volume 1 && volume 2 or a volume && a constant. Values are rounded to the
              nearest integer before performing the test. Output 1 for true and 0  for  false  at
              each voxel.

       -or    Test  for volume 1 || volume 2 or a volume || a constant. Values are rounded to the
              nearest integer before performing the test. Output 1 for true and 0  for  false  at
              each voxel.

       -not   Perform  logical  negation  on  a volume: convert non-zero to zero and zero to one.
              Values are rounded to the nearest integer before the negation.

       -isnan Test a volume for invalid values (NaN). Output 1 for invalid values and 0 for valid
              values.

       -nisnan
              Opposite of -isnan. Output 0 for invalid values and 1 for valid values.

       -count_valid
              Count the number of valid voxels across a series of volumes. If none of the volumes
              has valid data, then zero is written out (ie.  -zero  and  -ignore_nan  are  always
              assumed, unlike other cumulative operations).

Generic options for all commands:

       -help  Print summary of command-line options and exit.

       -version
              Print the program's version number and exit.

AUTHOR

       Peter Neelin

COPYRIGHTS

       Copyright © 1995 by Peter Neelin

SEE ALSO

       minccalc(1)

                                   $Date: 2004-05-20 21:52:08 $                       MINCMATH(1)