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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       -long  Superseded by -int.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 $