MINCMATH(1)							 MINC User's Guide						       MINCMATH(1)

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       -long  Superseded by -int.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. Out-
	      put 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.  Out-
	      put 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 (C) 1995 by Peter Neelin

SEE ALSO

       minccalc(1)

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