mincmath - perform simple math operations on minc files
mincmath [<options>] <in1>.mnc [<in2>.mnc...]
<out>.mnc
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.
Note that options can be specified in abbreviated form (as long as they are
unique) and can be given anywhere on the command line.
- -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- Superseded by -int.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.
- -constant value
- Specify a single constant.
- -const value
- Synonym for -constant.
- -const2 value1 value2
- Specify two constants.
- -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).
- -help
- Print summary of command-line options and exit.
- -version
- Print the program's version number and exit.
Peter Neelin
Copyright © 1995 by Peter Neelin
minccalc(1)