mincmath

mincmath perform simple math operations on minc files

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Superseded by -int.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