

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 8bit integer format. 
short  Store output voxels in 16bit integer format. 
int  Store output voxels in 32bit integer format. 
long  Superseded by int. 
float  Store output voxels in 32bit floating point format. 
double  
Store output voxels in 64bit 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 (NotANumber 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 nonzero 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 commandline options and exit. version Print the program’s version number and exit.
Peter Neelin
Copyright © 1995 by Peter Neelin
MINCMATH (1)  $Date: 20040520 21:52:08 $ 
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