MINCEXTRACT(1) MINC User's Guide MINCEXTRACT(1)NAME
mincextract - dump a hyperslab of MINC file data
SYNOPSIS
mincextract [options] mincfile
DESCRIPTION
mincextract dumps a chunk of MINC file data to standard output in the format of your choice.
OPTIONS -ascii Write out data as ascii strings (default)
-byte Write out data as 8-bit integers
-short Write out data as 16-bit integers
-int Write out data as 32-bit integers
-long Superseded by -int
-float Write out data as single precision floating-point values
-double
Write out data as double precision floating-point values
-filetype
Write out data in the type of the file
-signed
Write out signed data (applies only to integer types)
-unsigned
Write out unsigned data (applies only to integer types)
-range low high
Specify the range of output values
-normalize
Normalize integer pixel values to file max and min (Default)
-nonormalize
Turn off pixel normalization
-image_range low high
Specify the range of real image values for normalization
-image_minimum min
Specify the minimum real image value for normalization
-image_maximum max
Specify the maximum real image value for normalization
-start indexvector
Specifies corner of hyperslab (C conventions for indices). Indices are either separated by spaces (enclosed by quotes) or commas
(no quotes required).
-count indexvector
Specifies edge lengths of hyperslab to read. Indices are either separated by spaces (enclosed by quotes) or commas (no quotes
required).
-positive_direction
Flip images to always have positive direction.
-negative_direction
Flip images to always have negative direction.
-any_direction
Do not flip images (Default).
+xdirection
Flip images to give positive xspace:step value (left-to-right).
-xdirection
Flip images to give negative xspace:step value (right-to-left).
-xanydirection
Don't flip images along x-axis (default).
+ydirection
Flip images to give positive yspace:step value (post-to-ant).
-ydirection
Flip images to give negative yspace:step value (ant-to-post).
-yanydirection
Don't flip images along y-axis (default).
+zdirection
Flip images to give positive zspace:step value (inf-to-sup).
-zdirection
Flip images to give negative zspace:step value (sup-to-inf).
-zanydirection
Don't flip images along z-axis (default).
-help Print summary of command-line options and exit.
-version
Print the program's version number and exit.
AUTHOR
Peter Neelin
COPYRIGHTS
Copyright (C) 1993 by Peter Neelin
SEE ALSO minctoraw(1)
$Date: 2004-05-20 21:52:08 $ MINCEXTRACT(1)
Check Out this Related Man Page
MINCAVERAGE(1) MINC User's Guide MINCAVERAGE(1)NAME
mincaverage - average minc files
SYNOPSIS
mincaverage [<options>] <in1>.mnc [<in2>.mnc...] <out>.mnc
DESCRIPTION
Mincaverage averages minc files together. A range of optional behaviour is permitted as well: pre-normalizing volumes, creating a standard
deviation volume, averaging over 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).
-verbose
Print out progress information for each chunk of data copied (default).
-quiet Do not print out progress information.
-debug Print extra information (e.g. normalization factors).
-filelist filename
Specify a file containing a list of input file names. If "-" is given, then file names are read from stdin. 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.
-max_buffer_size_in_kb buffer-size
Specify the maximum size of the internal buffers (in kbytes). Default is 4096 kbytes.
Output type options
These options control the storage precision and size of individual voxel values in the output file.
-filetype
Don't do any type conversion (default).
-byte Write out 8-bit integer values.
-short Write out 16-bit integer values.
-int Write out 32-bit integer values.
-long Superseded by -int.
-float Write out single-precision floating point values.
-double
Write out double-precision floating point values.
-signed Write out values as signed integers (default for short and long). Ignored for floating point types.
-unsigned
Write out values as unsigned integers (default for byte). Ignored for floating point types.
-range min max
specifies the valid range of output voxel values in their integer representation. Default is the full range for the type and sign.
This option is ignored for floating point values. For it to have any effect, you must specify a type.
Averaging options-normalize
Normalize volumes to their global average before averaging them (based on the mean of voxels with value greater than 2 percent of
full range above the minimum).
-nonormalize
Do not normalize volumes (default).
-sdfile sdfile.mnc
Specify the name of an output standard deviation file, to be calculated in addition the mean that is normally calculated.
-copy_header
Copy all of the additional header information from the first input file (default for one input file).
-nocopy_header
Do not copy additional header information (default for many input files).
-avgdim dimname
Specify the name of a dimension over which we should be averaging (or calculating standard deviation). If normalization is done, it
still only applies to separate files only - no normalization is done within a file.
-binarize
Binarize the input volumes before calculating the average. The binarization is done by specifying a range of values that contribute
1 to the average. Normalization of the input is not permitted when performing binarization.
-binrange min max
Specify the range of values for binarization.
-binvalue value
Specify a single legal value (integer) for binarization. The range is set to be +/- 0.5 around this value to achieve an effective
rounding of input values.
-weights <w1,w2,...>
Specify a series of weights for averaging. The number of weighting values must match the number of input files and the values must
be provided as a single argument with commas or spaces as separators. The sum of the weights must be non-zero. If weights are used
with an averaging dimension, then only one input file can be specified.
-width_weighted
This option can only be used when averaging across a dimension (-avgdim option). It specifies that weighting should be done using
the width variable that corresponds to the averaging dimension. For example, using -width_weighted with -avgdim time will use the
time-width variable to weight the values.
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
$Date: 2004-05-20 21:52:07 $ MINCAVERAGE(1)