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

NAME
       minclookup - perform lookup table conversions on	minc files

SYNOPSIS
       minclookup [<options>] <in1>.mnc	<out>.mnc

DESCRIPTION
       Minclookup  will	 perform  a  lookup table operation on each voxel of a
       minc file. A lookup table consists of  a	 list  of  input  values  with
       matching	 output	 values.  Each voxel of	the input file is found	in the
       lookup table and	the corresponding output value is written  out.	 These
       output  values can be either scalar or vector values so,	for example, a
       colour lookup table would have four columns: one	column for input  val-
       ues and one column for each of red, green and blue output values.

       Lookup tables can take one of two forms:	continuous or discrete.

       A  continuous  lookup  table is for treating voxel values as continuous
       (real) values and converting values by doing interpolation between  the
       values  given in	the lookup table. A discrete lookup table treats input
       values as integers and deals with them as  completely  independent  en-
       tries, doing no interpolation.

       The  most  common use of	continuous lookup tables is for	converting in-
       tensity values into RGB colours.	To make	the lookup tables simpler, the
       input  values  are all rescaled into the	range zero to one. By default,
       the smallest value in the file maps to zero and	the  largest  maps  to
       one.  This value	is then	found in the lookup table, usually between two
       entries in the table (the table is always sorted	in ascending order  of
       input  values). Linear interpolation is then done on each output	column
       and the resultant value (or values) is written to the output  file.  If
       there is	more than one output value per input value, then the dimension
       vector_dimension	is added to the	output file with length	equal  to  the
       number  of output columns in the	lookup table. For input	values outside
       the range zero to one, the nearest table	value is used.

       Discrete	lookup tables are usually used	for  remapping	label  values.
       Each  input  value is treated as	an integer (it is not rescaled)	and if
       it is found in the lookup table,	then the corresponding value (or  val-
       ues)  is	 written  to  the output file. If it is	not found, then	a null
       value is	written	out (zero by default). No interpolation	is  done  with
       discrete	 lookup	tables - to get	a non-null output value, there must be
       an entry	in the table.

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.

       -buffer_size size
	      Specify the maximum size of the internal	buffers	 (in  kbytes).
	      Default is 10 MB.

       -filetype
	      Create an	output file with the same type as the first input file
	      (default).

       -byte  Store each voxel as an 8-bit integer.

       -short Store each voxel as a 16-bit integer.

       -int   Store each voxel as a 32-bit integer.

       -long  Superseded by -int.

       -float Store each voxel in 32-bit floating point	format.

       -double
	      Store each voxel in 64-bit floating point	format.

       -signed
	      Create an	output file with data stored in	a  signed  type.  This
	      option  is  meaningless  when used with floating point data for-
	      mats, which are always signed.

       -unsigned
	      Create an	output file with data stored in	an unsigned type. This
	      option  is  meaningless  when used with floating point data for-
	      mats.

       -valid_range min	max
	      Scale integer voxel values to fall between the  values  min  and
	      max.   By	default	integer	voxel values will be scaled to use the
	      entire range of the base type.  This option is meaningless  when
	      used with	floating point data formats.

Lookup table options
       -gray  Use a gray lookup	table to write out RGB values (default).

       -grey  Synonym for -gray.

       -hotmetal
	      Use a hot-metal lookup table to write out	RGB values.

       -spectral
	      Use a spectral (rainbow) lookup table to write out RGB values.

       -invert
	      Invert  the  lookup table	so that	the maximum value maps to zero
	      and the minimum value maps to one.  Applies only	to  continuous
	      lookup tables.

       -noinvert
	      Do  not  invert  the lookup table	- the minimum maps to zero and
	      the maximum maps to one (default).

       -range min max
	      Specify the range	of values that should map to the range of  the
	      lookup table (default is the full	range of the input file).

       -minimum	min
	      Specify  the  input  value that maps to the minimum value	in the
	      lookup table.

       -maximum	max
	      Specify the input	value that maps	to the maximum	value  in  the
	      lookup table.

       -lookup_table [file | -]
	      Specify  the name	of a file containing the lookup	table. If - is
	      given, the lookup	table is read from  the	 standard  input.  The
	      file  must have at least two columns: The	first column gives the
	      input values; the	other columns give  the	 corresponding	output
	      values.  For  a continuous lookup	table, the first column	should
	      contain a	value between zero and one inclusive Explicit  entries
	      for  both	 zero  and one should usually be given.	For a discrete
	      lookup table, the	first column should contain integer values. If
	      more  than one output column is given, then the output file will
	      have the dimension vector_dimension with a length	equal  to  the
	      number  of output	columns. The lines of the table	will be	sorted
	      if necessary so that the first column is in ascending order.

       -lut_string lookup-table-string
	      Specify the complete lookup table	as a single string. The	 semi-
	      colon character ";" is used to separate lines.

       -continuous
	      The  lookup  table  is continuous	(see description above): Input
	      values are treated as continuous (real) values and are  rescaled
	      to  the  range zero to one before	being looked up; interpolation
	      is done between values in	the table. This	is the default	behav-
	      iour.

       -discrete
	      The lookup table is discrete (see	description above): Input val-
	      ues are treated as integers and no interpolation is done between
	      input values.

       -null_value null-value-string
	      Specify a	null value to be used with discrete lookup tables when
	      a	value is not found in the lookup table.	 This  value  must  be
	      specified	 as  a	comma-separated	 list of values, with the same
	      number of	values as output columns in the	lookup table.

Generic	options	for all	commands:
       -help  Print summary of command-line options and	exit.

       -version
	      Print the	program's version number and exit.

EXAMPLES
       To get hot-metal	RGB images from	an MRI file:

	  minclookup -hotmetal input.mnc output.mnc

       To convert the labels in	a minc label file, use -discrete:

	  minclookup -discrete -lookup_table lookupfile	\
	     in_labels.mnc out_labels.mnc

       where lookupfile	is a file containing entries to	map label 2 to	4  and
       label 3 to 5:

	  2 4
	  3 5

       You could also specify this lookup table	on the command line:

	  minclookup -discrete -lut_string '2 4;3 5' \
	     in_labels.mnc out_labels.mnc

       To  get	a grey RGB file, with red for values less than the minimum and
       green for values	greater	than the minimum, you can give	two  zero  en-
       tries  and two one entries. The first zero is used for negative values,
       the second zero is used for interpolation to the	next entry.  There  is
       no  ambiguity  about  how to handle a value of exactly zero because the
       first and last values of	the table are handled in a special way to make
       sure  that  they	 are treated as	within range if	this sort of two-entry
       situation occurs.

	  minclookup -lookup_table - input.mnc output.mnc <<EOF
	  0 1 0	0
	  0 0 0	0
	  1 1 1	1
	  1 0 1	0
	  EOF

       To invert a scalar image, you could use minclookup:

	  minclookup -lut_string '0 1;1	0' in.mnc out.mnc

AUTHOR
       Peter Neelin

COPYRIGHTS
       Copyright (C) 1995 by Peter Neelin

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

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | General options | Lookup table options | Generic options for all commands: | EXAMPLES | AUTHOR | COPYRIGHTS

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