Provided by: minc-tools_2.3.00+dfsg-3build2_amd64 bug

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 values 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 entries, doing no interpolation.

       The  most  common  use of continuous lookup tables is for converting intensity 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 values) 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 formats, 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 formats.

       -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 semicolon 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
              behaviour.

       -discrete
              The  lookup  table is discrete (see description above): Input values 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 entries 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 © 1995 by Peter Neelin

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