minclookup - perform lookup table conversions on minc files
minclookup [<options>] <in1>.mnc <out>.mnc
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
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.
Note that options can be specified in abbreviated form (as long as they
are unique) and can be given anywhere on the command line.
-2 Create a MINC 2.0 format output file.
Overwrite an existing file.
Don’t overwrite an existing file (default).
Synonym for -noclobber.
Print out progress information for each chunk of data copied
-quiet Do not print out progress information.
Specify the maximum size of the internal buffers (in kbytes).
Default is 10 MB.
Create an output file with the same type as the first input file
-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.
Store each voxel in 64-bit floating point format.
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.
Create an output file with data stored in an unsigned type. This
option is meaningless when used with floating point data
-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.
Use a hot-metal lookup table to write out RGB values.
Use a spectral (rainbow) lookup table to write out RGB values.
Invert the lookup table so that the maximum value maps to zero
and the minimum value maps to one. Applies only to continuous
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).
Specify the input value that maps to the minimum value in the
Specify the input value that maps to the maximum value in the
-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.
Specify the complete lookup table as a single string. The
semicolon character ";" is used to separate lines.
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
The lookup table is discrete (see description above): Input
values are treated as integers and no interpolation is done
between input values.
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.
Print the program’s version number and exit.
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 \
where lookupfile is a file containing entries to map label 2 to 4 and
label 3 to 5:
You could also specify this lookup table on the command line:
minclookup -discrete -lut_string ’2 4;3 5’ \
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
To invert a scalar image, you could use minclookup:
minclookup -lut_string ’0 1;1 0’ in.mnc out.mnc
Copyright © 1995 by Peter Neelin
$Date: 2004-05-20 21:52:08 $