*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.

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