minclookup - Online in the Cloud

PROGRAM:

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

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