mincmakescalar

mincmakescalar - convert vector minc files to scalar mincmakescalar <options> <in>.mnc <out>.mnc

DESCRIPTION

Mincmakescalar converts vector minc files to scalar minc files. A vector minc file is one that contains the dimension vector_dimension as the fastest varying dimension of the image data and represents vector data at each voxel such as RGB images or gradient volumes. A scalar minc file does not contain the vector dimension and represents grayscale or intensity data.

A variety of conversion schemes are possible. The simplest is an average of the components of the vector. The magnitude of the vector at each voxel can also be computed. RGB volumes can be converted to greyscale by a standard linear combination. Finally, the user can supply a list of coefficients for a linear combination of vector components.

Some options will require a specific number of components on the input vectors (RGB data should have 3 components and the number of coefficients supplied for the linear combination should match the number of components on the input vectors), but the program will also accept input scalar data and will copy it through without modification.

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 output voxels as 8-bit integers.

-short
Store output voxels as 16-bit integers.

-int
Store output voxels as 32-bit integers

-long
Superseded by -int.

-float
Store output voxels as 32-bit floating point numbers.

-double
Store output voxels as 64-bit floating point numbers.

-signed
Create an output file with data stored in a signed type. This only has an effect if the one of the -byte, -short or -int options is specified.

-unsigned
Create an output file with data stored in an unsigned type. This only has an effect if the one of the -byte, -short or -int options is specified.

-valid_range min max
Create an output file with integer data stored in the specified restricted range. This only has an effect if the one of the -byte, -short or -int options is specified.

Conversion options

-magnitude
Compute the magnitude of each vector (default).

-average
Compute the average of the components of each vector.

-rgbtogrey
Convert RGB (3-component) files to greyscale using a linear combination with standard set of weighting coefficients.

-rgbtogray
Synonym for -rgbtogrey.

-linear c1,c2,c3,…
Compute a linear combination of the components of each vector using the specified coefficients (these weights must be given as a comma or space-separated list of numbers in a single command-line argument). The number of coefficients must match the number of components on the input vectors.

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 convert an RGB file to an grayscale file:

mincmakescalar -rgbtogrey rgb.mnc gray.mnc

To compute the gradient magnitude from a gradient volume

mincmakescalar -magnitude gradient.mnc magnitude.mnc

To convert an RGB file to a grayscale file using a different set of weighting factors for red, green and blue:

mincmakescalar -linear ‘0.2,0.5,0.3’ rgb.mnc gray.mnc

AUTHOR

Peter Neelin