This is the command mincmakescalar that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
mincmakescalar - convert vector minc files to scalar
mincmakescalar [<options>] <in>.mnc <out>.mnc
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.
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 (default).
-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 (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-long Superseded by -int.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.
Store output voxels as 64-bit floating point numbers.
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.
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
Compute the magnitude of each vector (default).
Compute the average of the components of each vector.
Convert RGB (3-component) files to greyscale using a linear combination with
standard set of weighting coefficients.
Synonym for -rgbtogrey.
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.
Print the program's version number and exit.
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
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