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mincmakescalar - convert vector minc files to scalar

mincmakescalar[<options>] <in>.mnc <out>.mnc

Mincmakescalarconverts vector minc files to scalar minc files. A vector minc file is one that contains the dimensionvector_dimensionas 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.

-2Create a MINC 2.0 format output file.-clobberOverwrite an existing file.-noclobberDon’t overwrite an existing file (default).-no_clobberSynonym for-noclobber.-verbosePrint out progress information for each chunk of data copied (default).-quietDo not print out progress information.-buffer_sizesizeSpecify the maximum size of the internal buffers (in kbytes). Default is 10 MB.-filetypeCreate an output file with the same type as the first input file (default).-byteStore output voxels as 8-bit integers.-shortStore output voxels as 16-bit integers.-intStore output voxels as 32-bit integers-longSuperseded by-int.-floatStore output voxels as 32-bit floating point numbers.-doubleStore output voxels as 64-bit floating point numbers.-signedCreate an output file with data stored in a signed type. This only has an effect if the one of the-byte,-shortor-intoptions is specified.-unsignedCreate an output file with data stored in an unsigned type. This only has an effect if the one of the-byte,-shortor-intoptions is specified.-valid_rangeminmaxCreate an output file with integer data stored in the specified restricted range. This only has an effect if the one of the-byte,-shortor-intoptions is specified.

-magnitudeCompute the magnitude of each vector (default).-averageCompute the average of the components of each vector.-rgbtogreyConvert RGB (3-component) files to greyscale using a linear combination with standard set of weighting coefficients.-rgbtograySynonym for-rgbtogrey.-linearc1,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.

-helpPrint summary of command-line options and exit.-versionPrint 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

Peter Neelin

Copyright © 1997 by Peter Neelin $Date: 2004-05-20 21:52:08 $