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Man Pages


Manual Reference Pages  -  RAWTOMINC (1)

NAME

rawtominc - converts a stream of binary image data to a minc format file

CONTENTS

Synopsis
Description
Pixel Value Specification
World Coordinates
Options
Dimension ordering
Input data type and range
Output data type and range
Scanning integers for range
Writing output file
Reading from input file
World coordinate conversion
Frame time and length specification
Imaging modality
Attribute specification
Generic options
Author
Copyrights

SYNOPSIS

rawtominc [options] output.mnc [[sz4] sz3] sz2 sz1

DESCRIPTION

Rawtominc reads a stream of binary data (byte, short, long, float or double) from standard input (unless the -input option is used) and writes it into the minc format file output.mnc. The user specifies the dimension sizes from slowest varying to fastest varying. At least two dimensions must be given (an image) but there can be up to four. Options give the user control over dimension names, data types and voxel to world coordinate conversion. Vector type data (such as RGB pixel data) can be read in as well.

PIXEL VALUE SPECIFICATION

Pixel values are specified by a type and a sign (e.g. signed short integer). They are also characterized by a range of legal values. For example, many scanners produce images stored with short integer pixel values. Some have values in the range 0 to 4095, others 0 to 32000, others -32768 to 32767. This range is the valid range, specified by the -range option (for floating point values, the valid range is the maximum and minimum of the whole dataset). Rawtominc allows the user to specify both the input type, sign and range as well as the output type, sign and range (read short values, store byte values, for example).

There is a further twist. Integer pixel values are generally taken to be simply scaled pixel representations of real (meaningful) physical values. Floating point values are taken to be the real value itself. Thus floating point values are scanned for the maximum and minimum, since they could be anything (they are stored in the MINC variables image-max and image-min). Integer values, however, are not scanned by default, since their range can be given by an option. To force scanning of integer values when the maximum and minimum are not known (some scanners produce files with variable ranges), use the option -scan_range.

WORLD COORDINATES

World coordinates refer to millimetric coordinates relative to some physical origin (either the scanner or some anatomical structure). Voxel coordinates are simply the indices into the image volume of a given voxel. It is worth describing briefly how MINC coordinate conversions work since this will affect how successful the new MINC file will be.

Each dimension of MINC image is specified by name - the spatial dimensions are xspace, yspace and zspace. The convention is that positive xspace coordinates run from the patient’s left side to right side, positive yspace coordinates run from patient posterior to anterior and positive zspace coordinates run from inferior to superior. For each of these spatial dimensions, the world coordinate conversion is specified by a pair of attributes: step and start. The xspace world coordinate, for example, is calculated using x = v*step + start, where x is the x world coordinate and v is the voxel count (starting at zero). Thus the magnitude of the step attribute specifies the distance between voxels and the sign of the step attribute specifies the orientation of the axis. Programs will use this information to display images with the correct aspect ratio and orientation, so make sure that you get it right. Many scanners store transverse images with the first pixel at the patient’s anterior/right side, so it would be necessary to give negative x and y step values. Other conventions have the opposite: first pixel at patient’s posterior/left, so step values are positive. Sometimes the first slice is inferior, so the z step should be positive. Other times it is superior, so z step is negative.

The image axes do not have to be aligned with the world coordinate axes. The axis directions are recorded in the file as direction cosines - unit vectors - one for each spatial axis. In this case, the step and start attributes described in the previous paragraph refer to distances along the axis, not to coordinates of the first voxel. This makes them invariant under a change of axis direction (the whole coordinate system can in fact be rotated just by changing the direction cosines). If the coordinate of the first voxel is known, then it can be converted (projected) to a set of start values by using the -origin option.

OPTIONS

Dimension ordering

-transverse
  Transverse images : [[time] z] y x (Default)
-sagittal
  Sagittal images : [[time] x] z y
-coronal Coronal images : [[time] y] z x
-time Time ordered images : [[z] time] y x
-xyz Dimension order : [[time] x] y z
-xzy Dimension order : [[time] x] z y
-yxz Dimension order : [[time] y] x z
-yzx Dimension order : [[time] y] z x
-zxy Dimension order : [[time] z] x y
-zyx Dimension order : [[time] z] y x
-dimorder dim1,dim2[,dim3[,dim4]]
  Specify an arbitrary dimension order, given by an comma-separated list of between 2 and 4 dimension names.
-vector size
  Gives the size of a vector dimension (always the fastest varying dimension). Default is no vector dimension.

Input data type and range

-byte 8-bit integer values (default).
-short 16-bit integer values.
-int 32-bit integer values.
-long Superseded by -int.
-float Single-precision floating point values.
-double Double-precision floating point values.
-signed Values are signed integers (default for short and long). Ignored for floating point types.
-unsigned
  Values are unsigned integers (default for byte). Ignored for floating point types.
-range min max
  specifies the valid range of pixel values. Default is the full range for the type and sign. This option is ignored for floating point values.
-real_range min max
  specifies the real range of image values that corresponds to the pixel values of option -range. Default is to not store the real image minimum and maximum. If -scan_range is used, then the image minimum and maximum corresponding to the scanned pixel minimum and maximum are calculated and stored. This option is ignored for floating point values.
-swap_bytes
  Input values (either -short or -int) need to be converted between Motorola (big-endian) and Intel (little-endian) data format. If "short" input is specified, adjacent bytes are swapped. If "int" input is specified, inner and outer byte pairs are swapped. This option has no effect with other input types.

Output data type and range

-obyte Store 8-bit integer values (default is input type).
-oshort Store 16-bit integer values (default is input type).
-oint Store 32-bit integer values (default is input type).
-olong Superseded by -oint.
-ofloat Single-precision floating point values (default is input type).
-odouble Double-precision floating point values (default is input type).
-osigned Values are signed integers (default for short and long). Ignored for floating point types. If output type is not specified, then default is input sign type.
-ounsigned
  Values are unsigned integers (default for byte). Ignored for floating point types. If output type is not specified, then default is input sign type.
-orange min max
  specifies the valid range of pixel values. Default is the full range for the type and sign. This option is ignored for floating point values. If output type and sign are not specified, then the default is the input range.

Scanning integers for range

-noscan_range
  Do not scan integer values for their minimum and maximum - assume that the -range option gives the appropriate range of pixel values (default). No rescaling of pixel values is done (unless the output type differs from the input type) and the created images are assumed to have a real (not pixel value) minimum and maximum of zero and one.
-scan_range
  Integer values are scanned for their minimum and maximum. Pixel values are rescaled to give the full range of pixel values and the real minimum and maximum are set to the pixel minimum and maximum (unless -real_range is used). This should be equivalent to converting the input to a floating point type and reading it in with -float -oshort (for example) assuming that -real_range is not used.

Writing output file

-2 Create MINC 2.0 format output files.
-clobber Overwrite existing minc file (default).
-noclobber
  Don’t overwrite existing minc file.

Reading from input file

-input inputfile
  Read input data from inputfile instead of standard input.
-skip length
  Skip the first length bytes of the input.

World coordinate conversion

-xstep xstep
  Step size for x dimension (default = none).
-ystep ystep
  Step size for y dimension (default = none).
-zstep zstep
  Step size for z dimension (default = none).
-xstart xstart
  Starting coordinate for x dimension (default = none). This is a distance parallel to the axis.
-ystart ystart
  Starting coordinate for y dimension (default = none). This is a distance parallel to the axis.
-zstart zstart
  Starting coordinate for z dimension (default = none). This is a distance parallel to the axis.
-xdircos x1 x2 x3
  Direction cosines for x dimension (default = none).
-ydircos y1 y2 y3
  Direction cosines for y dimension (default = none).
-zdircos z1 z2 z3
  Direction cosines for z dimension (default = none).
-origin o1 o2 o3
  Specify the spatial coordinates of the first voxel. If the direction cosines are not given or are the default ones, this option will give the same results as using the -start options. Otherwise, the coordinate is projected parallel to the axes to determine the appropriate start values.

Frame time and length specification

-frame_times t1,t2,t3,...
  Specify the start of each time frame. The number of values given must be equal to the length of the time dimension specified on the command line. All of the values given must be in one argument (no spaces between them, or the string must be quoted). Separation by spaces instead of commas is permitted.
-frame_widths w1,w2,w3,...
  Specify the length of each time frame. The comments for -frame_times apply here as well.

To set the start and step values for a functional file with a constant frame times, use the -dattribute flag described below as follows:

-dattribute time:step=1 -dattribute time:start=0

Imaging modality

-nomodality
  Do not store modality type in file (default).
-pet PET data.
-mri MRI data.
-spect SPECT data.
-gamma Data from a gamma camera.
-mrs MR spectroscopy data.
-mra MR angiography data.
-ct CT data.
-dsa DSA data
-dr Digital radiography data.

Attribute specification

-sattribute variable:attribute=value
  Specify that variable should be created with string attribute set to value. The complete specification, including variable, attribute and value, should be contained in only one argument to the program - quoting may be needed for strings containing blanks.
-dattribute variable:attribute=value :
  Like -sattribute, but for specifying double-precision attribute values.
-attribute variable:attribute=value
  Like -sattribute or -dattribute, except that the type is chosen by first trying to interpret the value as double precision - if that fails, then the value is assumed to be a string.

Generic options

-help Print summary of command-line options and exit.
-version Print the program’s version number and exit.

AUTHOR

Peter Neelin

COPYRIGHTS

Copyright © 1993 by Peter Neelin
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RAWTOMINC (1) $Date: 2005-02-09 19:27:18 $

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