This is the command rawtominc 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
PROGRAM:
NAME
rawtominc - converts a stream of binary image data to a minc format file
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.
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