rawtominc man page on DragonFly
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RAWTOMINC(1) MINC User's Guide RAWTOMINC(1)
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 maxi‐
mum 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 con‐
versions work since this will affect how successful the new MINC file
will be.
Each dimension of MINC image is specified by name - the spatial dimen‐
sions are xspace, yspace and zspace. The convention is that positive
xspace coordinates run from the patient's left side to right side, pos‐
itive 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 posi‐
tive. 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 (pro‐
jected) 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-sepa‐
rated 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) min‐
imum 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 argu‐
ment (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
$Date: 2005-02-09 19:27:18 $ RAWTOMINC(1)
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