Provided by: minc-tools_2.1.00-2_amd64 bug

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.

AUTHOR

       Peter Neelin

COPYRIGHTS

       Copyright © 1993 by Peter Neelin

                                   $Date: 2005/02/09 19:27:18 $                      RAWTOMINC(1)