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MINCRESAMPLE(1)		       MINC User's Guide	       MINCRESAMPLE(1)

NAME
       mincresample - resamples	a minc file along new spatial dimensions

SYNOPSIS
       mincresample [<options>]	<infile> <outfile>

DESCRIPTION
       Mincresample  will  resample  a	minc file along	new spatial dimensions
       with new	voxel positions. Each volume in	the input file (given  by  the
       spatial dimensions xspace, yspace and zspace) is	resampled according to
       the command-line	options. Non-spatial dimensions	are preserved in their
       original	order, but spatial dimensions can be re-ordered	to give	trans-
       verse, sagittal or coronal images. The new voxel	values are  calculated
       using tri-linear, tri-cubic or nearest-neighbour	interpolation.

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.  In	order to specify appropriate resampling	options, it is
       necessary to understand how MINC	coordinate conversions work.

       Each  dimension	of a MINC image	volume is specified by name - the spa-
       tial 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	 ante-
       rior 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 co-
       ordinate, 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.

       There is	a further twist: MINC files are	allowed	to have	non-orthogonal
       axes  with  the	dimensions  not	perfectly aligned with the named axis.
       There can be a direction_cosine attribute that gives the	true  orienta-
       tion  of	 the  axis.  For example, normally the xspace dimension	should
       line up with the	world x	axis, ie. direction cosine = (1,0,0); however,
       it is possible to have a	direction cosine of (0.9, 0.43589, 0).

       These  attributes (step,	start and direction_cosines) provide a conver-
       sion from voxel coordinates to world coordinates.  Combined with	a num-
       ber  of	elements or samples along an axis, they	provide	a complete de-
       scription of where the output sampling should be.  However, when	we are
       resampling  data, we are	frequently interested in a change of world co-
       ordinates: from an MRI scanner's	coordinate system to a	PET  scanner's
       coordinate  system,  for	 example,  or from a volume in its acquisition
       space to	coordinates in a standardized space. This change of world  co-
       ordinates  can  be specified through the	use of a transformation	(.xfm)
       file. Thus, in general, the resampling involves three  transformations:
       from the	input file's voxel coordinates to its world coordinates	(spec-
       ified by	the input file), from the input	world coordinates to the  out-
       put  world coordinates (specified by the	transformation file), and from
       the output file's world coordinates to its voxel	coordinates (specified
       by command-line options).

       In  general, direction cosines are rarely used -	axis re-orientation is
       specified by a change of	world coordinates (the	transformation	file).
       As  well,  resampling  positions	(output	world to voxel conversion) are
       often specified relative	to a model file	(ie.  resample	this  file  so
       that  it	 looks	like that file). Although there	are many options for a
       complete	specification of the transformation, one does not usually need
       to specify more than a few of them.

OPTIONS
       Note that options can be	specified in abbreviated form (as long as they
       are unique) and can be given anywhere on	the command line.

General	options
       -2     Create MINC 2.0 format output files.

       -clobber
	      Overwrite	an existing file.

       -noclobber
	      Don't overwrite an existing file (default).

       -verbose
	      Print out	progress information  for  each	 slice	computed  (de-
	      fault).

       -quiet Do not print out progress	information.

Resampling specification
       Options	that  give  the	 output	 sampling (all of the following	except
       -transformation)	are parsed in the order	that they appear on  the  com-
       mand  line.  Thus a command with	-like file.mnc -znelements 34 -zstep 2
       will give a sampling like that in file in file.mnc but with 34  samples
       at  2  mm along the zspace axis.	The default sampling is	taken from the
       input file, transformed according to any	transformation.

       -transformation file.xfm
	      Specify a	file giving the	world coordinate  transformation  (de-
	      fault is the identity transformation).

       -invert_transformation
	      Invert the transformation	before using it.

       -noinvert_transformation
	      Do no invert the transformation (default).

       -tfm_input_sampling
	      Transform	 the  input sampling (using the	transform specified by
	      -transformation) along with the data and use this	as the default
	      sampling (default).

       -use_input_sampling
	      Use  the	input sampling as the default sampling,	as is, without
	      transformation, even though the data is being  transformed  (old
	      behaviour).

       -like file.mnc
	      Specify a	model file that	gives the output world to voxel	trans-
	      formation	and number of elements (ie.  transform	this  file  so
	      that it looks like that one).

       -standard_sampling
	      Set the sampling to standard values (start = 0, step = 1,	direc-
	      tion cosines point along appropriate axes).

       -spacetype string
	      Set the name of the output  space	 (usually  native____  or  ta-
	      lairach_).

       -talairach
	      Set the name of the output space to talairach_.

       -units string
	      Set the units of the output space.

       -origin ox oy oz
	      Specify  the coordinate of the first voxel. This is not the same
	      as the start value if the	direction cosines are non-standard. As
	      well,  the  start	 is not	just a perpendicular projection	of the
	      origin onto the axis, it is  a  parallel	projection  (as	 in  a
	      multi-dimensional	 parallelogram	projection). The conversion is
	      handled properly by this option.

       -nelements nx ny	nz
	      Number of	elements along each of the world dimensions.

       -xnelements nx
	      Number of	elements along the xspace dimension.

       -ynelements ny
	      Number of	elements along the yspace dimension.

       -znelements nz
	      Number of	elements along the zspace dimension.

       -step xstep ystep zstep
	      Step between voxels along	each of	the world dimensions.

       -xstep xstep
	      Step between voxels along	the xspace dimension.

       -ystep ystep
	      Step between voxels along	the yspace dimension.

       -zstep zstep
	      Step between voxels along	the zspace dimension.

       -start xstart ystart zstart
	      Position of centre of first voxel	along each of the world	dimen-
	      sions.

       -xstart xstart
	      Position of centre of first voxel	along the xspace dimension.

       -ystart ystart
	      Position of centre of first voxel	along the yspace dimension.

       -zstart zstart
	      Position of centre of first voxel	along the zspace dimension.

       -dircos x1 x2 x3	y1 y2 y3 z1 z2 z3
	      Direction	cosines	for each of the	world axes.

       -xdircos	x1 x2 x3
	      Direction	cosines	for the	xspace dimension.

       -ydircos	y1 y2 y3
	      Direction	cosines	for the	yspace dimension.

       -zdircos	z1 z2 z3
	      Direction	cosines	for the	zspace dimension.

Dimension ordering
       The default is to preserve the original dimension order.

       -transverse
	      Write out	transverse slices.

       -sagittal
	      Write out	sagittal slices.

       -coronal
	      Write out	coronal	slices.

Output data type and range
       The default for type, sign and valid range is to	use those of the input
       file. If	type is	specified, then	both sign and valid range are  set  to
       the  default  for  that type. If	sign is	specified, then	valid range is
       set to the default for the type and sign.

       -byte  Store output voxels in 8-bit integer format.

       -short Store output voxels in 16-bit integer format.

       -int   Store output voxels in 32-bit integer format.

       -long  Superseded by -int.

       -float Store output voxels in 32-bit floating point format.

       -double
	      Store output voxels in 64-bit floating point format.

       -signed
	      Write out	values as  signed  integers  (default  for  short  and
	      long). Ignored for floating point	types.

       -unsigned
	      Write  out  values  as unsigned integers (default	for byte). Ig-
	      nored for	floating point types.

       -range min max
	      specifies	the valid range	of output voxel	values.	Default	is the
	      full  range  for	the  type and sign. This option	is ignored for
	      floating point values.

       -keep_real_range
	      Preserve the real	minimum	and maximum from the input volume,  so
	      that  values  are	scaled in the same way on output. This is par-
	      ticularly	useful for resampling label volumes where  interpolat-
	      ing intensity values does	not make sense.

       -nokeep_real_range
	      Recompute	 the  real  minimum and	maximum	for each output	slice.
	      This is the default.

Handling of undefined (invalid)	voxel values
       -fill  Output voxels that fall outside of the input volume  have	 unde-
	      fined  values.  When  the	-fill option is	used, these voxels are
	      given a value that is outside of the valid range (less than  the
	      valid minimum, if	the type, sign and valid range permit) so that
	      they can be detected by other software. The values of these vox-
	      els are not included in the image-max and	image-min variables.

       -nofill
	      Use  a  real/physical value (not voxel value) of zero for	points
	      outside of the input volume. These points	are  included  in  the
	      calculation  of  the image-max and image-min variables.  This is
	      the default.

       -fillvalue fillvalue
	      Specifies	a real/physical	value (not  voxel  value)  for	points
	      outside  of the input volume. The	points are not included	in the
	      calculation of the image-max and image-min variables.

Interpolation options
       -trilinear
	      Do a tri-linear interpolation between voxels. The	edges  of  the
	      volume  are  at the centre of the	first and last voxels of a di-
	      mension. This is the default.

       -tricubic
	      Do a tri-cubic interpolation between voxels. The	edges  of  the
	      volume  are  at the centre of the	first and last voxels of a di-
	      mension.

       -nearest_neighbour
	      Do nearest neighbour interpolation between voxels	(ie. find  the
	      voxel  closest to	the point and use its value). The edges	of the
	      volume are at the	edge of	the first and last voxels of a	dimen-
	      sion (centre +/- half voxel separation).

       -sinc  Do  renormalized	windowed-sinc interpolation between voxels, as
	      described	by Thacker et al. JMRI 10:582-588 (1999).

       -width n
	      Specifies	the half-width of the sinc  interpolation  kernel,  in
	      the range	from 1 to 10. The full sinc kernel width is n *	2 + 1,
	      and therefore varies from	3 to 21.  The default value is 5  giv-
	      ing a full-width of 11.

       -hanning
	      Use  a Hanning window with the sinc interpolant. This is the de-
	      fault.

       -hamming
	      Use a Hamming window with	the sinc interpolant.

Generic	options
       -help  Print summary of command-line options and	exit.

       -version
	      Print the	program's version number and exit.

EXAMPLES
       Resample	an individual's	brain in a standardized	space  on  a  standard
       sampling	grid:

	  mincresample individual.mnc in_std_space.mnc \
	     -transform	transform_to_standard_space.xfm	\
	     -like standard_sampling.mnc

       Resample	 an MRI	volume to be matched with a PET	volume,	but with finer
       resolution:

	  mincresample mri.mnc mri_resampled.mnc \
	     -transform	mri_to_pet.xfm -like pet.mnc \
	     -step 1 1 2 -xstart -0.5 -ystart -0.5 \
	     -nelements	256 256	64

       Turn a transverse volume	into a sagittal	volume:

	  mincresample transverse.mnc sagittal.mnc \
	     -sagittal -nearest

       Turn  a	256x256x64  (1x1x2mm)  transverse  volume   into   256x128x256
       (1x1x1mm) sagittal volume:

	  mincresample transverse.mnc sagittal.mnc -sagittal \
	     -zstep 1 -znelem 128

       Get a finer axial sampling on a PET volume:

	  mincresample pet_15_slices.mnc pet_46_slices.mnc \
	     -zstep 2 -znelements 46

AUTHOR
       Peter Neelin

COPYRIGHTS
       Copyright (C) 1993 by Peter Neelin

SEE ALSO
       mincreshape(1)

			 $Date:	2005-07-13 21:34:25 $	       MINCRESAMPLE(1)

NAME | SYNOPSIS | DESCRIPTION | WORLD COORDINATES | OPTIONS | General options | Resampling specification | Dimension ordering | Output data type and range | Handling of undefined (invalid) voxel values | Interpolation options | Generic options | EXAMPLES | AUTHOR | COPYRIGHTS | SEE ALSO

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