mincresample man page on DragonFly
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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
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.
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
description of where the output sampling should be. However, when we
are resampling data, we are frequently interested in a change of world
coordinates: 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
coordinates 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
(default).
-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
(default 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
talairach_).
-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).
Ignored 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
dimension. 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
dimension.
-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
default.
-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 © 1993 by Peter Neelin
SEE ALSO
mincreshape(1)
$Date: 2005-07-13 21:34:25 $ MINCRESAMPLE(1)
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