mincresample - resamples a minc file along new spatial
dimensions
mincresample [<options>] <infile>
<outfile>
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 transverse,
sagittal or coronal images. The new voxel values are calculated using
tri-linear, tri-cubic or nearest-neighbour interpolation.
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
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.
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
orientation 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
conversion from voxel coordinates to world coordinates. Combined with a
number 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 (specified by the input file), from the
input world coordinates to the output 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.
Note that options can be specified in abbreviated form (as long as
they are unique) and can be given anywhere on the command line.
- -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.
Options that give the output sampling (all of the following except
-transformation) are parsed in the order that they appear on the
command 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 transformation
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, direction
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 dimensions.
- -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.
The default is to preserve the original dimension order.
- -transverse
- Write out transverse slices.
- -sagittal
- Write out sagittal slices.
- -coronal
- Write out coronal slices.
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 particularly useful
for resampling label volumes where interpolating intensity values does not
make sense.
- -nokeep_real_range
- Recompute the real minimum and maximum for each output slice. This is the
default.
- -fill
- Output voxels that fall outside of the input volume have undefined 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 voxels 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.
- -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 dimension (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 giving 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.
- -help
- Print summary of command-line options and exit.
- -version
- Print the program's version number and exit.
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
Copyright © 1993 by Peter Neelin