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
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
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,
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.
Overwrite an existing file.
Don’t overwrite an existing file (default).
Print out progress information for each slice computed
-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.
Specify a file giving the world coordinate transformation
(default is the identity transformation).
Invert the transformation before using it.
Do no invert the transformation (default).
Transform the input sampling (using the transform specified by
-transformation) along with the data and use this as the default
Use the input sampling as the default sampling, as is, without
transformation, even though the data is being transformed (old
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).
Set the sampling to standard values (start = 0, step = 1,
direction cosines point along appropriate axes).
Set the name of the output space (usually native____ or
Set the name of the output space to talairach_.
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.
Number of elements along the xspace dimension.
Number of elements along the yspace dimension.
Number of elements along the zspace dimension.
-step xstep ystep zstep
Step between voxels along each of the world dimensions.
Step between voxels along the xspace dimension.
Step between voxels along the yspace dimension.
Step between voxels along the zspace dimension.
-start xstart ystart zstart
Position of centre of first voxel along each of the world
Position of centre of first voxel along the xspace dimension.
Position of centre of first voxel along the yspace dimension.
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.
Write out transverse slices.
Write out sagittal slices.
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.
Store output voxels in 64-bit floating point format.
Write out values as signed integers (default for short and
long). Ignored for floating point types.
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.
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.
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
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
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
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.
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.
Do a tri-cubic interpolation between voxels. The edges of the
volume are at the centre of the first and last voxels of a
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).
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.
Use a Hanning window with the sinc interpolant. This is the
Use a Hamming window with the sinc interpolant.
-help Print summary of command-line options and exit.
Print the program’s version number and exit.
Resample an individual’s brain in a standardized space on a standard
mincresample individual.mnc in_std_space.mnc \
-transform transform_to_standard_space.xfm \
Resample an MRI volume to be matched with a PET volume, but with finer
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 \
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
$Date: 2005-07-13 21:34:25 $