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.

-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 <xstep> <ystep> <zstep>: Position of centre of first voxel along each of the world dimensions.

-xstart <xstep>: Position of centre of first voxel along the xspace dimension.

-ystart <ystep>: Position of centre of first voxel along the yspace dimension.

-zstart <zstep>: 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: Write out bytes values.

-short: Write out short integer values.

-int: Write out 32-bit integer values.

-long: Superseded by -int.

-float: Write out single-precision floating point values.

-double: Write out double-precision floating point values.

-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).

-help: Print summary of command-line options and abort.

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

Peter Neelin

Copyright 1993 by Peter Neelin