|-2||Create MINC 2.0 format output files.|
|-clobber||Overwrite an existing file.|
|Dont overwrite an existing file (default).|
|Print out progress information for each slice computed (default).|
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 programs version number and exit.
Resample an individuals brain in a standardized space on a standard sampling grid:
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 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 \
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
|MINCRESAMPLE (1)||$Date: 2005-07-13 21:34:25 $|