itk_resample

resample a MINC volume using ITK with spline interpolation and .xfm transforms

itk_resample <input> <output.mnc> [options]

DESCRIPTION

itk_resample resamples a medical image volume onto a new sampling grid. It supports MINC .xfm and ITK transformation files to map voxel coordinates between the input and output volumes. The interpolation is performed using B-spline interpolation with a configurable spline order (default order 2).

A target sampling grid can be specified with --like to match the geometry (dimensions, voxel sizes, start coordinates, and direction cosines) of an existing file, or with --uniformize to create an isotropic grid at a given step size.

Label volumes can be resampled with nearest-neighbour interpolation using the --labels flag, and optional look-up table remapping with --lut_string. Anti-aliasing prefiltering is available via the --aa flag for downsampling operations.

OPTIONS

--verbose

Print verbose information during processing.

--clobber

Overwrite the output file if it already exists.

--like file

Resample the input to match the sampling grid of file (dimensions, voxel spacing, starts, and direction cosines).

--transform xfm

Apply the specified MINC .xfm transformation file during resampling.

--itk_transform file

Apply the specified ITK-format transformation file during resampling.

--order n

Set the B-spline interpolation order (0 to 5). Order 0 is nearest-neighbour, order 1 is trilinear, and orders 2-5 are higher-order B-splines. Default is 2.

--uniformize step

Resample the volume onto an isotropic grid with the given step size (in mm).

--invert_transform

Invert the transformation before applying it.

--labels

Treat the input as a label volume. Uses nearest-neighbour interpolation (order 0).

--byte

Store output voxels as unsigned 8-bit bytes.

--short

Store output voxels as signed 16-bit short integers.

--ushort

Store output voxels as unsigned 16-bit short integers.

--int

Store output voxels as signed 32-bit integers.

--uint

Store output voxels as unsigned 32-bit integers.

--float

Store output voxels as 32-bit floating point.

--double

Store output voxels as 64-bit double-precision floating point.

--lut_string str

Apply a label look-up table remapping specified as a semicolon-separated string of old:new pairs (e.g., “1:2;3:4”).

--aa

Enable anti-aliasing prefiltering. Useful when downsampling to prevent aliasing artefacts.

--background val

Set the background (fill) value for voxels that fall outside the input volume. Default is 0.

EXAMPLES

Resample a volume to match the geometry of another file:

itk_resample input.mnc output.mnc --like template.mnc

Resample using a transformation with trilinear interpolation:

itk_resample input.mnc output.mnc --like template.mnc --transform input_to_template.xfm --order 1

Resample a label volume with an inverted transform:

itk_resample labels.mnc resampled_labels.mnc --like target.mnc --transform t1_to_target.xfm --invert_transform --labels

Create an isotropic 1 mm volume:

itk_resample input.mnc output_1mm.mnc --uniformize 1.0

Resample with anti-aliasing for downsampling:

itk_resample hires.mnc lores.mnc --like lores_template.mnc --aa --clobber

AUTHOR

Vladimir S. Fonov - Montreal Neurological Institute, McGill University.

COPYRIGHTS

Copyright (C) Vladimir S. Fonov, McConnell Brain Imaging Centre, McGill University.

SEE ALSO

itk_convert, mincresample, itk_convert_xfm, resample_grid