【MRtrix】MRtrixを用いた解像度の変更 ~Upsampling~

SYNOPSIS

     Modify the grid of an image without interpolation (cropping or padding) or
     by regridding to an image grid with modified orientation, location and or
     resolution. The image content remains in place in real world coordinates.

USAGE

     mrgrid [ options ] input operation output

        input        input image to be regridded.

        operation    the operation to be performed, one of: regrid, crop, pad.

        output       the output image.


DESCRIPTION

     - regrid: This operation performs changes of the voxel grid that require
     interpolation of the image such as changing the resolution or location and
     orientation of the voxel grid. If the image is down-sampled, the
     appropriate smoothing is automatically applied using Gaussian smoothing
     unless nearest neighbour interpolation is selected or oversample is
     changed explicitly. The resolution can only be changed for spatial
     dimensions. 

     - crop: The image extent after cropping, can be specified either manually
     for each axis dimensions, or via a mask or reference image. The image can
     be cropped to the extent of a mask. This is useful for axially-acquired
     brain images, where the image size can be reduced by a factor of 2 by
     removing the empty space on either side of the brain. Note that cropping
     does not extend the image beyond the original FOV unless explicitly
     specified (via -crop_unbound or negative -axis extent).

     - pad: Analogously to cropping, padding increases the FOV of an image
     without image interpolation. Pad and crop can be performed simultaneously
     by specifying signed specifier argument values to the -axis option.

     This command encapsulates and extends the functionality of the superseded
     commands 'mrpad', 'mrcrop' and 'mrresize'. Note the difference in -axis
     convention used for 'mrcrop' and 'mrpad' (see -axis option description).

EXAMPLE USAGES

     Crop and pad the first axis:
       $ mrgrid in.mif crop -axis 0 10,-5 out.mif
     This removes 10 voxels on the lower and pads with 5 on the upper bound,
     which is equivalent to padding with the negated specifier (mrgrid in.mif
     pad -axis 0 -10,5 out.mif).

     Right-pad the image to the number of voxels of a reference image:
       $ mrgrid in.mif pad -as ref.mif -all_axes -axis 3 0,0 out.mif -fill nan
     This pads the image on the upper bound of all axes except for the volume
     dimension. The headers of in.mif and ref.mif are ignored and the output
     image uses NAN values to fill in voxels outside the original range of
     in.mif.

     Regrid and interpolate to match the voxel grid of a reference image:
       $ mrgrid in.mif regrid -template ref.mif -scale 1,1,0.5 out.mif -fill nan
     The -template instructs to regrid in.mif to match the voxel grid of
     ref.mif (voxel size, grid orientation and voxel centres). The -scale
     option overwrites the voxel scaling factor yielding voxel sizes in the
     third dimension that are twice as coarse as those of the template image.

Regridding options (involves image interpolation, applied to spatial axes only)

  -template image
     match the input image grid (voxel spacing, image size, header
     transformation) to that of a reference image. The image resolution
     relative to the template image can be changed with one of -size, -voxel,
     -scale.

  -size dims
     define the size (number of voxels) in each spatial dimension for the
     output image. This should be specified as a comma-separated list.

  -voxel size
     define the new voxel size for the output image. This can be specified
     either as a single value to be used for all spatial dimensions, or as a
     comma-separated list of the size for each voxel dimension.

  -scale factor
     scale the image resolution by the supplied factor. This can be specified
     either as a single value to be used for all dimensions, or as a
     comma-separated list of scale factors for each dimension.

  -interp method
     set the interpolation method to use when reslicing (choices: nearest,
     linear, cubic, sinc. Default: cubic).

  -oversample factor
     set the amount of over-sampling (in the target space) to perform when
     regridding. This is particularly relevant when downsamping a
     high-resolution image to a low-resolution image, to avoid aliasing
     artefacts. This can consist of a single integer, or a comma-separated list
     of 3 integers if different oversampling factors are desired along the
     different axes. Default is determined from ratio of voxel dimensions
     (disabled for nearest-neighbour interpolation).

Pad and crop options (no image interpolation is performed, header transformation is adjusted)

  -as reference image
     pad or crop the input image on the upper bound to match the specified
     reference image grid. This operation ignores differences in image
     transformation between input and reference image.

  -uniform number
     pad or crop the input image by a uniform number of voxels on all sides

  -mask image
     crop the input image according to the spatial extent of a mask image. The
     mask must share a common voxel grid with the input image but differences
     in image transformations are ignored. Note that even though only 3
     dimensions are cropped when using a mask, the bounds are computed by
     checking the extent for all dimensions. Note that by default a gap of 1
     voxel is left at all edges of the image to allow valid trilinear
     interpolation. This gap can be modified with the -uniform option but by
     default it does not extend beyond the FOV unless -crop_unbound is used.

  -crop_unbound
     Allow padding beyond the original FOV when cropping.

  -axis index spec  (multiple uses permitted)
     pad or crop the input image along the provided axis (defined by index).
     The specifier argument defines the number of voxels added or removed on
     the lower or upper end of the axis (-axis index delta_lower,delta_upper)
     or acts as a voxel selection range (-axis index start:stop). In both
     modes, values are relative to the input image (overriding all other
     extent-specifying options). Negative delta specifier values trigger the
     inverse operation (pad instead of crop and vice versa) and negative range
     specifier trigger padding. Note that the deprecated commands 'mrcrop' and
     'mrpad' used range-based and delta-based -axis indices, respectively.

  -all_axes
     Crop or pad all, not just spatial axes.

General options

  -fill number
     Use number as the out of bounds value. nan, inf and -inf are valid
     arguments. (Default: 0.0)

Stride options

  -strides spec
     specify the strides of the output data in memory; either as a
     comma-separated list of (signed) integers, or as a template image from
     which the strides shall be extracted and used. The actual strides produced
     will depend on whether the output image format can support it.

Data type options

  -datatype spec
     specify output image data type. Valid choices are: float32, float32le,
     float32be, float64, float64le, float64be, int64, uint64, int64le,
     uint64le, int64be, uint64be, int32, uint32, int32le, uint32le, int32be,
     uint32be, int16, uint16, int16le, uint16le, int16be, uint16be, cfloat32,
     cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be, int8, uint8,
     bit.

Standard options

  -info
     display information messages.

  -quiet
     do not display information messages or progress status; alternatively,
     this can be achieved by setting the MRTRIX_QUIET environment variable to a
     non-empty string.

  -debug
     display debugging messages.

  -force
     force overwrite of output files (caution: using the same file as input and
     output might cause unexpected behaviour).

  -nthreads number
     use this number of threads in multi-threaded applications (set to 0 to
     disable multi-threading).

  -config key value  (multiple uses permitted)
     temporarily set the value of an MRtrix config file entry.

  -help
     display this information page and exit.

  -version
     display version information and exit.