Package 'rpyANTs' reference manual

Title:	An Alternative Advanced Normalization Tools ('ANTs')
Description:	Provides portable access from 'R' to biomedical image processing toolbox 'ANTs' by Avants et al. (2009) <doi:10.54294/uvnhin> via seamless integration with the 'Python' implementation 'ANTsPy'. Allows biomedical images to be processed in 'Python' and analyzed in 'R', and vice versa via shared memory. See 'citation("rpyANTs")' for more reference information.
Authors:	Zhengjia Wang [aut, cre]
Maintainer:	Zhengjia Wang <[email protected]>
License:	Apache License 2.0
Version:	0.0.3.9006
Built:	2024-11-08 18:18:34 UTC
Source:	https://github.com/dipterix/rpyANTs

Get 'ANTsPy' module

Description

Get 'ANTsPy' module

Usage

ants

load_ants(force = FALSE, error_if_missing = TRUE)
ants

load_ants(force = FALSE, error_if_missing = TRUE)

Arguments

`force`	whether to force reloading `ants` module; default is false
`error_if_missing`	whether to raise errors when the module is unable to load; default is true.

Value

A 'Python' module if successfully loaded. If error_if_missing is set to false and module is unable to load, return NULL

Apply a transform list to map an image from one domain to another

Description

See ants$apply_transforms for more details.

Usage

ants_apply_transforms(
  fixed,
  moving,
  transformlist,
  interpolator = c("linear", "nearestNeighbor", "gaussian", "genericLabel", "bSpline",
    "cosineWindowedSinc", "welchWindowedSinc", "hammingWindowedSinc",
    "lanczosWindowedSinc"),
  imagetype = 0L,
  whichtoinvert = NULL,
  compose = NULL,
  defaultvalue = 0,
  verbose = FALSE,
  ...
)
ants_apply_transforms(
  fixed,
  moving,
  transformlist,
  interpolator = c("linear", "nearestNeighbor", "gaussian", "genericLabel", "bSpline",
    "cosineWindowedSinc", "welchWindowedSinc", "hammingWindowedSinc",
    "lanczosWindowedSinc"),
  imagetype = 0L,
  whichtoinvert = NULL,
  compose = NULL,
  defaultvalue = 0,
  verbose = FALSE,
  ...
)

Arguments

`fixed`	fixed image defining domain into which the moving image is transformed
`moving`	moving image to be mapped to fixed space
`transformlist`	list of strings (path to transforms) generated by `ants_registration` where each transform is a file name
`interpolator`	how to interpolate the image; see 'Usage'
`imagetype`	integer: 0 (scalar), 1 (vector), 2 (tensor), 3 (time-series), used when the fixed and moving images have different mode (dimensions)
`whichtoinvert`	either `NULL`, `None` ('Python'), or a vector of logical with same length as `transformlist`; print `ants$apply_transforms` to see detailed descriptions
`compose`	optional character pointing to a valid file location
`defaultvalue`	numerical value for mappings outside the image domain
`verbose`	whether to verbose application of transform
`...`	must be named arguments passing to further methods

Value

Transformed image. The image will share the same space as fixed.

Examples


if(interactive() && ants_available()) {
  ants <- load_ants()
  fixed <- as_ANTsImage( ants$get_ants_data('r16') )
  moving <- as_ANTsImage( ants$get_ants_data('r64') )
  fixed <- ants_resample_image(fixed, c(64, 64), TRUE, "linear")
  moving <- ants_resample_image(moving, c(64,64), TRUE, "linear")

  mytx <- ants_registration(fixed = fixed,
                            moving = moving,
                            type_of_transform = 'SyN')
  mywarpedimage <- ants_apply_transforms(
    fixed = fixed,
    moving = moving,
    transformlist = mytx$fwdtransforms
  )

  par(mfrow = c(1,3), mar = c(0,0,3,0))
  pal <- gray.colors(256)
  image(fixed[], asp = 1, axes = FALSE, col = pal,
        ylim = c(1, 0), main = "Reference")
  image(moving[], asp = 1, axes = FALSE, col = pal,
        ylim = c(1, 0), main = "Moving")
  image(mywarpedimage[], asp = 1, axes = FALSE, col = pal,
        ylim = c(1, 0), main = "Moving reg+resamp into Reference")
}

if(interactive() && ants_available()) {
  ants <- load_ants()
  fixed <- as_ANTsImage( ants$get_ants_data('r16') )
  moving <- as_ANTsImage( ants$get_ants_data('r64') )
  fixed <- ants_resample_image(fixed, c(64, 64), TRUE, "linear")
  moving <- ants_resample_image(moving, c(64,64), TRUE, "linear")

  mytx <- ants_registration(fixed = fixed,
                            moving = moving,
                            type_of_transform = 'SyN')
  mywarpedimage <- ants_apply_transforms(
    fixed = fixed,
    moving = moving,
    transformlist = mytx$fwdtransforms
  )

  par(mfrow = c(1,3), mar = c(0,0,3,0))
  pal <- gray.colors(256)
  image(fixed[], asp = 1, axes = FALSE, col = pal,
        ylim = c(1, 0), main = "Reference")
  image(moving[], asp = 1, axes = FALSE, col = pal,
        ylim = c(1, 0), main = "Moving")
  image(mywarpedimage[], asp = 1, axes = FALSE, col = pal,
        ylim = c(1, 0), main = "Moving reg+resamp into Reference")
}

Apply a transform list to map points from one domain to another

Description

See ants$apply_transforms_to_points for more details. Please note point mapping goes the opposite direction of image mapping (see ants_apply_transforms), for both reasons of convention and engineering.

Usage

ants_apply_transforms_to_points(
  dim,
  points,
  transformlist,
  whichtoinvert = NULL,
  verbose = FALSE,
  ...
)
ants_apply_transforms_to_points(
  dim,
  points,
  transformlist,
  whichtoinvert = NULL,
  verbose = FALSE,
  ...
)

Arguments

`dim`	dimensions of the transformation
`points`	data frame containing columns `'x'`, `'y'`, `'z'`, `'t'` (depending on `dim`)
`transformlist`	list of strings (path to transforms) generated by `ants_registration` where each transform is a file name
`whichtoinvert`	either `NULL`, `None` ('Python'), or a vector of logical with same length as `transformlist`; print `ants$apply_transforms_to_points` to see detailed descriptions
`verbose`	whether to verbose application of transform
`...`	ignored

Value

Transformed points in data frame (R object)

Examples


if(interactive() && ants_available()) {
  ants <- load_ants()
  fixed <- as_ANTsImage( ants$get_ants_data('r16') )
  moving <- as_ANTsImage( ants$get_ants_data('r27') )

  reg <- ants_registration(
    fixed = fixed, moving = moving,
    type_of_transform = "antsRegistrationSyNRepro[a]")

  pts <- data.frame(
    x = c(128, 127),
    y = c(101, 111)
  )

  ptsw = ants_apply_transforms_to_points(2, pts, reg$fwdtransforms)
  ptsw
}

if(interactive() && ants_available()) {
  ants <- load_ants()
  fixed <- as_ANTsImage( ants$get_ants_data('r16') )
  moving <- as_ANTsImage( ants$get_ants_data('r27') )

  reg <- ants_registration(
    fixed = fixed, moving = moving,
    type_of_transform = "antsRegistrationSyNRepro[a]")

  pts <- data.frame(
    x = c(128, 127),
    y = c(101, 111)
  )

  ptsw = ants_apply_transforms_to_points(2, pts, reg$fwdtransforms)
  ptsw
}

Check if 'ANTs' is available

Description

Check if 'ANTs' is available

Usage

ants_available(module = c("ants", "antspynet"))
ants_available(module = c("ants", "antspynet"))

Arguments

module

either 'ants' or 'antspynet'; default is 'ants'

Value

Logical, whether 'ANTs' or 'ANTsPyNet' is available

Motion correction

Description

Print ants$motion_correction to see the original document

Usage

ants_motion_correction(
  x,
  fixed = NULL,
  type_of_transform = "BOLDRigid",
  mask = NULL,
  fdOffset = 50,
  outprefix = "",
  verbose = FALSE,
  ...
)
ants_motion_correction(
  x,
  fixed = NULL,
  type_of_transform = "BOLDRigid",
  mask = NULL,
  fdOffset = 50,
  outprefix = "",
  verbose = FALSE,
  ...
)

Arguments

`x`	input image, usually 'fMRI' series
`fixed`	fixed image to register all timepoints to
`type_of_transform`	see `ants_registration`
`mask`	mask for image
`fdOffset`	offset value to use in frame-wise displacement calculation
`outprefix`	save path
`verbose`	whether to verbose the messages
`...`	passed to registration methods

Value

Motion-corrected image

Examples


if(interactive() && ants_available()) {
  fi <- as_ANTsImage(ants$get_ants_data('ch2'))
  mytx <- ants_motion_correction( fi )

  par(mfrow = c(1, 2), mar = c(1,1,1,1))
  image(fi[,,91], asp = 1, axes = FALSE)
  image(mytx$motion_corrected[,,91], asp = 1, axes = FALSE)
}

if(interactive() && ants_available()) {
  fi <- as_ANTsImage(ants$get_ants_data('ch2'))
  mytx <- ants_motion_correction( fi )

  par(mfrow = c(1, 2), mar = c(1,1,1,1))
  image(fi[,,91], asp = 1, axes = FALSE)
  image(mytx$motion_corrected[,,91], asp = 1, axes = FALSE)
}

Plot single `'ANTsImage'`

Description

Plot single 'ANTsImage'

Usage

ants_plot(
  image,
  overlay = NULL,
  blend = FALSE,
  alpha = 1,
  cmap = "Greys_r",
  overlay_cmap = "turbo",
  overlay_alpha = 0.9,
  vminol = NULL,
  vmaxol = NULL,
  cbar = FALSE,
  cbar_length = 0.8,
  cbar_dx = 0,
  cbar_vertical = TRUE,
  axis = 0,
  nslices = 12,
  slices = NULL,
  ncol = NULL,
  slice_buffer = NULL,
  black_bg = TRUE,
  bg_thresh_quant = 0.01,
  bg_val_quant = 0.99,
  domain_image_map = NULL,
  crop = FALSE,
  scale = FALSE,
  reverse = FALSE,
  title = "",
  title_fontsize = 20,
  title_dx = 0,
  title_dy = 0,
  filename = NULL,
  dpi = 500,
  figsize = 1.5,
  reorient = TRUE,
  resample = TRUE,
  force_agg = FALSE,
  close_figure = TRUE
)
ants_plot(
  image,
  overlay = NULL,
  blend = FALSE,
  alpha = 1,
  cmap = "Greys_r",
  overlay_cmap = "turbo",
  overlay_alpha = 0.9,
  vminol = NULL,
  vmaxol = NULL,
  cbar = FALSE,
  cbar_length = 0.8,
  cbar_dx = 0,
  cbar_vertical = TRUE,
  axis = 0,
  nslices = 12,
  slices = NULL,
  ncol = NULL,
  slice_buffer = NULL,
  black_bg = TRUE,
  bg_thresh_quant = 0.01,
  bg_val_quant = 0.99,
  domain_image_map = NULL,
  crop = FALSE,
  scale = FALSE,
  reverse = FALSE,
  title = "",
  title_fontsize = 20,
  title_dx = 0,
  title_dy = 0,
  filename = NULL,
  dpi = 500,
  figsize = 1.5,
  reorient = TRUE,
  resample = TRUE,
  force_agg = FALSE,
  close_figure = TRUE
)

Arguments

`image`	`'ANTsImage'`, or something can be converted to `'ANTsImage'`
`overlay`	overlay `'ANTsImage'`, can be `NULL`, optional
`blend`	whether to blend image with overlay; default is false
`cmap`, `alpha`	image color map and transparency
`overlay_cmap`, `overlay_alpha`	overlay color map and transparency
`vminol`, `vmaxol`	I could not find its usage
`cbar`	whether to draw color legend
`cbar_length`, `cbar_dx`, `cbar_vertical`	legend position and size
`axis`	see 'Details'
`nslices`, `slices`, `ncol`	controls slice to show
`slice_buffer`	performance
`black_bg`, `bg_thresh_quant`, `bg_val_quant`	controls background
`domain_image_map`	optional `'ANTsImage'`
`crop`, `scale`, `reverse`	whether to crop, scale, or reverse the image according to background
`title`, `title_fontsize`, `title_dx`, `title_dy`	image title
`filename`, `dpi`, `figsize`	needed when saving to file
`reorient`	whether to reorient to `'LAI'` before plotting; default is true
`resample`	whether to resample
`force_agg`	whether to force graphic engine to use `'agg'` device; default is false
`close_figure`	whether to close figure when returning the function

Details

By default, images will be reoriented to 'LAI' orientation before plotting. So, if axis=0, the images will be ordered from the left side of the brain to the right side of the brain. If axis=1, the images will be ordered from the anterior (front) of the brain to the posterior (back) of the brain. And if axis=2, the images will be ordered from the inferior (bottom) of the brain to the superior (top) of the brain.

Value

Nothing

Examples



if(interactive() && ants_available()) {
  ants <- load_ants()
  img <- ants$image_read(ants$get_ants_data('mni'))

  ants_plot(
    img, nslices = 12, black_bg = FALSE,
    bg_thresh_quant = 0.05, bg_val_quant = 1.0, axis = 2,
    cbar = TRUE, crop = TRUE, reverse = TRUE, cbar_vertical = FALSE,
    ncol = 4, title = "Axial view of MNI brain"
  )
}


if(interactive() && ants_available()) {
  ants <- load_ants()
  img <- ants$image_read(ants$get_ants_data('mni'))

  ants_plot(
    img, nslices = 12, black_bg = FALSE,
    bg_thresh_quant = 0.05, bg_val_quant = 1.0, axis = 2,
    cbar = TRUE, crop = TRUE, reverse = TRUE, cbar_vertical = FALSE,
    ncol = 4, title = "Axial view of MNI brain"
  )
}

Plot multiple `'ANTsImage'`

Description

R-friendly wrapper function for ants$plot_grid

Usage

ants_plot_grid(
  images,
  shape = NULL,
  slices = 0,
  axes = 2,
  figsize = 1,
  rpad = 0,
  cpad = 0,
  vmin = NULL,
  vmax = NULL,
  colorbar = TRUE,
  cmap = "Greys_r",
  title = "",
  tfontsize = 20,
  title_dx = 0,
  title_dy = 0,
  rlabels = NULL,
  rfontsize = 14,
  rfontcolor = "black",
  rfacecolor = "white",
  clabels = NULL,
  cfontsize = 14,
  cfontcolor = "black",
  cfacecolor = "white",
  filename = NULL,
  dpi = 400,
  transparent = TRUE,
  ...,
  force_agg = FALSE,
  close_figure = TRUE
)
ants_plot_grid(
  images,
  shape = NULL,
  slices = 0,
  axes = 2,
  figsize = 1,
  rpad = 0,
  cpad = 0,
  vmin = NULL,
  vmax = NULL,
  colorbar = TRUE,
  cmap = "Greys_r",
  title = "",
  tfontsize = 20,
  title_dx = 0,
  title_dy = 0,
  rlabels = NULL,
  rfontsize = 14,
  rfontcolor = "black",
  rfacecolor = "white",
  clabels = NULL,
  cfontsize = 14,
  cfontcolor = "black",
  cfacecolor = "white",
  filename = NULL,
  dpi = 400,
  transparent = TRUE,
  ...,
  force_agg = FALSE,
  close_figure = TRUE
)

Arguments

`images`	a single `'ANTsImage'`, list, or nested list of `'ANTsImage'`
`shape`	shape of grid, default is using dimensions of `images`
`slices`	length of one or equaling to length of `slices`, slice number to plot
`axes`	`0` for `'sagittal'`, `1` for `'coronal'`, `2` for `'axial'`; default is `2`
`figsize`, `rpad`, `cpad`, `colorbar`, `cmap`, `transparent`	graphical parameters
`vmin`, `vmax`	value threshold for the image
`title`	title of figure
`title_dx`, `title_dy`, `tfontsize`	controls title margin and size
`rlabels`, `clabels`	row and column labels
`rfontsize`, `rfontcolor`, `rfacecolor`, `cfontsize`, `cfontcolor`, `cfacecolor`	row and column font size, color, and background color
`filename`, `dpi`	parameters to save figures
`...`	passed to `ants$plot_grid`; make sure all entries are named
`force_agg`	whether to force graphic engine to use `'agg'` device; default is false
`close_figure`	whether to close figure when returning the function

Value

Nothing

Examples


if(interactive() && ants_available()) {
  ants <- load_ants()
  image1 <- ants$image_read(ants$get_ants_data('mni'))
  image2 <- image1$smooth_image(1.0)
  image3 <- image1$smooth_image(2.0)
  image4 <- image1$smooth_image(3.0)

  ants_plot_grid(
    list(image1, image2, image3, image4),
    slices = 100, title = "4x1 Grid"
  )

  ants_plot_grid(
    list(image1, image2, image3, image4),
    shape = c(2, 2),
    slices = 100, title = "2x2 Grid"
  )
  ants_plot_grid(
    list(image1, image2, image3, image4),
    shape = c(2, 2), axes = c(0,1,2,1),
    slices = 100, title = "2x2 Grid (diff. anatomical slices)"
  )

}



if(interactive() && ants_available()) {
  ants <- load_ants()
  image1 <- ants$image_read(ants$get_ants_data('mni'))
  image2 <- image1$smooth_image(1.0)
  image3 <- image1$smooth_image(2.0)
  image4 <- image1$smooth_image(3.0)

  ants_plot_grid(
    list(image1, image2, image3, image4),
    slices = 100, title = "4x1 Grid"
  )

  ants_plot_grid(
    list(image1, image2, image3, image4),
    shape = c(2, 2),
    slices = 100, title = "2x2 Grid"
  )
  ants_plot_grid(
    list(image1, image2, image3, image4),
    shape = c(2, 2), axes = c(0,1,2,1),
    slices = 100, title = "2x2 Grid (diff. anatomical slices)"
  )

}

Register two images using 'ANTs'

Description

Usage

ants_registration(
  fixed,
  moving,
  type_of_transform = "SyN",
  initial_transform = NULL,
  outprefix = tempfile(),
  mask = NULL,
  grad_step = 0.2,
  flow_sigma = 3,
  total_sigma = 0,
  aff_metric = c("mattes", "GC", "meansquares"),
  aff_sampling = 32,
  aff_random_sampling_rate = 0.2,
  syn_metric = c("mattes", "CC", "meansquares", "demons"),
  syn_sampling = 32,
  reg_iterations = c(40, 20, 0),
  aff_iterations = c(2100, 1200, 1200, 10),
  aff_shrink_factors = c(6, 4, 2, 1),
  aff_smoothing_sigmas = c(3, 2, 1, 0),
  write_composite_transform = FALSE,
  verbose = FALSE,
  smoothing_in_mm = FALSE,
  ...
)
ants_registration(
  fixed,
  moving,
  type_of_transform = "SyN",
  initial_transform = NULL,
  outprefix = tempfile(),
  mask = NULL,
  grad_step = 0.2,
  flow_sigma = 3,
  total_sigma = 0,
  aff_metric = c("mattes", "GC", "meansquares"),
  aff_sampling = 32,
  aff_random_sampling_rate = 0.2,
  syn_metric = c("mattes", "CC", "meansquares", "demons"),
  syn_sampling = 32,
  reg_iterations = c(40, 20, 0),
  aff_iterations = c(2100, 1200, 1200, 10),
  aff_shrink_factors = c(6, 4, 2, 1),
  aff_smoothing_sigmas = c(3, 2, 1, 0),
  write_composite_transform = FALSE,
  verbose = FALSE,
  smoothing_in_mm = FALSE,
  ...
)

Arguments

`fixed`	fixed image to which we register the moving image, can be character path to 'NIfTI' image, or `'ANTsImage'` instance, `'oro.nifti'` object, `'niftiImage'` from package `'RNifti'`, or `'threeBrain.nii'` from package `'threeBrain'`; see also `as_ANTsImage`
`moving`	moving image to be mapped to fixed space; see also `as_ANTsImage`
`type_of_transform`	a linear or non-linear registration type; print `ants$registration` to see details
`initial_transform`	optional list of strings; transforms to apply prior to registration
`outprefix`	output file to save results
`mask`	image mask; see also `as_ANTsImage`
`grad_step`, `flow_sigma`, `total_sigma`	optimization parameters
`aff_metric`	the metric for the 'affine' transformation, choices are `'GC'`, `'mattes'`, `'meansquares'`
`aff_sampling`, `aff_random_sampling_rate`, `aff_iterations`, `aff_shrink_factors`, `aff_smoothing_sigmas`	controls 'affine' transform
`syn_metric`	the metric for the `'SyN'` transformation, choices are `'GC'`, `'mattes'`, `'meansquares'`, `'demons'`
`syn_sampling`, `reg_iterations`	controls the `'SyN'` transform
`write_composite_transform`	whether the composite transform (and its inverse, if it exists) should be written to an 'HDF5' composite file; default is false
`verbose`	verbose the progress
`smoothing_in_mm`	logical, currently only impacts low dimensional registration
`...`	others passed to `ants$registration`

Details

Function family ants_registration* align images (specified by moving) to fixed. Here are descriptions of the variations:

ants_registration: Simple wrapper function for 'Python' implementation ants.registration, providing various of registration options
ants_registration_halpern1: Rigid-body registration designed for 'Casey-Halpern' lab, mainly used for aligning 'MRI' to 'CT' (or the other way around)

Value

A 'Python' dictionary of aligned images and transform files.

Examples


if(interactive() && ants_available()) {

  ants <- load_ants()

  # check the python documentation here for detailed explanation
  print(ants$registration)

  # example to register
  fi <- ants$image_read(ants$get_ants_data('r16'))
  mo <- ants$image_read(ants$get_ants_data('r64'))

  # resample to speed up this example
  fi <- ants$resample_image(fi, list(60L,60L), TRUE, 0L)
  mo <- ants$resample_image(mo, list(60L,60L), TRUE, 0L)

  # SDR transform
  transform <- ants_registration(
    fixed=fi, moving=mo, type_of_transform = 'SyN' )

  ants$plot(fi, overlay = transform$warpedmovout, overlay_alpha = 0.3)


}


if(interactive() && ants_available()) {

  ants <- load_ants()

  # check the python documentation here for detailed explanation
  print(ants$registration)

  # example to register
  fi <- ants$image_read(ants$get_ants_data('r16'))
  mo <- ants$image_read(ants$get_ants_data('r64'))

  # resample to speed up this example
  fi <- ants$resample_image(fi, list(60L,60L), TRUE, 0L)
  mo <- ants$resample_image(mo, list(60L,60L), TRUE, 0L)

  # SDR transform
  transform <- ants_registration(
    fixed=fi, moving=mo, type_of_transform = 'SyN' )

  ants$plot(fi, overlay = transform$warpedmovout, overlay_alpha = 0.3)


}

Resample image

Description

See ants$resample_image for more details

Usage

ants_resample_image(
  x,
  resample_params,
  use_voxels = FALSE,
  interp_type = c("linear", "nn", "guassian", "sinc", "bspline")
)
ants_resample_image(
  x,
  resample_params,
  use_voxels = FALSE,
  interp_type = c("linear", "nn", "guassian", "sinc", "bspline")
)

Arguments

`x`	input image
`resample_params`	either relative number or absolute integers
`use_voxels`	whether the `resample_params` should be treated as new dimension `use_voxels=TRUE`, or the new dimension should be calculated based on current dimension and `resample_params` combined (`use_voxels=FALSE` then `resample_params` will be treated as relative number); default is `FALSE`
`interp_type`	interpolation type; either integer or character; see 'Usage' for available options

Value

Resampled image

Examples



if(interactive() && ants_available()) {
  ants <- load_ants()
  fi <- as_ANTsImage(ants$get_ants_data("r16"))

  # linear (interp_type = 0 or "linear)
  filin <- ants_resample_image(fi, c(50, 60), TRUE, "linear")

  # nearest neighbor (interp_type = 1 or "nn)
  finn <- ants_resample_image(fi, c(50, 60), TRUE, "nn")

  par(mfrow = c(1, 3), mar = c(0, 0, 0, 0))
  pal <- gray.colors(256, start = 0)

  image(fi[], asp = 1, axes = FALSE,
        ylim = c(1,0), col = pal)
  image(filin[], asp = 1, axes = FALSE,
        ylim = c(1,0), col = pal)
  image(finn[], asp = 1, axes = FALSE,
        ylim = c(1,0), col = pal)
}


if(interactive() && ants_available()) {
  ants <- load_ants()
  fi <- as_ANTsImage(ants$get_ants_data("r16"))

  # linear (interp_type = 0 or "linear)
  filin <- ants_resample_image(fi, c(50, 60), TRUE, "linear")

  # nearest neighbor (interp_type = 1 or "nn)
  finn <- ants_resample_image(fi, c(50, 60), TRUE, "nn")

  par(mfrow = c(1, 3), mar = c(0, 0, 0, 0))
  pal <- gray.colors(256, start = 0)

  image(fi[], asp = 1, axes = FALSE,
        ylim = c(1,0), col = pal)
  image(filin[], asp = 1, axes = FALSE,
        ylim = c(1,0), col = pal)
  image(finn[], asp = 1, axes = FALSE,
        ylim = c(1,0), col = pal)
}

Get `'ANTsPyNet'` module

Description

Get 'ANTsPyNet' module

Usage

load_antspynet(force = FALSE, error_if_missing = TRUE)
load_antspynet(force = FALSE, error_if_missing = TRUE)

Arguments

`force`	whether to force reloading `antspynet` module; default is false
`error_if_missing`	whether to raise errors when the module is unable to load; default is true.

Value

A 'Python' module if successfully loaded. If error_if_missing is set to false and module is unable to load, return NULL

Extract brain and strip skull

Description

Print antspynet$brain_extraction to see the original documentation.

Usage

antspynet_brain_extraction(
  x,
  modality = c("t1", "t1nobrainer", "t1combined", "flair", "t2", "t2star", "bold", "fa",
    "t1t2infant", "t1infant", "t2infant"),
  verbose = FALSE
)
antspynet_brain_extraction(
  x,
  modality = c("t1", "t1nobrainer", "t1combined", "flair", "t2", "t2star", "bold", "fa",
    "t1t2infant", "t1infant", "t2infant"),
  verbose = FALSE
)

Arguments

`x`	input image or image path
`modality`	modality type
`verbose`	whether to print out process to the screen

Value

Brain mask image

Process brain image prior to segmentation

Description

Strip skulls, normalize intensity, align and re-sample to template. This procedure is needed for many antspynet functions since the deep neural networks are trained in template spaces

Usage

antspynet_preprocess_brain_image(
  x,
  truncate_intensity = c(0.01, 0.99),
  brain_extraction_modality = c("none", "t1", "t1v0", "t1nobrainer", "t1combined",
    "flair", "t2", "bold", "fa", "t1infant", "t2infant"),
  template_transform_type = c("None", "Affine", "Rigid"),
  template = c("biobank", "croppedMni152"),
  do_bias_correction = TRUE,
  return_bias_field = FALSE,
  do_denoising = TRUE,
  intensity_matching_type = c("regression", "histogram"),
  reference_image = NULL,
  intensity_normalization_type = NULL,
  verbose = TRUE
)
antspynet_preprocess_brain_image(
  x,
  truncate_intensity = c(0.01, 0.99),
  brain_extraction_modality = c("none", "t1", "t1v0", "t1nobrainer", "t1combined",
    "flair", "t2", "bold", "fa", "t1infant", "t2infant"),
  template_transform_type = c("None", "Affine", "Rigid"),
  template = c("biobank", "croppedMni152"),
  do_bias_correction = TRUE,
  return_bias_field = FALSE,
  do_denoising = TRUE,
  intensity_matching_type = c("regression", "histogram"),
  reference_image = NULL,
  intensity_normalization_type = NULL,
  verbose = TRUE
)

Arguments

`x`	`'ANTsImage'` or path to image to process
`truncate_intensity`	defines the quantile threshold for truncating the image intensity
`brain_extraction_modality`	character of length 1, perform brain extraction modality
`template_transform_type`	either `'Rigid'` or `'Affine'` align to template brain
`template`	template image (not skull-stripped) or string, e.g. `'biobank'`, `'croppedMni152'`
`do_bias_correction`	whether to perform bias field correction
`return_bias_field`	return bias field as an additional output without bias correcting the image
`do_denoising`	whether to remove noises using non-local means
`intensity_matching_type`	either `'regression'` or `'histogram'`; only is performed if `reference_image` is not `NULL`.
`reference_image`	`'ANTsImage'` or path to image, or `NULL`
`intensity_normalization_type`	either re-scale the intensities to `c(0, 1)` (`'01'`), or for zero-mean, unit variance (`'0mean'`); if `NULL` normalization is not performed
`verbose`	print progress to the screen

Value

Dictionary with images after process. The images are registered and re-sampled into template.

Examples


library(rpyANTs)
if(interactive() && ants_available("antspynet")) {
  image_path <- ants$get_ants_data('r30')
  preprocessed <- antspynet_preprocess_brain_image(
    image_path, verbose = FALSE
  )

  # Compare
  orig_img <- as_ANTsImage(image_path)
  new_img <- preprocessed$preprocessed_image
  pal <- grDevices::gray.colors(256, start = 0, end = 1)

  par(mfrow = c(1, 2), mar = c(0.1, 0.1, 0.1, 0.1),
      bg = "black", fg = "white")
  image(orig_img[], asp = 1, axes = FALSE,
        col = pal, ylim = c(1, 0))
  image(new_img[], asp = 1, axes = FALSE,
        col = pal, ylim = c(1, 0))

}


library(rpyANTs)
if(interactive() && ants_available("antspynet")) {
  image_path <- ants$get_ants_data('r30')
  preprocessed <- antspynet_preprocess_brain_image(
    image_path, verbose = FALSE
  )

  # Compare
  orig_img <- as_ANTsImage(image_path)
  new_img <- preprocessed$preprocessed_image
  pal <- grDevices::gray.colors(256, start = 0, end = 1)

  par(mfrow = c(1, 2), mar = c(0.1, 0.1, 0.1, 0.1),
      bg = "black", fg = "white")
  image(orig_img[], asp = 1, axes = FALSE,
        col = pal, ylim = c(1, 0))
  image(new_img[], asp = 1, axes = FALSE,
        col = pal, ylim = c(1, 0))

}

Imaging segmentation using `antspynet`

Description

Supports Desikan-Killiany-Tourville labeling and deep 'Atropos'.

Usage

antspynet_desikan_killiany_tourville_labeling(
  x,
  do_preprocessing = TRUE,
  return_probability_images = FALSE,
  do_lobar_parcellation = FALSE,
  verbose = TRUE
)

antspynet_deep_atropos(
  x,
  do_preprocessing = TRUE,
  use_spatial_priors = TRUE,
  aseg_only = TRUE,
  verbose = TRUE
)
antspynet_desikan_killiany_tourville_labeling(
  x,
  do_preprocessing = TRUE,
  return_probability_images = FALSE,
  do_lobar_parcellation = FALSE,
  verbose = TRUE
)

antspynet_deep_atropos(
  x,
  do_preprocessing = TRUE,
  use_spatial_priors = TRUE,
  aseg_only = TRUE,
  verbose = TRUE
)

Arguments

`x`	`'NIfTI'` image or path to the image that is to be segmented
`do_preprocessing`	whether `x` is in native space and needs the be registered to template brain before performing segmentation; default is true since the model is trained with template brain. If you want to manually process the image, see `antspynet_preprocess_brain_image`
`return_probability_images`	whether to return probability images
`do_lobar_parcellation`	whether to perform lobar 'parcellation'
`verbose`	whether to print out the messages
`use_spatial_priors`	whether to use `'MNI'` partial tissue priors
`aseg_only`	whether to just return the segmented image

Value

One or a list of 'ANTsImage' image instances. Please print out antspynet$desikan_killiany_tourville_labeling or antspynet$deep_atropos to see the details.

Examples



# Print Python documents
if(interactive() && ants_available("antspynet")) {
  antspynet <- load_antspynet()

  print(antspynet$deep_atropos)

  print(antspynet$desikan_killiany_tourville_labeling)
}


# Print Python documents
if(interactive() && ants_available("antspynet")) {
  antspynet <- load_antspynet()

  print(antspynet$deep_atropos)

  print(antspynet$desikan_killiany_tourville_labeling)
}

Load data as `'ANTsImage'` class

Description

Load data as 'ANTsImage' class

Usage

as_ANTsImage(x, strict = FALSE)
as_ANTsImage(x, strict = FALSE)

Arguments

`x`	data to be converted; this can be an `'ANTsImage'` instance, character, `'oro.nifti'` object, `'niftiImage'` from package `'RNifti'`, or `'threeBrain.nii'` from package `'threeBrain'`
`strict`	whether `x` should not be `NULL`

Value

An 'ANTsImage' instance; use ants$ANTsImage to see the 'Python' documentation

Examples


if(interactive() && ants_available()) {

  ants <- load_ants()

  # Python string
  x1 <- ants$get_ants_data('r16')
  as_ANTsImage( x1 )

  # R character
  nii_path <- system.file(package = "RNifti",
                          "extdata", "example.nii.gz")
  as_ANTsImage( nii_path )

  # niftiImage object
  x2 <- RNifti::readNifti(nii_path)
  as_ANTsImage( x2 )

}

if(interactive() && ants_available()) {

  ants <- load_ants()

  # Python string
  x1 <- ants$get_ants_data('r16')
  as_ANTsImage( x1 )

  # R character
  nii_path <- system.file(package = "RNifti",
                          "extdata", "example.nii.gz")
  as_ANTsImage( nii_path )

  # niftiImage object
  x2 <- RNifti::readNifti(nii_path)
  as_ANTsImage( x2 )

}

Convert to `'ANTsTransform'`

Description

Convert to 'ANTsTransform'

Usage

as_ANTsTransform(x, ...)

## Default S3 method:
as_ANTsTransform(x, dimension = 3, ...)

## S3 method for class 'ants.core.ants_transform.ANTsTransform'
as_ANTsTransform(x, ...)

## S3 method for class 'ants.core.ants_image.ANTsImage'
as_ANTsTransform(x, ...)

## S3 method for class 'numpy.ndarray'
as_ANTsTransform(x, ...)

## S3 method for class 'character'
as_ANTsTransform(x, ...)
as_ANTsTransform(x, ...)

## Default S3 method:
as_ANTsTransform(x, dimension = 3, ...)

## S3 method for class 'ants.core.ants_transform.ANTsTransform'
as_ANTsTransform(x, ...)

## S3 method for class 'ants.core.ants_image.ANTsImage'
as_ANTsTransform(x, ...)

## S3 method for class 'numpy.ndarray'
as_ANTsTransform(x, ...)

## S3 method for class 'character'
as_ANTsTransform(x, ...)

Arguments

`x`	'affine' matrix or `'numpy'` array, character path to the matrix, `'ANTsTransform'`, `'ANTsImage'` as displacement field.
`...`	passed to other methods
`dimension`	expected transform space dimension; default is 3

Value

An 'ANTsTransform' object

Examples


if(interactive() && ants_available()) {

  mat <- matrix(c(
    0, -1, 0, 128,
    1, 0, 0, -128,
    0, 0, -1, 128,
    0, 0,  0,   1
  ), ncol = 4, byrow = TRUE)

  trans <- as_ANTsTransform(mat)
  trans

  # apply transform
  trans$apply_to_point(c(120, 400, 1))

  # same results
  mat %*% c(120, 400, 1, 1)

  trans[] == mat

}

if(interactive() && ants_available()) {

  mat <- matrix(c(
    0, -1, 0, 128,
    1, 0, 0, -128,
    0, 0, -1, 128,
    0, 0,  0,   1
  ), ncol = 4, byrow = TRUE)

  trans <- as_ANTsTransform(mat)
  trans

  # apply transform
  trans$apply_to_point(c(120, 400, 1))

  # same results
  mat %*% c(120, 400, 1, 1)

  trans[] == mat

}

Truncate and correct 'MRI' intensity

Description

Uses ants.abp_n4 to truncate and correct intensity

Usage

correct_intensity(image, mask = NULL, intensity_truncation = c(0.025, 0.975))
correct_intensity(image, mask = NULL, intensity_truncation = c(0.025, 0.975))

Arguments

`image`	'MRI' image to be corrected, will be passed to `as_ANTsImage`
`mask`	binary mask image
`intensity_truncation`	numerical length of two, quantile probabilities to truncate.

Value

An 'ANTsImage' instance

Examples


if(interactive() && ants_available()) {
  ants <- load_ants()
  scale <- (0.1 + outer(
    seq(0, 1, length.out = 256)^6,
    seq(0, 1, length.out = 256)^2,
    FUN = "+"
  )) / 6
  img = ants$image_read(ants$get_ants_data('r16')) * scale

  corrected <- correct_intensity(img)

  pal <- gray.colors(255, start = 0)
  par(mfrow = c(1, 2), mar = c(0.1, 0.1, 2.1, 0.1),
      bg = "black", fg = "white")
  image(img[], asp = 1, axes = FALSE,
        col = pal, ylim = c(1, 0),
        main = "Original", col.main = "white")
  image(corrected[], asp = 1, axes = FALSE,
        col = pal, ylim = c(1, 0),
        main = "Corrected", col.main = "white")

}

if(interactive() && ants_available()) {
  ants <- load_ants()
  scale <- (0.1 + outer(
    seq(0, 1, length.out = 256)^6,
    seq(0, 1, length.out = 256)^2,
    FUN = "+"
  )) / 6
  img = ants$image_read(ants$get_ants_data('r16')) * scale

  corrected <- correct_intensity(img)

  pal <- gray.colors(255, start = 0)
  par(mfrow = c(1, 2), mar = c(0.1, 0.1, 2.1, 0.1),
      bg = "black", fg = "white")
  image(img[], asp = 1, axes = FALSE,
        col = pal, ylim = c(1, 0),
        main = "Original", col.main = "white")
  image(corrected[], asp = 1, axes = FALSE,
        col = pal, ylim = c(1, 0),
        main = "Corrected", col.main = "white")

}

Ensure the template directory is downloaded

Description

Ensure the template directory is downloaded

Usage

ensure_template(name = BUILTIN_TEMPLATES)
ensure_template(name = BUILTIN_TEMPLATES)

Arguments

name

name of the template, commonly known as 'MNI152' templates; choices are "mni_icbm152_nlin_asym_09a", "mni_icbm152_nlin_asym_09b", and "mni_icbm152_nlin_asym_09c".

Value

The downloaded template path

Examples


# Do not run for testing as this will download the template
if(FALSE) {

# Default is `mni_icbm152_nlin_asym_09a`
ensure_template()
ensure_template("mni_icbm152_nlin_asym_09a")

# Using MNI152b
ensure_template("mni_icbm152_nlin_asym_09b")

}


# Do not run for testing as this will download the template
if(FALSE) {

# Default is `mni_icbm152_nlin_asym_09a`
ensure_template()
ensure_template("mni_icbm152_nlin_asym_09a")

# Using MNI152b
ensure_template("mni_icbm152_nlin_asym_09b")

}

'ANTs' functions for 'Halpern' lab

Description

'ANTs' functions for 'Halpern' lab

Usage

halpern_register_ct_mri(
  fixed,
  moving,
  outprefix,
  fixed_is_ct = TRUE,
  verbose = TRUE
)

halpern_register_template_mri(
  fixed,
  moving,
  outprefix,
  mask = NULL,
  verbose = TRUE
)

halpern_apply_transform_template_mri(roi_folder, outprefix, verbose = TRUE)
halpern_register_ct_mri(
  fixed,
  moving,
  outprefix,
  fixed_is_ct = TRUE,
  verbose = TRUE
)

halpern_register_template_mri(
  fixed,
  moving,
  outprefix,
  mask = NULL,
  verbose = TRUE
)

halpern_apply_transform_template_mri(roi_folder, outprefix, verbose = TRUE)

Arguments

`fixed`	fixed image as template
`moving`	moving image that is to be registered into `fixed`
`outprefix`	output prefix, needs to be absolute path prefix
`fixed_is_ct`	whether `fixed` is 'CT'
`verbose`	whether to verbose the progress; default is true
`mask`	mask file for template (skull-stripped)
`roi_folder`	template 'ROI' or atlas folder in which the image atlases or masks will be transformed into subject's native brain

Value

A list of result configurations

Install 'ANTs' via 'ANTsPy'

Description

Install 'ANTs' via 'ANTsPy'

Usage

install_ants(python_ver = "3.11", verbose = TRUE)
install_ants(python_ver = "3.11", verbose = TRUE)

Arguments

`python_ver`	'Python' version, see `configure_conda`; default is `"3.11"` since `'ANTsPy'` is compiled for all platforms under this version
`verbose`	whether to print the installation messages

Value

This function returns nothing.

Check if an object is a 3D 'affine' transform matrix

Description

Check if an object is a 3D 'affine' transform matrix

Usage

is_affine3D(x, ...)

## Default S3 method:
is_affine3D(x, strict = TRUE, ...)

## S3 method for class 'ants.core.ants_transform.ANTsTransform'
is_affine3D(x, ...)
is_affine3D(x, ...)

## Default S3 method:
is_affine3D(x, strict = TRUE, ...)

## S3 method for class 'ants.core.ants_transform.ANTsTransform'
is_affine3D(x, ...)

Arguments

`x`	R or Python object, accepted forms are numeric `matrix`, `'ANTsTransform'`, or `character` (path to transform matrix)
`...`	passed to other methods
`strict`	whether the last element should be always 1

Value

A logical value whether the object can be loaded as a 4-by-4 matrix.

Examples


# not affine
is_affine3D(1)

# 3x3 matrix is not as it is treated as 2D transform
is_affine3D(matrix(rnorm(9), nrow = 3))

# 3x4 matrix
x <- matrix(rnorm(12), nrow = 3)
is_affine3D(x)

# 4x4 matrix
x <- rbind(x, c(0,0,0,1))
is_affine3D(x)

if(interactive() && ants_available()) {

  ants <- load_ants()
  x <- ants$new_ants_transform(dimension = 3L)
  is_affine3D(x)

  # save the parameters
  f <- tempfile(fileext = ".mat")
  ants$write_transform(x, f)
  is_affine3D(f)

}




# not affine
is_affine3D(1)

# 3x3 matrix is not as it is treated as 2D transform
is_affine3D(matrix(rnorm(9), nrow = 3))

# 3x4 matrix
x <- matrix(rnorm(12), nrow = 3)
is_affine3D(x)

# 4x4 matrix
x <- rbind(x, c(0,0,0,1))
is_affine3D(x)

if(interactive() && ants_available()) {

  ants <- load_ants()
  x <- ants$new_ants_transform(dimension = 3L)
  is_affine3D(x)

  # save the parameters
  f <- tempfile(fileext = ".mat")
  ants$write_transform(x, f)
  is_affine3D(f)

}

Get 'Python' main process environment

Description

Get 'Python' main process environment

Usage

py
py

Format

An object of class python.builtin.module (inherits from python.builtin.object) of length 1.

Value

The 'Python' main process as a module

Get 'Python' built-in object

Description

Get 'Python' built-in object

Usage

py_builtin(name, convert = TRUE)
py_builtin(name, convert = TRUE)

Arguments

`name`	object name
`convert`	see `import_builtins`

Value

A python built-in object specified by name

Examples


if(interactive() && ants_available()) {


# ------ Basic case: use python `int` as an R function ---------
py_int <- py_builtin("int")

# a is an R object now
a <- py_int(9)
print(a)
class(a)

# ------ Use python `int` as a Python function -----------------
py_int2 <- py_builtin("int", convert = FALSE)

# b in a python object
b <- py_int2(9)

# There is no '[1] ' when printing
print(b)
class(b)

# convert to R object
py_to_r(b)



}

if(interactive() && ants_available()) {


# ------ Basic case: use python `int` as an R function ---------
py_int <- py_builtin("int")

# a is an R object now
a <- py_int(9)
print(a)
class(a)

# ------ Use python `int` as a Python function -----------------
py_int2 <- py_builtin("int", convert = FALSE)

# b in a python object
b <- py_int2(9)

# There is no '[1] ' when printing
print(b)
class(b)

# convert to R object
py_to_r(b)



}

List in 'Python'

Description

List in 'Python'

Usage

py_list(..., convert = FALSE)
py_list(..., convert = FALSE)

Arguments

`...`	passing to `list` ('Python')
`convert`	whether to convert the results back into R; default is no

Value

List instance, or an R vector if converted

Examples



if(interactive() && ants_available()) {

  py_list(list(1,2,3))
  py_list(c(1,2,3))

  py_list(array(1:9, c(3,3)))
  py_list(list(list(1:3), letters[1:3]))

}
if(interactive() && ants_available()) {

  py_list(list(1,2,3))
  py_list(c(1,2,3))

  py_list(array(1:9, c(3,3)))
  py_list(list(list(1:3), letters[1:3]))

}

Slice index in 'Python' arrays

Description

Slice index in 'Python' arrays

Usage

py_slice(...)
py_slice(...)

Arguments

...

passing to slice ('Python')

Value

Index slice instance

Examples



if(interactive() && ants_available()) {

  x <- np_array(array(seq(20), c(4, 5)))

  # equivalent to x[::2]
  x[py_slice(NULL, NULL, 2L)]

}
if(interactive() && ants_available()) {

  x <- np_array(array(seq(20), c(4, 5)))

  # equivalent to x[::2]
  x[py_slice(NULL, NULL, 2L)]

}

Process 'T1' image

Description

Process 'MRI' and align with template brains

Usage

t1_preprocess(
  t1_path,
  templates = "mni_icbm152_nlin_asym_09a",
  work_path = ".",
  verbose = TRUE
)
t1_preprocess(
  t1_path,
  templates = "mni_icbm152_nlin_asym_09a",
  work_path = ".",
  verbose = TRUE
)

Arguments

`t1_path`	path to a 'T1' image
`templates`	template to use; default is `'mni_icbm152_nlin_asym_09a'`,
`work_path`	working path, must be a directory
`verbose`	whether to verbose the progress

Value

Nothing will be returned. Please check work_path for results.

Package 'rpyANTs'

Help Index

Get 'ANTsPy' module

Description

Usage

Arguments

Value

See Also

Apply a transform list to map an image from one domain to another

Description

Usage

Arguments

Value

See Also

Examples

Apply a transform list to map points from one domain to another

Description

Usage

Arguments

Value

See Also

Examples

Check if 'ANTs' is available

Description

Usage

Arguments

Value

See Also

Motion correction

Description

Usage

Arguments

Value

Examples

Plot single 'ANTsImage'

Description

Usage

Arguments

Details

Value

Examples

Plot multiple 'ANTsImage'

Description

Usage

Arguments

Value

Examples

Register two images using 'ANTs'

Description

Usage

Arguments

Details

Value

Examples

Resample image

Description

Usage

Arguments

Value

Examples

Get 'ANTsPyNet' module

Description

Usage

Arguments

Value

See Also

Extract brain and strip skull

Description

Usage

Arguments

Value

Process brain image prior to segmentation

Description

Usage

Arguments

Value

See Also

Examples

Imaging segmentation using antspynet

Description

Plot single `'ANTsImage'`

Plot multiple `'ANTsImage'`

Get `'ANTsPyNet'` module

Imaging segmentation using `antspynet`

Load data as `'ANTsImage'` class

Convert to `'ANTsTransform'`