Simple motion_correction function.

motion corrects 4D time series imaging data

.motion_correction(
  img,
  fixed = NULL,
  moreaccurate = 1,
  txtype = "Affine",
  verbose = FALSE,
  num_threads = 1,
  seed = NULL
)

Arguments

img	4D antsImage
fixed	target fixed image
moreaccurate	0, 1 or 2 with higher values being more accurte (use 2 for real applications, 0 for testing)
txtype	Transformation type
verbose	verbosity boolean
num_threads	will execute Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = num_threads) before running to attempt a more reproducible result. See https://github.com/ANTsX/ANTs/wiki/antsRegistration-reproducibility-issues for discussion. If NULL, will not set anything.
seed	will execute Sys.setenv(ANTS_RANDOM_SEED = seed) before running to attempt a more reproducible result. See https://github.com/ANTsX/ANTs/wiki/antsRegistration-reproducibility-issues for discussion. If NULL, will not set anything.

Value

list of outputs

Note

This function may give different results on multiple runs.

Author

Avants BB

Examples

set.seed(1000)
testimg<-makeImage( c(10,10,10,5),  rnorm(  5000  ) )
testimg<-iMath(testimg,"PadImage",5)
mocorr <-.motion_correction( testimg, num_threads = 1, seed = 10)
aimg_to_array = function(x) {
if (is.antsImage(x)) {
   x = as.array(x)
}
x
}
amocorr = lapply(mocorr, aimg_to_array)
mocorr2 <-.motion_correction( testimg, num_threads = 1, seed = 10)
amocorr2 = lapply(mocorr2, aimg_to_array)
testthat::expect_equal(mocorr, mocorr2)
testthat::expect_equal(amocorr, amocorr2)

# This function may give different results on multiple runs
# without setting the seed