quantifyCBF: quantifyCBF

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

quantifyCBF

Description

Computes CBF from ASL - pasl or pcasl

Usage

quantifyCBF(perfusion, mask, parameters, M0val = NA, outlierValue = 0.02)

Arguments

perfusion	input asl matrix
mask	3D image mask (antsImage)
parameters	list with entries for sequence and m0 (at minimimum)
M0val	baseline M0 value (optional)
outlierValue	trim outliers by this fractional value (optional)

Value

a list is output with 3 types of cbf images

Author(s)

Avants BB, Kandel B, Duda JT

Examples

## Not run: 
if (!exists("fn")) {
  fn <- getANTsRData("pcasl")
}
# PEDS029_20101110_pcasl_1.nii.gz # high motion subject
asl <- antsImageRead(fn)
# image available at http://files.figshare.com/1701182/PEDS012_20131101.zip
pcasl.bayesian <- aslPerfusion(asl,
  dorobust = 0., useDenoiser = 4, skip = 11, useBayesian = 1000,
  moreaccurate = 0, verbose = T, maskThresh = 0.5
) # throw away lots of data
# user might compare to useDenoiser=FALSE
pcasl.parameters <- list(sequence = "pcasl", m0 = pcasl.bayesian$m0)
cbf <- quantifyCBF(
  pcasl.bayesian$perfusion, pcasl.bayesian$mask,
  pcasl.parameters
)
meancbf <- cbf$kmeancbf
print(mean(meancbf[pcasl.bayesian$mask == 1]))
antsImageWrite(meancbf, "temp.nii.gz")
pcasl.processing <- aslPerfusion(asl,
  moreaccurate = 0,
  dorobust = 0.95, useDenoiser = NULL, skip = 5, useBayesian = 0
)
# user might compare to useDenoiser=FALSE
pcasl.parameters <- list(sequence = "pcasl", m0 = pcasl.processing$m0)
cbf <- quantifyCBF(pcasl.processing$perfusion, pcasl.processing$mask, pcasl.parameters)
meancbf <- cbf$kmeancbf
print(mean(meancbf[pcasl.processing$mask == 1]))
antsImageWrite(meancbf, "temp2.nii.gz")
plot(meancbf, slices = "1x50x1")

## End(Not run)

stnava/ANTsR documentation built on April 16, 2024, 12:17 a.m.