Description Usage Arguments Value Author(s) Examples

This function will estimate perfusion from an ASL time series using a (robust) regression approach. It will do motion correction, compcorr, factor out nuisance variables and use regression to estimate the perfusion itself. It will mask the image too based on a simple procedure ( should fix this in the future by allowing the user to optionally pass a mask in from the outside ). WARNING: the function will estimate the m0 image from the mean of the control tags assuming that the data is acquired T C T C as is most of JJ's data. Quantitative CBF can be obtained by mutiplying the output of this function by a scalar.

1 2 3 4 5 |

`asl` |
input asl image |

`maskThresh` |
for estimating a brain mask |

`moreaccurate` |
zero, one or two with the last being the most accurate |

`dorobust` |
robustness parameter, lower value keeps more data |

`m0` |
known M0 if any |

`skip` |
stride to speed up robust regression weight estimates |

`mask` |
known brain mask |

`checkmeansignal` |
throw out volumes with mean lower than this thresh |

`moco_results` |
passes prior motion results so moco does not get repeated |

`regweights` |
known temporal weights on regression solution, if any |

`useDenoiser` |
use the aslDenoiser if this value is a range gt than zero |

`useBayesian` |
strength of bayesian prior |

`verbose` |
bool |

`ncompcor` |
number of compcor parameters |

`N3` |
bool correct target image before motion corr |

output a list of relevant objects

Avants BB

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ```
# image available at http://files.figshare.com/1701182/PEDS012_20131101.zip
# fn<-'PEDS012_20131101_pcasl_1.nii.gz'
# asl<-antsImageRead(fn,4)
set.seed(1)
nvox <- 5*5*5*10
dims <- c(5,5,5,10)
asl <- makeImage( dims , rnorm( nvox )+500 ) %>% iMath("PadImage" , 2 )
aslmean <- getAverageOfTimeSeries( asl )
aslmask <- getMask( aslmean , 0.001 , Inf )
aslmat<-timeseries2matrix( asl, aslmask )
for ( i in 1:10 ) aslmat[,i*2]<-aslmat[,i*2]*2
asl<-matrix2timeseries( asl, aslmask, aslmat )
# NOT WORKING
## Not run:
pcasl.processing <- aslPerfusion( asl, moreaccurate=1, dorobust=0 )
testthat::expect_equal(mean(pcasl.processing$m1), 62.2115522470984)
pcasl.processing <- aslPerfusion( asl, moreaccurate=1, ncompcor=2 )
# allow some rejection
pcasl.processing <- aslPerfusion( asl, moreaccurate=1, dorobust=0.925 )
## End(Not run)
``` |

neuroconductor-devel/ANTsR documentation built on March 8, 2019, 2:13 a.m.

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