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Comments (7)

stnava avatar stnava commented on August 30, 2024

@jeffduda see comments in this issue .... if you want to continue with the iMath business, please make sure changes are backward compatible ... i.e. keep iBind and %>% documentation and other things in iMath working.

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bkandel avatar bkandel commented on August 30, 2024

I fixed the issues in aslCensoring.

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bkandel avatar bkandel commented on August 30, 2024

Currently seeing:

Name: antsSpatialICAfMRI

Title: Perform spatial ICA on fMRI bold data.

Aliases: antsSpatialICAfMRI

** Examples

set.seed( 123 )
boldImages <- list()
n=16
nvox <- n_n_n*12
dims <- c(n,n,n,12)
boldImages[[1]] <- makeImage( dims , rnorm( nvox )+500 ) %>% iMath("PadImage" , 4 )
boldImages[[2]] <- makeImage( dims , rnorm( nvox )+500 ) %>% iMath("PadImage" , 4 )
boldImages[[3]] <- makeImage( dims , rnorm( nvox )+500 ) %>% iMath("PadImage" , 4 )

cleanBoldImages <- list()
for( i in 1:length( boldImages ) )

  • {
  • fmri <- preprocessfMRI( boldImages[[i]], residualizeMatrix=FALSE )
  • if( i == 1 ) maskImage <- fmri$maskImage
  • cleanBoldImages[[i]] <- fmri$cleanBoldImage
  • }

icaResults <- antsSpatialICAfMRI( cleanBoldImages, maskImage,

  • numberOfICAComponents = 2 )
    Error in svd(scale(x %*% t(x))) : infinite or missing values in 'x'
    Calls: antsSpatialICAfMRI -> whiten -> svd
    Execution halted

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stnava avatar stnava commented on August 30, 2024

yes - tried to fi that yesterday --- somewhat platform/run specific ... problem is preprocessfMRI now returns some junk (all zero) images ... not sure why.

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stnava avatar stnava commented on August 30, 2024

ok this antsSpatialICAfMRI issue is fixed now

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bkandel avatar bkandel commented on August 30, 2024

Currently aslDenoiseR example still fails.

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bkandel avatar bkandel commented on August 30, 2024

These all appear to be fixed now, so closing.

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