residuals in 3dLMEr

AFNI Message Board
1

Hello,
I was wondering if any more progress had been made to implementing the “residuals” option in 3dLMEr? This was brought up in the following thread a few months ago (https://afni.nimh.nih.gov/afni/community/board/read.php?1,162874,163747#msg-163747), but I know how things get busy! - and I see the option is still commented out in github. I updated R to 4.0 and now 3dLME will not run, and I need a way to get residuals so that I can output into 3dFWHMx -ACF to correct for multiple comparisons. If this option is not available in 3dLMEr, any other suggested strategies for determining cluster size thresholds? Thank you!

2

Option -resid in 3dLMEr has been turned on in the updated version on github, and will be available in the next AFNI release.

3

That’s great! And just to confirm, 3dLMEr runs well with R 4.0 versions, correct? (I know there were problems with 3dLME.) Also, do you have an estimate of when this will be available, and if there will be a notice sent out when this is released? Thanks so much!

4

just to confirm, 3dLMEr runs well with R 4.0 versions, correct?

There might be some issue with R 4.0 on Mac, but it should be fine on Linux machines.

do you have an estimate of when this will be available, and if there will be a notice sent out when this is released?

If you cannot wait for the next official release, directly download the following and put it in your AFNI binary directory: https://afni.nimh.nih.gov/sscc/staff/gangc/pub/3dLMEr.R

5

Thank you very much for your help!

6

Hello,

Just a follow up on this thread,

I’m using 3dLMEr Version 0.1.0 (April 11, 2021) and there is now the -resid option but I keep getting this error when I use it :


Package snow loaded successfully!

Error in Stat[, , kk, 1] <- parApply(cl, inData[, , kk, ], c(1, 2), runLME,  : 
  number of items to replace is not a multiple of replacement length
Execution halted

The model work well when I don’t use it though. (I am running on CentOS 7.9, with AFNI_21.1.08 ‘Domitian’ using R version 3.6.0).

Any idea what can cause this ?

Thanks in advance,

David Munoz