3dICC - model specification and InputFile

AFNI Message Board
1

Hi AFNI experts,

I’m trying to set up a couple of reliability analyses but there are some details that I’m not sure about.

I’m referring to the HBM paper (https://doi.org/10.1002/hbm.23909) and AFNI documentation on 3dICC (https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dICC.html)

  1. I’m trying a whole brain ICC, and I’m then planning to use ICC(3,1). The paper lists 4 model strategies, some with and some without regularization. I don’t see how I can set up, for example RME with 3dICC.
    Am I missing something here? is it possible to set up these model strategies or not? if not, what is 3dICC using then?

  2. I have a very similar data set to the one described in the HBM paper. I’m interested in the reliability of emotional effects (e.g., Emotional vs Neutral, or Pleasant vs Unpleasant). Something similar to what done here: https://doi.org/10.1016/j.dcn.2018.03.010
    What is the InputFile for -dataTable? a tFile for the contrast of interest for each subject?

thank you,
ns

2

I don’t see how I can set up, for example RME with 3dICC.

RME and RMME are not currently implemented in 3dICC.

What is the InputFile for -dataTable?

The contrast for each session from each subject

a tFile for the contrast of interest for each subject?

Yes, the t-statistic associated with each contrast.

3

I successfully ran ICC(3,1) with a GM mask based on TT_N27 covering the whole brain.

I had issues running ICC(2,1) with a mask covering amygdala and fusiform gyrus.

sub-brik 11contains t-stat for a contrast of interest:

#!/usr/bin/env tcsh
3dICC -prefix ICC2_N40_amyIT. -jobs 2
-model ‘1+(1|session)+(1|Subj)’
-mask amy.IT_mask.+tlrc.
-dataTable
Subj session InputFile
s1 one 3051.FP.stats.VAL.GLT.+tlrc’[11]’
s1 two 3051.SP.stats.VAL.GLT.+tlrc’[11]’
s2 one 3052.FP.stats.VAL.GLT.+tlrc’[11]’
s2 two 3052.SP.stats.VAL.GLT.+tlrc’[11]’
s3 one 3055.FP.stats.VAL.GLT.+tlrc’[11]’
s3 two 3055.SP.stats.VAL.GLT.+tlrc’[11]’
s4 one 3061.FP.stats.VAL.GLT.+tlrc’[11]’
s4 two 3061.SP.stats.VAL.GLT.+tlrc’[11]’
.
.
.
.

Output:
Reading input files now…

Reading input files for effect estimates: Done!

Loading required package: lme4
Loading required package: Matrix
If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or something else
is likely inappropriate.

[1] “Great, test run passed at voxel (21, 25, 20)!”
Error in asMethod(object) : not a positive definite matrix
Calls: nrow … asMethod → as → .class1 → as → asMethod → as → asMethod
Execution halted

Thank you,
ns

4

sub-brik 11contains t-stat for a contrast of interest:

Why t-stat only as input? Which type of model are you trying to adopt?