3dICC error

Dear AFNI experts,

I try to run 3dICC on ‘very preliminary data’ (so very small sample size).
I would like to quantify networks similarity across 3 subjects.

3dICC -prefix myICC -jobs 4                                   \
          -mask mask.nii.gz      \
          -model  '1+Network+(1|Subj)'                        \
          -dataTable      \
Subj 	Network 	InputFile \
s1 	N1 	thresh_zstat13.nii.gz \
s1 	N2	thresh_zstat8.nii.gz \
s2 	N1 	thresh_zstat17.nii.gz \
s2 	N2 	thresh_zstat13.nii.gz \
s3 	N1 	thresh_zstat9.nii.gz \
s3 	N2 	thresh_zstat10.nii.gz

When I ran 3dICC, it failed:

***** Summary information of data structure *****
3 subjects : s1 s2 s3
6 response values
2 levels for factor Network : N1 N2

Contingency tables of subject distributions among the categorical variables:

***** End of data structure information *****

Reading input files now…


Range of input data: [-6.717, 14.814]

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, 43, 23)!”
Error in asMethod(object) : not a positive definite matrix
Calls: nrow … asMethod → as → .class1 → as → asMethod → as → asMethod
Exécution arrêtée

Do you have any idea about why it failed?

Many thanks in advance.


Hi, Carole-

This may not be the source of the program’s error (will defer to Gang on this), but I wonder if the same file should be used for two different subjects? The same exact file:


… appears for both S1 and S2.


Yes, thank you.
Yes in fact it’s not the same file.
I deleted the complete path to make my message more readable but it’s really 2 different files. :slight_smile:


3dICC is designed to estimate ICC when an effect/measurement is obtained two or more times (like sessions in fMRI scanning) among subjects. What is the repetition variable in your case? Could you describe your data structure?