3dICC error

Hi,

I use the following 3dICC command and have an error of ‘object ‘runMeta’ not found’ below ‘*****’. Kindly help.

Phoebe

3dICC -prefix MDH_co2_pco2_max_decon_icc
-mask MDH_brain_al_mask_xcereb.nii
-model “1+Session+(1|Subj)”
-dataTable
Subj Session InputFile
mdh001 CO2 mdh001_bold_co2_pco2_max_decon+tlrc’[0]’
mdh003 CO2 mdh003_bold_co2_pco2_max_decon+tlrc’[0]’
mdh004 CO2 mdh004_bold_co2_pco2_max_decon+tlrc’[0]’
mdh005 CO2 mdh005_bold_co2_pco2_max_decon+tlrc’[0]’
mdh008 CO2 mdh008_bold_co2_pco2_max_decon+tlrc’[0]’
mdh009 CO2 mdh009_bold_co2_pco2_max_decon+tlrc’[0]’
mdh010 CO2 mdh010_bold_co2_pco2_max_decon+tlrc’[0]’
mdh011 CO2 mdh011_bold_co2_pco2_max_decon+tlrc’[0]’
mdh013 CO2 mdh013_bold_co2_pco2_max_decon+tlrc’[0]’
mdh014 CO2 mdh014_bold_co2_pco2_max_decon+tlrc’[0]’
mdh017 CO2 mdh017_bold_co2_pco2_max_decon+tlrc’[0]’
mdh001 REST mdh001_bold_rest_pco2_max_decon+tlrc’[0]’
mdh003 REST mdh003_bold_rest_pco2_max_decon+tlrc’[0]’
mdh004 REST mdh004_bold_rest_pco2_max_decon+tlrc’[0]’
mdh005 REST mdh005_bold_rest_pco2_max_decon+tlrc’[0]’
mdh008 REST mdh008_bold_rest_pco2_max_decon+tlrc’[0]’
mdh009 REST mdh009_bold_rest_pco2_max_decon+tlrc’[0]’
mdh010 REST mdh010_bold_rest_pco2_max_decon+tlrc’[0]’
mdh011 REST mdh011_bold_rest_pco2_max_decon+tlrc’[0]’
mdh013 REST mdh013_bold_rest_pco2_max_decon+tlrc’[0]’
mdh014 REST mdh014_bold_rest_pco2_max_decon+tlrc’[0]’
mdh017 REST mdh017_bold_rest_pco2_max_decon+tlrc’[0]’


++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
11 subjects : mdh001 mdh003 mdh004 mdh005 mdh008 mdh009 mdh010 mdh011 mdh013 mdh014 mdh017
22 response values
2 levels for factor Session : CO2 REST

Contingency tables of subject distributions among the categorical variables:

***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
11 subjects : mdh001 mdh003 mdh004 mdh005 mdh008 mdh009 mdh010 mdh011 mdh013 mdh014 mdh017
22 response values
2 levels for factor Session : CO2 REST

Contingency tables of subject distributions among the categorical variables:

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

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 (53, 63, 50)!”
[1] “Start to compute 151 slices along Z axis. You can monitor the progress”
[1] “and estimate the total run time as shown below.”
[1] “07/04/20 19:41:00.144”
Error in apply(comArr[, , kk, ], c(1, 2), runMeta, dataframe = lop$dataStr, :
object ‘runMeta’ not found
Calls: aperm → apply → match.fun
Execution halted

Phoebe, what is your AFNI version?

afni -ver

You may have to update your AFNI. Also, use multiple CPUs with the -jobs option if possible.

Hi Gang,

Thanks for your reply.
I just updated AFNI and it seems to work. However, it prompts with the following warning (after ****) after Slice 15.
Any suggestion?

Thanks in advance.
Phoebe.


Loading required package: lme4
Loading required package: Matrix

Range of input data: [-0.053, 1.651]

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 (85, 130, 81)!”
[1] “Start to compute 151 slices along Z axis. You can monitor the progress”
[1] “and estimate the total run time as shown below.”
[1] “07/14/20 19:24:08.224”
Z slice # 1 done: 07/14/20 19:24:08.676
Z slice # 2 done: 07/14/20 19:24:08.911
Z slice # 3 done: 07/14/20 19:24:09.137
Z slice # 4 done: 07/14/20 19:24:09.364
Z slice # 5 done: 07/14/20 19:24:09.595
Z slice # 6 done: 07/14/20 19:24:09.834
Z slice # 7 done: 07/14/20 19:24:10.063
Z slice # 8 done: 07/14/20 19:24:10.303
Z slice # 9 done: 07/14/20 19:24:10.532
Z slice # 10 done: 07/14/20 19:24:11.298
Z slice # 11 done: 07/14/20 19:24:12.572
boundary (singular) fit: see ?isSingular
Z slice # 12 done: 07/14/20 19:24:14.297
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
Z slice # 13 done: 07/14/20 19:24:16.326
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
Z slice # 14 done: 07/14/20 19:24:19.159
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
Z slice # 15 done: 07/14/20 19:24:23.239
boundary (singular) fit: see ?isSingular

Phoebe, those warnings aside, did 3dICC complete the analysis? The warnings are just an indicator that the model hits the parameter boundary at probably a small number of voxels. Don’t worry about it.

Hi Gang,

It has been running for almost 24 hours by now and it didn’t finish yet. No dataset is output.

Phoebe.