3dISC issue

AFNI Message Board
1

AFNI version info (afni -ver): 26.1.05

R version is 4.5.1

I am having an issue with 3dISC command - I am running it in HPC environment.

The command is
```

3dISC -prefix ./ISC_group -mask ../schaefer_atlas/MNI152_T1_1mm_brain_mask.nii.gz -model '1+(1|Subj1)+(1|Subj2)'
-dataTable \
Subj1 Subj2 InputFile \
s1 s2 {mri_dir}/{mri}/CP_sub01_sub02_run05.nii.gz \
s1 s3 {mri_dir}/{mri}/CP_sub01_sub03_run05.nii.gz \
s1 s4 {mri_dir}/{mri}/CP_sub01_sub04_run05.nii.gz \

etc

```

I basically using the same command structure as shown in the documentation for the command.

I am looking to calculate the group average of the ISC.

The slurm file I receive contains the follwing:

During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_COLLATE failed, using "C"
3: Setting LC_TIME failed, using "C"
4: Setting LC_MESSAGES failed, using "C"
5: Setting LC_MONETARY failed, using "C"
6: Setting LC_PAPER failed, using "C"
7: Setting LC_MEASUREMENT failed, using "C"

as well as

++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
18 subjects in set1 : s1 s11 s12 s13 s14 s15 s16 s17 s18 s19 s2 s3 s4 s5 s6 s7 s8 s9
18 subjects in set2 : s11 s12 s13 s14 s15 s16 s17 s18 s19 s2 s20 s3 s4 s5 s6 s7 s8 s9
19 subjects in total: s1 s11 s12 s13 s14 s15 s16 s17 s18 s19 s2 s3 s4 s5 s6 s7 s8 s9 s20
171 response values

Contingency tables of subject distributions among the categorical variables:

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

and then this additional message after it reads all the input files

Reading input files for effect estimates: Done!

Range of input data: [-0.497, 0.903]

If the program hangs for an extended period (e.g., more than 5
minutes), terminate the process as it likely indicates an issue with
the model specification or other factors.

Loading required package: lme4
Loading required package: Matrix
boundary (singular) fit: see help('isSingular')
[1] "Great, test run passed at voxel (95, 102, 25)!"
[1] "Start to compute 48 slices along Z axis. You can monitor the progress"
[1] "and estimate the total run time as shown below."
[1] "06/18/26 16:23:39.510"
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')

and continues with same message (I presume that it is for each voxel).

So I am wondering how to (a) correct for the initial warning messages at the beginning? Or can they be ignored in this care?

What are the potential issues in regards the 'singularity error message'? I am calculating the group average across all pairs and there is no additional covariate I am including in statistical model.

Thank you in advance.

Regards,

Arun

2

Arun,

Regardless of those warning messages, was an output file successfully generated? If so, do the results appear reasonable and consistent with your expectations?

Gang Chen

3

Hi Gang,

The output looks good - the results seem reasonable to me. I guess it produced the results even with the warnings.

Thank you,

Arun

4

Arun,

Glad to know that the results generated by 3dISC look reasonable. Those warnings are largely benign. For example, the following indicates that R could not detect your operating system's language and region settings, and has fallen back to the default "C" locale.


The slurm file I receive contains the follwing:

During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_COLLATE failed, using "C"
3: Setting LC_TIME failed, using "C"
4: Setting LC_MESSAGES failed, using "C"
5: Setting LC_MONETARY failed, using "C"
6: Setting LC_PAPER failed, using "C"
7: Setting LC_MEASUREMENT failed, using "C"

As for the warning:

boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')

it means that the model failed to converge for some voxels, which is not surprising since overfitting may occur for voxels along the edge of the brain.

Gang Chen

5

Gang

Thank you for explanation.

Arun