AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
August 11, 2022 10:33AM
Hello,

I am using 3dLMEr to model the relationship between functional connectivity and risk for psychopathology based on parental report. Each subject has two reporters (maternal, paternal) and a risk classification label based on that reporter (high, low). I also have covariates of no-interest (age, sex assigned at birth, study site). I am interested in the risk x reporter interaction and the command I've been using is below:

3dLMEr -prefix "${homeDir}/out/${seed}/3dLMEr_${seed}_${hemi}_WB_conn_riskXreporter.nii.gz" -jobs 15 \
-qVars 'AGE' \
-qVarCenters "${center}" \
-gltCode risk_by_reporter 'RISK : 1*high -1*low REPORTER : 1*maternal -1*paternal' \
-gltCode maternal_high-low 'RISK : 1*high -1*low REPORTER : 1*maternal' \
-gltCode paternal_high-low 'RISK : 1*high -1*low REPORTER : 1*paternal' \
-gltCode high_maternal-paternal 'RISK : 1*high REPORTER : 1*maternal -1*paternal' \
-gltCode low_maternal-paternal 'RISK : 1*low REPORTER : 1*maternal -1*paternal' \
-gltCode risk_high-low 'RISK : 1*high -1*low' \
-gltCode reporter_maternal-paternal 'REPORTER : 1*maternal -1*paternal' \
-mask "${templates}/MNI152_T1_2.4mm_gm.nii.gz" \
-model 'RISK*REPORTER+AGE+SEX+(1|SITE_ID)+(1|Subj)' \
-dataTable @${homeDir}/${seed}_${hemi}_WB_conn_LMEr_table_riskXreporter.tsv

When I include GLTs examining anything other than main effects across other factors (first 5 GLTs), I get the following error after all the necessary R packages are confirmed:
......
Loading required package: phia
Loading required package: car
Loading required package: carData
Error in if (is.na(lop$gltList[[n]])) gltRes[[n]] <- tryCatch(testInteractions(fm, :
the condition has length > 1
Execution halted

When only the main effect GLTs are included (last two GLTs), there is no error and the program runs successfully with output.

Am I specifying GLTs incorrectly when modeling the interaction and subsequent contrasts within other factors? Any help on why these models are not running successfully would be appreciated.
Subject Author Posted

Error in 3dLMEr GLT specification

tjkeding August 11, 2022 10:33AM

Re: Error in 3dLMEr GLT specification

gang August 12, 2022 06:29AM

Re: Error in 3dLMEr GLT specification

tjkeding August 12, 2022 09:10AM

Re: Error in 3dLMEr GLT specification

gang August 12, 2022 01:04PM