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:

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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  

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March 14, 2023 04:35PM
Hello AFNI folks,

I am looking to structure a group analysis using voxel-level data as a predictor rather than the response variable. More specifically, I want to fit an LMEr model at each voxel, where symptoms at a follow-up time point are being explained by an interaction between a 'risk' variable (between-subject) and functional connectivity at that voxel at baseline (also between subject, but each voxel/subject will have unique FC values). My approach is as follows:

1. Create a new .nii file for each subject (with the same grid as FC maps) containing the symptom value to be predicted for each voxel - here, because the symptom score does not vary within-subject, the .nii file would contain the same symptom value for all voxels.
2. Create a data table using the examples from 3dLME, with a 'BRAIN_FC' column containing the path to the FC map for that subject. The table would also include the between-subject 'risk' variable, other between-subject covariates, and the InputFile column contains the .nii file created in (1).
3. Use the following command to test for an interaction between risk and FC at baseline to predict symptoms:

3dLMEr -prefix ${out}/3dLMEr_${seed}_${hemi}_brainXrisk_combined.nii.gz -jobs 15 \
-mask ${templates}/MNI152_T1_2.4mm_gm.nii.gz \
-qVars "COV1,COV3" \
-qVarCenters "0.0,0.0" \
-gltCode risk_high-low 'RISK : 1*high -1*low' \
-gltCode brain 'BRAIN_FC :' \
-gltCode brainXrisk_high-low 'BRAIN_FC : RISK : 1*high -1*low' \
-model 'RISK*BRAIN_FC+COV1+COV2+COV3+(1|COV4)' \
-dataTable @${out}/LMEr_tables/${seed}_${hemi}_brainXrisk_combined.tsv

COV1, 2, and 3 are between-subject covariates (2 continuous, 1 categorical) and COV4 is a 'site' variable for which we want to model a random intercept.

When I attempt to run this model, I get the following error:
** Error:
Incorrect level coding in variable BRAIN_FC : :

I have also attempted to use the -vVars option with BRAIN_FC column as input and taken out the -gltCode for the BRAIN_FC main effect and continue to get this error. Any advice on my approach, a better way of modeling this question, or help troubleshooting this error would be greatly appreciated!
Subject Author Posted

3dLMEr - Using functional connectivity as a predictor

tjkeding March 14, 2023 04:35PM

Re: 3dLMEr - Using functional connectivity as a predictor

gang March 15, 2023 11:33AM

Re: 3dLMEr - Using functional connectivity as a predictor

tjkeding March 15, 2023 01:33PM

Re: 3dLMEr - Using functional connectivity as a predictor

gang March 16, 2023 07:47AM

Re: 3dLMEr - Using functional connectivity as a predictor Attachments

tjkeding March 16, 2023 09:52AM

Re: 3dLMEr - Using functional connectivity as a predictor

tjkeding March 16, 2023 10:07AM

Re: 3dLMEr - Using functional connectivity as a predictor

gang March 16, 2023 10:46AM

Re: 3dLMEr - Using functional connectivity as a predictor

tjkeding March 16, 2023 11:57AM

Re: 3dLMEr - Using functional connectivity as a predictor

gang March 16, 2023 05:11PM

Re: 3dLMEr - Using functional connectivity as a predictor

tjkeding March 16, 2023 05:32PM