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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

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Omar Maximo
November 04, 2021 04:37PM
Hi AFNI,

I'm trying to run a linear mixed model using 3dLME between 2 groups across 3 different sessions/time points (some subjects have missing data) while controlling for age, sex, and framewise displacement. I just want to make sure my script looks ok. I'm trying to model a group x session interaction while controlling for the aforementioned variables. With ~1+RT, Im specifying different intercepts and slopes for subjects. Is there something I'm missing?

module load rc/afni/20.1.18-foss-2017b-Python-2.7.14
module load R/3.2.0-goolf-1.7.20

3dLME -prefix /FC_data/group_analysis/results_3dLME_DMN.nii -jobs 10 \
-model 'Group*Session+Age+Sex+FD' \
-qVars 'Age,FD' \
-ranEff '~1+RT' \
-SS_type 3 \
-dataTable \
Subj Group Session Age Sex FD InputFile \
sub-control01 HC 1 28 2 0.1217738 /FC_data/DMN/connmap_sub-control01_ses-01_DMN.nii \
sub-control01 HC 2 28 2 0.1749546 /FC_data/DMN/connmap_sub-control01_ses-02_DMN.nii \
sub-control01 HC 3 28 2 0.150672 /FC_data/DMN/connmap_sub-control01_ses-03_DMN.nii \
sub-control02 HC 1 23 1 0.1281235 /FC_data/DMN/connmap_sub-control02_ses-01_DMN.nii \
sub-control03 HC 1 25 1 0.1455679 /FC_data/DMN/connmap_sub-control03_ses-01_DMN.nii \
sub-control03 HC 2 25 1 0.3276477 /FC_data/DMN/connmap_sub-control03_ses-02_DMN.nii \
..........
sub-patient01 FEP 1 25 1 0.1971614 /FC_data/DMN/connmap_sub-patient01_ses-01_DMN.nii \
sub-patient01 FEP 2 25 1 0.2590447 /FC_data/DMN/connmap_sub-patient01_ses-02_DMN.nii \
sub-patient01 FEP 3 25 1 0.254582 /FC_data/DMN/connmap_sub-patient01_ses-03_DMN.nii \
sub-patient02 FEP 2 30 2 0.1924839 /FC_data/DMN/connmap_sub-patient02_ses-02_DMN.nii \
..........

Thanks,
O.
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Subject Author Posted

3dLME script

Omar Maximo November 04, 2021 04:37PM

Re: 3dLME script

gang November 05, 2021 10:39AM

Re: 3dLME script

Omar Maximo November 11, 2021 11:26AM

Re: 3dLME script

gang November 15, 2021 10:19AM

Re: 3dLME script

Omar Maximo November 15, 2021 03:07PM

Re: 3dLME script

gang November 16, 2021 07:47AM