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  

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YC
February 15, 2023 12:07PM
Hi AFNI expert,

I have questions regarding setting up 3dLME, to look if betwee-subject factor (Group: control, patient) and within-subject variable (Time: Time 1 and Time 2) account for significant variance in the brain activity. I am mostly interested in effect of Broup By Time interaction. I ran into error when I run the script : Incorrect level coding in variable cond: v1.

Please let me know what seeting in my script caused that error. Thank you! Here is my script:

3dLME \
-prefix Ctrl29_vs_Pat36_V1-V2 \
-jobs 2 \
-mask $brain_mask \
-model 'cond*group' \
-ranEff '~1' \
-SS_type 3 \
-num_glt 8 \
-gltLabel 1 'v1' -gltCode 1 'cond : 1*v1' \
-gltLabel 2 'v2' -gltCode 2 'cond : 1*v2' \
-gltLabel 3 'ctrl' -gltCode 3 'group : 1*ctrl' \
-gltLabel 4 'pat' -gltCode 4 'group : 1*pat' \
-gltLabel 5 'v1-v2' -gltCode 5 'cond : 1*v1 -1*v2' \
-gltLabel 6 'ctrl-pat' -gltCode 6 'group : 1*ctrl -1*pat' \
-gltLabel 7 'ctrl_v1-v2' -gltCode 7 'cond : 1*v1 -1*v2 group : 1*ctrl' \
-gltLabel 8 'pat_v1-v2' -gltCode 8 'cond : 1*v1 -1*v2 group : 1*pat' \
-num_glf 1 \
-glfLabel 1 'GroupByTime' -glfCode 1 'group : 1*ctrl -1*pat cond : 1*v1 -1*v2' \
-dataTable \
Subj cond group InputFile \
s1 v1 ctrl '$c1v1' \
s1 v2 ctrl '$c1v2' \
s2 v1 ctrl '$c2v1' \
s2 v2 ctrl '$c2v2' \
s3 v1 ctrl '$c3v1' \
...
...
s30 v1 pat '$p1v1' \
s30 v2 pat '$p1v2' \
s31 v1 pat '$p2v1' \
s31 v2 pat '$p2v2' \
s32 v1 pat '$p3v1' \
s32 v2 pat '$p3v2' \
s33 v1 pat '$p4v1' \
...
...
Subject Author Posted

Errors running 3dLME (incorrect level coding in variable cond)

YC February 15, 2023 12:07PM

Re: Errors running 3dLME (incorrect level coding in variable cond)

gang February 16, 2023 09:31AM

Re: Errors running 3dLME (incorrect level coding in variable cond)

YC February 16, 2023 02:42PM

Re: Errors running 3dLME (incorrect level coding in variable cond)

gang February 16, 2023 05:14PM