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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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nhannawa
June 13, 2018 09:14AM
Hi AFNI Team,

I am working on an longitudinal analysis involving an fMRI paradigm with 3 visits. As a substantial number of patients had only two visits, I believe it is appropriate to use linear mixed effects analysis to be able to include those patients with missing data. My model fails and I am unsure why -

Does first-level analysis need to be conducted within AFNI? I am unsure if this is what is causing my problem. For example, I have previously analysed this data within FSL - am I able to use results from my first level analysis in FSL (e.g. cope files or t-statistics in standard space, for each subject/visit) as the inputs for 3dLME?

Otherwise, can you see any problem with my model specification below? Currently, it only contains 2 subjects, as I wanted to be sure it worked before including them all!

Thanks,
Naomi

3dLME -prefix LME_fMRI_fsl -jobs 2 \
-model 'Visit+Time_dif+Base_DD+Base_Age' \
-qVars 'Time_dif,Base_DD,Base_Age' \
-num_glt 3 \
-num_glf 1 \
-gltLabel 1 'Visit_1_2' -gltCode 1 'Visit : 1*v1 -1*v2' \
-gltLabel 2 'Visit_2_3' -gltCode 2 'Visit : 1*v2 -1*v3' \
-gltLabel 3 'Effect_of_time' -gltCode 3 'Time_dif :' \
-glfLabel 1 'Main_effect_visit' -glfCode 1 ' Visit : 1*v1 -1*v2 & 1*v1 -1*v3' \
-ranEff '~1' -SS_type 3 \
-dbgArgs \
-dataTable \
Subj Visit Time_dif Base_DD Base_Age InputFile \
s1 v1 0 4.71 56.15 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V1/001_V1/1_run_Naomi.feat/reg_standard/stats/cope8.nii.gz \
s1 v1 0 4.71 56.15 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V1/001_V1/2_run_Naomi.feat/reg_standard/stats/cope8.nii.gz \
s1 v2 625 4.71 56.15 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V2/001_V2/1_run_Naomi++.feat/reg_standard/stats/cope8.nii.gz \
s1 v2 625 4.71 56.15 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V2/001_V2/2_run_Naomi+.feat/reg_standard/stats/cope8.nii.gz \
s1 v3 1150 4.71 56.15 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V3/001_V3/1_run_Naomi.feat/reg_standard/stats/cope8.nii.gz \
s1 v3 1150 4.71 56.15 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V3/001_V3/2_run_Naomi.feat/reg_standard/stats/cope8.nii.gz \
s2 v1 0 2.58 54.28 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V1/002_V1/1_run_Naomi.feat/reg_standard/stats/cope8.nii.gz \
s2 v1 0 2.58 54.28 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V1/002_V1/2_run_Naomi.feat/reg_standard/stats/cope8.nii.gz \
s2 v2 571 2.58 54.28 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V2/002_V2/1_run_Naomi.feat/reg_standard/stats/cope8.nii.gz \
s2 v2 571 2.58 54.28 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V2/002_V2/2_run_Naomi+.feat/reg_standard/stats/cope8.nii.gz \
s2 v3 1210 2.58 54.28 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V3/002_V3/1_run_Naomi++.feat/reg_standard/stats/cope8.nii.gz \
s2 v3 1210 2.58 54.28 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V3/002_V3/2_run_Naomi.feat/reg_standard/stats/cope8.nii.gz
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Subject Author Posted

3dLME inputs

nhannawa June 13, 2018 09:14AM

Re: 3dLME inputs

gang June 13, 2018 11:51AM

Re: 3dLME inputs

nhannawa June 14, 2018 07:19AM