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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
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



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