Group level model

Hi,

I am looking for some advice on the most appropriate way to model some seed-based resting-state fMRI data at the group level. The data consists of three groups: Patients, Siblings, and Controls. I would like to be able to compare Patients and Controls, Patients and Siblings, and Siblings and Controls, with the idea being that then I can separate functional connectivity associated with disease vs associated with genetic vulnerability, and thus perhaps identify protective mechanisms in the Sibling group (whom obviously don’t suffer).

The Sibling group are related to the patient group, although the sizes are not even (i.e. for many, but not all patients, one of their siblings was scanned). Thus, the data are not balanced across groups, and there is some correlation between patients and their siblings (where they exist!).

Would it be possible (advisable?) to use 3dMEMA to model these data and include a covariate to account for a between sibling effect? Alternatively I have considered just doing T-tests to make the above comparisons.

Any advice would be most welcome.

Thanks

Joe

Joe,

For the comparison between Patients and Controls, and the contrast between Siblings and Controls, two-sample t-test should be good enough using, for example, 3dttest++.

The situation is a little tricky with the comparison between Patients and Siblings. One possibility is to try linear mixed-effects modeling through 3dLME:

3dLME -prefix …
-model ‘group’
-ranEff ‘~group|Subj’
-num_glt 3
-gltLabel 1 patient -gltCode 1 ‘group : 1patient’
-gltLabel 2 control -gltCode 2 'group : 1
control’
-gltLabel 3 pat_vs_ctrl -gltCode 3 ‘group : 1patient -1control’
-dataTable
Subj group InputFile
Fam1 patient …
Fam1 sibling …

Hi Gang,

Thanks very much for your advice. After a bit of playing around I’ve managed to get the model to estimate using the following script (see below). Is this the correct way to specify the random and fixed effects for what I am trying to do?

As I mentioned before not all patients have a sibling (and vice versa). Therefore, in the RFX part of the design matrix they have their own regressor (not shared with any other subject), does this mean I am essentially censoring them out of the model?

Thanks

Joe

/cubric/software/afni.versions/16.2.18/3dLME -prefix /home/sapjw12/scratch/Xav_BPD/level2.final/BPvsSIB.nuc_acc.bilateral.8mm.nii.gz
-model ‘group’
-ranEff ‘~1|family’
-num_glt 3
-gltLabel 1 patient -gltCode 1 ‘group : 1patient’
-gltLabel 2 sibling -gltCode 2 'group : 1
sibling’
-gltLabel 3 pat_vs_sibling -gltCode 3 ‘group : 1patient -1sibling’
-dataTable
Subj family group InputFile
102 Fam02 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/102/102.corr_Z.nuc_acc.bilateral.8mm.nii.gz
103 Fam03 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/103/103.corr_Z.nuc_acc.bilateral.8mm.nii.gz
105 Fam05 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/105/105.corr_Z.nuc_acc.bilateral.8mm.nii.gz
107 Fam07 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/107/107.corr_Z.nuc_acc.bilateral.8mm.nii.gz
108 Fam08 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/108/108.corr_Z.nuc_acc.bilateral.8mm.nii.gz
111 Fam11 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/111/111.corr_Z.nuc_acc.bilateral.8mm.nii.gz
112 Fam12 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/112/112.corr_Z.nuc_acc.bilateral.8mm.nii.gz
114 Fam14 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/114/114.corr_Z.nuc_acc.bilateral.8mm.nii.gz
116 Fam16 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/116/116.corr_Z.nuc_acc.bilateral.8mm.nii.gz
117 Fam17 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/117/117.corr_Z.nuc_acc.bilateral.8mm.nii.gz
119 Fam19 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/119/119.corr_Z.nuc_acc.bilateral.8mm.nii.gz
120 Fam20 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/120/120.corr_Z.nuc_acc.bilateral.8mm.nii.gz
121 Fam21 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/121/121.corr_Z.nuc_acc.bilateral.8mm.nii.gz
122 Fam22 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/122/122.corr_Z.nuc_acc.bilateral.8mm.nii.gz
123 Fam23 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/123/123.corr_Z.nuc_acc.bilateral.8mm.nii.gz
124 Fam24 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/124/124.corr_Z.nuc_acc.bilateral.8mm.nii.gz
125 Fam25 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/125/125.corr_Z.nuc_acc.bilateral.8mm.nii.gz
127 Fam27 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/127/127.corr_Z.nuc_acc.bilateral.8mm.nii.gz
128 Fam28 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/128/128.corr_Z.nuc_acc.bilateral.8mm.nii.gz
131 Fam31 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/131/131.corr_Z.nuc_acc.bilateral.8mm.nii.gz
133 Fam33 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/133/133.corr_Z.nuc_acc.bilateral.8mm.nii.gz
134 Fam34 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/134/134.corr_Z.nuc_acc.bilateral.8mm.nii.gz
135 Fam35 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/135/135.corr_Z.nuc_acc.bilateral.8mm.nii.gz
136 Fam36 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/136/136.corr_Z.nuc_acc.bilateral.8mm.nii.gz
137 Fam37 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/137/137.corr_Z.nuc_acc.bilateral.8mm.nii.gz
138 Fam38 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/138/138.corr_Z.nuc_acc.bilateral.8mm.nii.gz
141 Fam41 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/141/141.corr_Z.nuc_acc.bilateral.8mm.nii.gz
142 Fam42 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/142/142.corr_Z.nuc_acc.bilateral.8mm.nii.gz
143 Fam43 patient /home/sapjw12/scratch/Xav_BPD/level1.NEW/143/143.corr_Z.nuc_acc.bilateral.8mm.nii.gz
502 Fam02 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/502/502.corr_Z.nuc_acc.bilateral.8mm.nii.gz
503 Fam03 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/503/503.corr_Z.nuc_acc.bilateral.8mm.nii.gz
504 Fam04 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/504/504.corr_Z.nuc_acc.bilateral.8mm.nii.gz
505 Fam05 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/505/505.corr_Z.nuc_acc.bilateral.8mm.nii.gz
506 Fam06 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/506/506.corr_Z.nuc_acc.bilateral.8mm.nii.gz
507 Fam07 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/507/507.corr_Z.nuc_acc.bilateral.8mm.nii.gz
508 Fam08 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/508/508.corr_Z.nuc_acc.bilateral.8mm.nii.gz
509 Fam09 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/509/509.corr_Z.nuc_acc.bilateral.8mm.nii.gz
511 Fam11 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/511/511.corr_Z.nuc_acc.bilateral.8mm.nii.gz
512 Fam12 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/512/512.corr_Z.nuc_acc.bilateral.8mm.nii.gz
513 Fam13 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/513/513.corr_Z.nuc_acc.bilateral.8mm.nii.gz
514 Fam14 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/514/514.corr_Z.nuc_acc.bilateral.8mm.nii.gz
517 Fam17 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/517/517.corr_Z.nuc_acc.bilateral.8mm.nii.gz
518 Fam18 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/518/518.corr_Z.nuc_acc.bilateral.8mm.nii.gz
519 Fam19 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/519/519.corr_Z.nuc_acc.bilateral.8mm.nii.gz
520 Fam20 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/520/520.corr_Z.nuc_acc.bilateral.8mm.nii.gz
521 Fam21 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/521/521.corr_Z.nuc_acc.bilateral.8mm.nii.gz
522 Fam22 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/522/522.corr_Z.nuc_acc.bilateral.8mm.nii.gz
524 Fam24 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/524/524.corr_Z.nuc_acc.bilateral.8mm.nii.gz
525 Fam25 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/525/525.corr_Z.nuc_acc.bilateral.8mm.nii.gz
527 Fam27 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/527/527.corr_Z.nuc_acc.bilateral.8mm.nii.gz
528 Fam28 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/528/528.corr_Z.nuc_acc.bilateral.8mm.nii.gz
529 Fam29 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/529/529.corr_Z.nuc_acc.bilateral.8mm.nii.gz
530 Fam30 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/530/530.corr_Z.nuc_acc.bilateral.8mm.nii.gz
531 Fam31 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/531/531.corr_Z.nuc_acc.bilateral.8mm.nii.gz
533 Fam33 sibling /home/sapjw12/scratch/Xav_BPD/level1.NEW/533/533.corr_Z.nuc_acc.bilateral.8mm.nii.gz

Joe,

With your setting, try this:

-model ‘group’ \
-ranEff ‘~group|Subj’ \

The first columns (“Subj” and “family”) are essentially the same thing. And 3dLME assumes that “Subj” is the only random-effects factor.