In
order to apply lme to your family data you must order your design
matrix and MRI data (eg. cortical thickness) in a way that you have all the assessments for
the first cluster (family) then all the assesments for the second
and so on. Then you need to built a vector "ni" of length equals to
the number of clusters in your data. Each entry of that vector
contains the number of elements in the corresponding cluster (the
vector is ordered according to the previous ordering of your
clusters).
Alternatively
you could use something like
[M,Y,ni]
= sortData(M,1,Y,sID); (sorts the data)
as
explained in the wiki. All you need to do is assign the same subject
ID (sID) to the elements within a family and add a fake time
variable to the matrix of covariates M. After sorting the design
matrix an data you then remove the fake time variable from your
design matrix.