Hello!

I'm currently playing which my data and am unsure about the statistical test to use.

I have MRI data from 25 patients. I have 4 (predetermined) lesion types and a control area from which I obtained MRI values. Not all patients have all lesion types, some patients have several of the same lesion types. I would like to know if MRI values differ significantly between the lesion types (and control). I have possibly two covariates - scanner type (I used two) and area size.

Data looks something like this;
scanner subject lesiontype area value
1 1 1 4.5 850
1 1 3 3.7 456
1 1 3 3.3 387
1 2 2 5.4 658
etc

I don't think an ANCOVA would work as the data isn't independent (subject 1 has both lesion type 1 and 3). Repeated measures doesn't work because of missing data (subject 1 doesn't have lesion type 2). Regression analysis seems to work but I may violate independence here too.

Next I grouped my data together to get only one average value for lesion type;
scanner subject lesiontype area value
1 1 1 4.5 850
1 1 3 3.3 387
1 2 2 5.4 658
etc

I still have missing data (lesion type 2 for subject 1), but was now able to do a Generalised Estimating equations or GEE (for longitudinal data, nested data or correlated data). Here I used subject as subject variable and lesiontype as within subject variable (which I can recode to run several models and compare the groups).

Unfortunately I don't know enough about this statistical test to know whether this is the way forward? I can only find examples for longitudinal data. Will there be issues here? Which statistical test would be best to analyse this data?

Many, many thanks!